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Duan J, Qin H, Sun M, Fu Y, Lang J, Zhang A, Qin Z, Guo Z, Xu H, Li X, Wang C, Zhang L. Occurrence and genotypic identification of Blastocystis sp., Enterocytozoon bieneusi, and Giardia duodenalis in dairy cattle in Heilongjiang Province, China. Parasitol Int 2024; 100:102871. [PMID: 38403046 DOI: 10.1016/j.parint.2024.102871] [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: 01/11/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Blastocystis sp., Enterocytozoon bieneusi, and Giardia duodenalis are three common zoonotic intestinal parasites, and cattle are important hosts of these three intestinal protozoa. In this study, 1632 fecal samples were collected from dairy farms in Heilongjiang Province, China, and screened for Blastocystis sp., E. bieneusi, and G. duodenalis using polymerase chain reaction. Of these, 149 (9.13%) were positive for three zoonotic pathogens, including 104 (6.40%), 22 (1.35%), and 23 (1.41%) for Blastocystis sp., E. bieneusi, and G. duodenalis, respectively. Based on partial SSU rRNA gene sequencing analysis, 104 positive samples of Blastocystis sp. were found, and a total of nine known subtypes were identified, including ST10 (61), ST3 (18), ST14 (6), ST26 (7), ST24 (3), ST25 (2), ST1 (2), ST5 (2), and ST21 (1). Among these, three subtypes (ST1, ST3, and ST5) were recognized as zoonotic subtypes, and two subtypes (ST10 and ST14) were specific to animals. All 23 Giardia duodenalis-positive samples belonged to assemblage E (n = 23) based on sequenced beta-giardin (bg) and triosephosphate isomerase (tpi) genes. Three known genotypes of E. bieneusi, namely J (n = 9), I (n = 6), and BEB4 (n = 7), were identified by sequence analysis of the internal transcriptional spacer region gene. Our study provides basic data for prevention and control in Heilongjiang Province; however, further research is required to better understand the prevalence and public health significance of these pathogens in the Heilongjiang region.
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Affiliation(s)
- Junxia Duan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, Henan Province, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Huikai Qin
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, Henan Province, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Mengqing Sun
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, Henan Province, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Yin Fu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, Henan Province, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Jiashu Lang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, Henan Province, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Aihui Zhang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang Province, PR China
| | - Ziyang Qin
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, Henan Province, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Zhenxuan Guo
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, Henan Province, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Huiyan Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, Henan Province, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China.
| | - Xiaoying Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, Henan Province, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China.
| | - Chunren Wang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang Province, PR China
| | - Longxian Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, Henan Province, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China.
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Upadhyay S, Das K, Ghosal A, Manna S, Saito-Nakano Y, Dutta S, Nozaki T, Ganguly S. Multi-locus sequence analysis reveals phylogenetically segregated Entamoeba histolytica population. Parasitol Int 2024; 100:102861. [PMID: 38244854 DOI: 10.1016/j.parint.2024.102861] [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: 10/31/2023] [Revised: 01/09/2024] [Accepted: 01/13/2024] [Indexed: 01/22/2024]
Abstract
Amoebiasis, caused by the enteric parasite, Entamoeba histolytica, is one of the major food- and water-borne parasitic diseases in developing countries with improper sanitation and poor hygiene. Infection with E. histolytica has diverse disease outcomes, which are determined by the genetic diversity of the infecting strains. Comparative genetic analysis of infecting E. histolytica strains associated with differential disease outcomes from different geographical regions of the world is important to identify the specific genetic patterns of the pathogen that trigger certain disease outcomes of Amoebiasis. The strategy is able to elucidate the genealogical relation and population structure of infecting E. histolytica strains from different geographical regions. In the present study, we have performed a comparative genetic analysis of circulating E. histolytica strains identified from different parts of the world, including our study region, based on five tRNA-linked short tandem repeat (STR) loci (i.e., D-A, NK2, R-R, STGA-D and A-L) and evaluated their potential associations with differential disease outcomes of Amoebiasis. A number of regional-specific, emerging haplotypes of E. histolytica, significantly associated with specific disease outcomes have been identified. Haplotypes, which have a significant positive association with asymptomatic and amoebic liver abscess outcomes, showed a significant negative association with diarrheal outcome, or vice versa. Comparative multi-locus analysis revealed that E. histolytica isolates from our study region are phylogenetically segregated from the isolates of other geographical regions. This study provides a crucial overview of the population structure and emerging pattern of the enteric parasite, E. histolytica.
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Affiliation(s)
- Shashi Upadhyay
- Department of Allied Health Science, School of Health Science and Technology, University of Petroleum and Energy Studies, Dehradun 248007, India
| | - Koushik Das
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India.
| | - Ajanta Ghosal
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Suvendu Manna
- Department of HSE & Civil Engineering, School of Engineering, University of Petroleum and Energy Studies, Dehradun 248007, India
| | - Yumiko Saito-Nakano
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Shanta Dutta
- Department of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sandipan Ganguly
- Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India.
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Qi Y, Wang J, Lu N, Qi X, Yang C, Liu B, Lu Y, Gu Y, Tan W, Zhu C, Ai L, Rao J, Mao Y, Yi H, Li Y, Yue M. Potential novel Colpodella spp. (phylum Apicomplexa) and high prevalence of Colpodella spp. in goat-attached Haemaphysalis longicornis ticks in Shandong province, China. Ticks Tick Borne Dis 2024; 15:102328. [PMID: 38432073 DOI: 10.1016/j.ttbdis.2024.102328] [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: 06/11/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024]
Abstract
Tick-borne Apicomplexan parasites pose a significant threat to both public health and animal husbandry. Identifying potential pathogenic parasites and gathering their epidemiological data are essential for prospectively preventing and controlling infections. In the present study, genomic DNA of ticks collected from two goat flocks (Goatflock1 and Goatflock2) and one dog group (Doggroup) were extracted and the 18S rRNA gene of Babesia/Theileria/Colpodella spp. was amplified by PCR and sequenced. Phylogenetic analysis was conducted based on the obtained sequences. The differences in pathogen positive rates between ticks of different groups were statistically analyzed using the Chi-square or continuity-adjusted Chi-square test. As a result, two pathogenic Theileria (T.) luwenshuni genotypes, one novel pathogenic Colpodella sp. HLJ genotype, and two potential novel Colpodella spp. (referred to as Colpodella sp. struthionis and Colpodella sp. yiyuansis in this study) were identified in the Haemaphysalis (H.) longicornis ticks. Ticks of Goatflock2 had a significantly higher positive rate of Colpodella spp. than those from Goatflock1 (χ2=92.10; P = 8.2 × 10-22) and Doggroup (χ2=42.34; P = 7.7 × 10-11), and a significantly higher positive rate of T. luwenshuni than Doggroup (χ2=5.38; P = 0.02). However, the positive rates of T. luwenshuni between Goatflock1 and Goatflock2 were not significantly different (χ2=2.02; P = 0.16), and so as the positive rates of both pathogens between Goatflock1 and Doggroup groups (P > 0.05). For either Colpodella spp. or T. luwenshuni, no significant difference was found in prevalence between male and female ticks. These findings underscore the potential importance of Colpodella spp. in domestic animal-attached ticks, as our study revealed two novel Colpodella spp. and identified Colpodella spp. in H. longicornis for the first time. The study also sheds light on goats' potential roles in the transmission of Colpodella spp. to ticks and provides crucial epidemiological data of pathogenic Theileria and Colpodella. These data may help physicians, veterinarians, and public health officers prepare suitable detection and treatment methods and develop prevention and control strategies.
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Affiliation(s)
- Yong Qi
- Huadong Research Institute for Medicine and Biotechniques, 210002, #293 Zhongshandonglu, Nanjing, Jiangsu, China
| | - Junhu Wang
- Huadong Research Institute for Medicine and Biotechniques, 210002, #293 Zhongshandonglu, Nanjing, Jiangsu, China
| | - Nianhong Lu
- Huadong Research Institute for Medicine and Biotechniques, 210002, #293 Zhongshandonglu, Nanjing, Jiangsu, China
| | - Xin Qi
- The Second People's Hospital of Yiyuan County, 256100, Zibo, Shandong, China
| | - Chaoyue Yang
- Army Medical University, 400038, Chongqing, China
| | - Bing Liu
- Department of Disease Control and Prevention, Rocket Force Characteristic Medical Center, 100088, 16 Xinjiekouwai street, Xicheng District, Beijing, China
| | - Yongfeng Lu
- Administration for Drug and Instrument Supervision and Inspection of PLAJLSF, 100071, Beijing, China
| | - Yuan Gu
- The Ninth Outpatient Department, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu province, 210002, China
| | - Weilong Tan
- Huadong Research Institute for Medicine and Biotechniques, 210002, #293 Zhongshandonglu, Nanjing, Jiangsu, China
| | - Changqiang Zhu
- Huadong Research Institute for Medicine and Biotechniques, 210002, #293 Zhongshandonglu, Nanjing, Jiangsu, China
| | - Lele Ai
- Huadong Research Institute for Medicine and Biotechniques, 210002, #293 Zhongshandonglu, Nanjing, Jiangsu, China
| | - Jixian Rao
- Huadong Research Institute for Medicine and Biotechniques, 210002, #293 Zhongshandonglu, Nanjing, Jiangsu, China
| | - Yingqing Mao
- Huadong Research Institute for Medicine and Biotechniques, 210002, #293 Zhongshandonglu, Nanjing, Jiangsu, China
| | - Haiming Yi
- Huadong Research Institute for Medicine and Biotechniques, 210002, #293 Zhongshandonglu, Nanjing, Jiangsu, China
| | - Yuexi Li
- Huadong Research Institute for Medicine and Biotechniques, 210002, #293 Zhongshandonglu, Nanjing, Jiangsu, China
| | - Ming Yue
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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Wu LS, Luo X, Tan M, Zhang LJ, Luo HF, Huang G, Huang P, Chen J, Chen Y. Prevalence of thalassemia-carrier couples and fertility risk assessment. Int J Hematol 2024; 119:374-382. [PMID: 38411864 DOI: 10.1007/s12185-024-03722-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/28/2024]
Abstract
Thalassemia is a highly prevalent hematologic disease in Guizhou, China. This study aimed to determine the epidemiological characteristics of thalassemia in couples at childbearing age and assess the neonatal risk of thalassemia in this subpopulation. A cohort of 4481 couples at childbearing age were recruited for thalassemia carrier screening by both traditional hematological tests and next-generation sequencing. Of them, 1314 (14.66%) thalassemia carriers were identified, including 857 (9.76%) α-thalassemia, 391 (4.36%) β-thalassemia, and 48 (0.54%) composite α and β-thalassemia. A total of 12 α-globin gene alterations and 16 β-globin mutations were detected, including four novel thalassemia mutations. SEA was the most common α-thalassemia genotype (26.86%), CD41-42 the most common β-thalassemia genotype (36.57%), and αα/- α3.7 + CD41-42 the most common composite α- and β-thalassemia genotype (18.75%). Ethnically, the Zhuang had the highest rate of thalassemia gene carriers among the ethnic groups. Geographically, Qiannan had the highest rate of thalassemia gene carriers. In addition, 38 of the 48 couples with composite α- and β-thalassemia were high-risk thalassemia carriers, and 4 carrying the -SEA/αα gene needed fertility guidance.
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Affiliation(s)
- Liu-Song Wu
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Xi Luo
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Mei Tan
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Li-Jun Zhang
- Department of Pediatrics, The Qian-Nan-Zhou People's Hospital of Guizhou, Guizhou, China
| | - Hong-Fang Luo
- Department of Pediatrics, The 2nd Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Ge Huang
- Clinical Laboratory, The Qian-Dong-Nan People's Hospital of Guizhou, Guizhou, China
| | - Pei Huang
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Jindong Chen
- Exploring Health, LLC., 3 Lanyue Rd., Huangpu District, Guangzhou, 510663, China.
- Department of Urology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
| | - Yan Chen
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China.
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China.
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China.
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Sasaki A, Takeshima H, Yamashita S, Ichita C, Kawachi J, Naito W, Ohashi Y, Takeuchi C, Fukuda M, Furuichi Y, Yamamichi N, Ando T, Kobara H, Kotera T, Itoi T, Sumida C, Hamada A, Koizumi K, Ushijima T. Severe induction of aberrant DNA methylation by nodular gastritis in adults. J Gastroenterol 2024:10.1007/s00535-024-02094-y. [PMID: 38499886 DOI: 10.1007/s00535-024-02094-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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/29/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Nodular gastritis (NG) is characterized by marked antral lymphoid follicle formation, and is a strong risk factor for diffuse-type gastric cancer in adults. However, it is unknown whether aberrant DNA methylation, which is induced by atrophic gastritis (AG) and is a risk for gastric cancer, is induced by NG. Here, we analyzed methylation induction by NG. METHODS Gastric mucosal samples were obtained from non-cancerous antral tissues of 16 NG and 20 AG patients with gastric cancer and 5 NG and 6 AG patients without, all age- and gender-matched. Genome-wide methylation analysis and expression analysis were conducted by a BeadChip array and RNA-sequencing, respectively. RESULTS Clustering analysis of non-cancerous antral tissues of NG and AG patients with gastric cancer was conducted using methylation levels of 585 promoter CpG islands (CGIs) of methylation-resistant genes, and a large fraction of NG samples formed a cluster with strong methylation induction. Promoter CGIs of CDH1 and DAPK1 tumor-suppressor genes were more methylated in NG than in AG. Notably, methylation levels of these genes were also higher in the antrum of NG patients without cancer. Genes related to lymphoid follicle formation, such as CXCL13/CXCR5 and CXCL12/CXCR4, had higher expression in NG, and genes involved in DNA demethylation TET2 and IDH1, had only half the expression in NG. CONCLUSIONS Severe aberrant methylation, involving multiple tumor-suppressor genes, was induced in the gastric antrum and body of patients with NG, in accordance with their high gastric cancer risk.
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Affiliation(s)
- Akiko Sasaki
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Chikamasa Ichita
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Jun Kawachi
- Department of General Surgery, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Wataru Naito
- Department of Diagnostic Pathology, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Yui Ohashi
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Chihiro Takeuchi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Masahide Fukuda
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Yumi Furuichi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
- Department of Gastroenterological Surgery, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Nobutake Yamamichi
- Center for Epidemiology and Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takayuki Ando
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Hideki Kobara
- Department of Gastroenterology and Neurology, Kagawa University, Kagawa, Japan
| | - Tohru Kotera
- Department of Medical Examination, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Takao Itoi
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo, Japan
| | - Chihiro Sumida
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Akinobu Hamada
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazuya Koizumi
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan.
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Sarenje KL, van Zwetselaar M, Kumburu H, Sonda T, Mmbaga B, Ngalamika O, Maimbolwa MC, Siame A, Munsaka S, Kwenda G. Antimicrobial resistance and heterogeneity of Neisseria gonorrhoeae isolated from patients attending sexually transmitted infection clinics in Lusaka, Zambia. BMC Genomics 2024; 25:290. [PMID: 38500064 PMCID: PMC10949682 DOI: 10.1186/s12864-024-10155-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) of Neisseria gonorrhoeae is a threat to public health as strains have developed resistance to antimicrobials available for the treatment of gonorrhea. Whole genome sequencing (WGS) can detect and predict antimicrobial resistance to enhance the control and prevention of gonorrhea. Data on the molecular epidemiology of N. gonorrhoeae is sparse in Zambia. This study aimed to determine the genetic diversity of N. gonorrhoeae isolated from patients attending sexually transmitted infection (STI) clinics in Lusaka, Zambia. METHODS A cross-sectional study that sequenced 38 N. gonorrhoeae isolated from 122 patients with gonorrhea from 2019 to 2020 was conducted. The AMR profiles were determined by the E-test, and the DNA was extracted using the NucliSens easyMaG magnetic device. Whole genome sequencing was performed on the Illumina NextSeq550 platform. The Bacterial analysis pipeline (BAP) that is readily available at: https://cge.cbs.dtu.dk/services/CGEpipeline-1.1 was used for the identification of the species, assembling the genome, multi-locus sequence typing (MLST), detection of plasmids and AMR genes. Phylogeny by single nucleotide polymorphisms (SNPs) was determined with the CCphylo dataset. RESULTS The most frequent STs with 18.4% of isolates each were ST7363, ST1921 and ST1582, followed by ST1583 (13%), novel ST17026 (7.9%), ST1588 (7.9%), ST1596 (5.3%), ST11181 (5.3%), ST11750 (2.6/%) and ST11241 (2.6%) among the 38 genotyped isolates. The blaTeM-1B and tetM (55%) was the most prevalent combination of AMR genes, followed by blaTeM-1B (18.4%), tetM (15.8%), and the combination of blaTeM-1B, ermT, and tetL was 2.6% of the isolates. The AMR phenotypes were predicted in ciprofloxacin, penicillin, tetracycline, azithromycin, and cefixime. The combination of mutations 23.7% was gryA (S91F), parC (E91G), ponA (L421) and rpsJ (V57M), followed by 18.4% in gyrA (S91F), ponA (L421P), rpsJ (V57M), and 18.4% in gyrA (D95G, S91F), ponA (L421P), and rpsJ (V57M). The combinations in gyrA (D95G, S91F) and rpsJ (V57M), and gyrA (D95G, S91F), parC (E91F), ponA (L421P) and rpsJ (V57M) were 13.2% each of the isolates. Plasmid TEM-1 (84.2%), tetM (15.8%), and gonococcal genetic island (GGI) was detected in all isolates. CONCLUSION This study revealed remarkable heterogeneity of N. gonorrhoeae with blaTEM-1, tetM, ponA, gyrA, and parC genes associated with high resistance to penicillin, tetracycline, and ciprofloxacin demanding revision of the standard treatment guidelines and improved antimicrobial stewardship in Zambia.
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Affiliation(s)
- Kelvin Lutambo Sarenje
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, P.O. Box 50110, Zambia.
- Department of Dermato-venereology, University Teaching Hospital, Lusaka, Zambia.
| | | | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Blandina Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Owen Ngalamika
- Department of Dermato-venereology, University Teaching Hospital, Lusaka, Zambia
| | - Margaret C Maimbolwa
- Department of Midwifery Child, and Women's Health, School of Nursing Sciences, University of Zambia, Lusaka, Zambia
| | - Amon Siame
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Sody Munsaka
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, P.O. Box 50110, Zambia
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, P.O. Box 50110, Zambia
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7
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Jacobsen S, Faber M, Altmann B, Mas Marques A, Bock CT, Niendorf S. Impact of the COVID-19 pandemic on norovirus circulation in Germany. Int J Med Microbiol 2024; 314:151600. [PMID: 38246091 DOI: 10.1016/j.ijmm.2024.151600] [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: 10/31/2023] [Revised: 12/14/2023] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Human norovirus is a major cause of viral gastroenteritis in all age groups. The virus is constantly and rapidly changing, allowing mutations and recombination events to create great diversity of circulating viruses. With the start of the COVID-19 pandemic in 2020, a wide range of public health measures were introduced worldwide to control human-to-human transmission of SARS-CoV-2. In Germany, control measures such as distance rules, contact restrictions, personal protection equipment as well as intensive hand hygiene were introduced. To better understand the effect of the measures to control the COVID-19 pandemic on incidence and the molecular epidemiological dynamics of norovirus outbreaks in Germany, we analyzed national notification data between July 2017 and December 2022 and characterized norovirus sequences circulating between January 2018 and December 2022. Compared to a reference period before the pandemic, the incidence of notified norovirus gastroenteritis decreased by 89.7% to 9.6 per 100,000 during the 2020/2021 norovirus season, corresponding to an incidence rate ratio (IRR) of 0.10. Samples from 539 outbreaks were genotyped in two regions of the viral genome from pre-pandemic (January 2018 to February 2020) and samples from 208 outbreaks during pandemic time period (March 2020 to December 2022). As expected, norovirus outbreaks were mainly found in child care facilities and nursing homes. In total, 36 genotypes were detected in the study period. A high proportion of recombinant strains (86%) was found in patients, the proportion of detected recombinant viruses did not vary between the pre-pandemic and pandemic phase. The proportion of the predominant recombinant strain GII.4 Sydney[P16] was unchanged before pandemic and during pandemic at 37.5%. The diversity of most common genotypes in nursing homes and child care facilities showed a different proportion of genotypes causing outbreaks. In nursing homes as well as in child care facilities GII.4 Sydney[P16] was predominant during the whole study period. Compared to the nursing homes, a greater variety of genotypes at the expense of GII.4 Sydney[P16] was detected in child care facilities. Furthermore, the overall proportion of recombinant strain GII.3[P12] increased during the pandemic, due to outbreaks in child care facilities. The COVID-19 pandemic had a high impact on the occurrence of sporadic cases and norovirus outbreaks in Germany, leading to a near suppression of the typical norovirus winter season following the start of the pandemic. The number of norovirus-associated outbreak samples sent to the Consultant Laboratory dropped by 63% during the pandemic. We could not identify a clear influence on circulating norovirus genotypes. The dominance of GII.4 Sydney recombinant strains was independent from the pandemic. Further studies are needed to follow up on the diversity of less predominant genotypes to see if the pandemic could have acted as a bottleneck to the spread of previously minoritized genotypes like GII.3[P12].
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Affiliation(s)
- Sonja Jacobsen
- Consultant Laboratory for Norovirus, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Mirko Faber
- Department of Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Britta Altmann
- Department of Infectious Disease, Robert Koch Institute, 13353 Berlin, Germany
| | - Andreas Mas Marques
- Consultant Laboratory for Norovirus, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - C-Thomas Bock
- Department of Infectious Disease, Robert Koch Institute, 13353 Berlin, Germany
| | - Sandra Niendorf
- Consultant Laboratory for Norovirus, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany.
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8
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Wu H, Zhou L, Wang F, Chen Z, Lu Y. Molecular epidemiology and phylogeny of the emerging zoonotic virus Rocahepevirus: A global genetic analysis. Infect Genet Evol 2024; 118:105557. [PMID: 38244748 DOI: 10.1016/j.meegid.2024.105557] [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: 12/22/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/22/2024]
Abstract
Human infections with Rocahepevirus ratti genotype C1 (HEV-C1) in Hong Kong of China, Canada, Spain, and France have drawn worldwide concern towards Rocahepevirus. This study conducted a global genetic analysis of Rocahepevirus, aiming to furnish comprehensive molecular insights and promote further research. We retrieved 817 Rocahepevirus sequences from the GenBank database through October 31, 2023, categorizing them according to research, sample collection area and date, genotype, host, and sequence length. Subsequently, we conducted descriptive epidemiological, phylogenetic evolutionary, and protein polymorphism (in length and identity) analyses on these sequences. Rocahepevirus genomes were identified across twenty-eight countries, predominantly in Asia (71.73%, 586/817) and Europe (26.44%, 216/817). The HEV-C1 dominates Rocahepevirus (77.2%, 631/817), while newly discovered Rocahepevirus genotypes (C3/C4/C5 and other unclassified genotypes) were primarily identified in Europe (25/120) and China (91/120). Muridae animals (72.5%, 592/817) serve as the primary hosts for Rocahepevirus, with other hosts encompassing species from the families Soricidae, Hominidae, Mustelidae, and Cricetidae. Additionally, Rocahepevirus genomes (C1 genotype) were identified in sewage samples recently. The phylogenetic evolution of Rocahepevirus exhibits considerable variation. Specifically, HEV-C1 can be classified into at least six genetic groups (G1 to G6), with human HEV-C1 distributed across multiple evolutionary clades. The overall ORF1 and ORF2 amino acid sequence lengths were significantly different (P < 0.001) across Rocahepevirus genotypes. HEV-C1/C2/C3 and HEV-C4/C5 displayed substantial differences in amino acid sequence identity (58.4%-59.6%). The identification of Rocahepevirus genomes has expanded across numerous countries, particularly in European and Asian countries, coinciding with an expanding host range and emergence of new genotypes. The evolutionary path of Rocahepevirus is intricate, where the HEV-C1 dominates globally and internally forms multiple evolutionary groups (G1 to G6), exhibiting diverse genetic variation within human HEV-C1. Significant differences exist in the protein polymorphism (in length and identity) across Rocahepevirus genotypes. Given Rocahepevirus's shift from an animal virus to a zoonotic pathogen, worldwide cooperation in monitoring Rocahepevirus genomes is vital.
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Affiliation(s)
- Han Wu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai 200032, China
| | - Lu Zhou
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai 200032, China
| | - Fengge Wang
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai 200032, China
| | - Zixiang Chen
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai 200032, China
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai 200032, China.
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9
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Hanke K, Rykalina V, Koppe U, Gunsenheimer-Bartmeyer B, Heuer D, Meixenberger K. Developing a next level integrated genomic surveillance: Advances in the molecular epidemiology of HIV in Germany. Int J Med Microbiol 2024; 314:151606. [PMID: 38278002 DOI: 10.1016/j.ijmm.2024.151606] [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: 10/31/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Advances in the molecular epidemiological studies of the Human Immunodeficiency Virus (HIV) at the Robert Koch Institute (RKI) by laboratory and bioinformatic automation should allow the processing of larger numbers of samples and more comprehensive and faster data analysis in order to provide a higher resolution of the current HIV infection situation in near real-time and a better understanding of the dynamic of the German HIV epidemic. The early detection of the emergence and transmission of new HIV variants is important for the adaption of diagnostics and treatment guidelines. Likewise, the molecular epidemiological detection and characterization of spatially limited HIV outbreaks or rapidly growing sub-epidemics is of great importance in order to interrupt the transmission pathways by regionally adapting prevention strategies. These aims are becoming even more important in the context of the SARS-CoV2 pandemic and the Ukrainian refugee movement, which both have effects on the German HIV epidemic that should be monitored to identify starting points for targeted public health measures in a timely manner. To this end, a next level integrated genomic surveillance of HIV is to be established.
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Affiliation(s)
- Kirsten Hanke
- Unit 18: Sexually transmitted bacterial Pathogens (STI) and HIV, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.
| | - Vera Rykalina
- Unit 18: Sexually transmitted bacterial Pathogens (STI) and HIV, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Uwe Koppe
- Unit 34: HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | | | - Dagmar Heuer
- Unit 18: Sexually transmitted bacterial Pathogens (STI) and HIV, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Karolin Meixenberger
- Unit 18: Sexually transmitted bacterial Pathogens (STI) and HIV, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
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10
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Allen JL, Bushell RN, Noormohammadi AH, Stent AW, Whiteley P, Browning GF, Marenda MS. Pasteurella multocida ST20 is widespread in Australian poultry farms and may infect wild waterbirds. Vet Microbiol 2024; 290:109990. [PMID: 38228079 DOI: 10.1016/j.vetmic.2024.109990] [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: 08/26/2023] [Revised: 12/16/2023] [Accepted: 01/09/2024] [Indexed: 01/18/2024]
Abstract
The bacterial agent that causes fowl cholera, Pasteurella multocida, was isolated from two deceased wild waterbirds in Victoria, Australia, in 2013. Whole genome sequence analysis placed the isolates into ST20, a subtype described in farmed chickens from Queensland, Australia and more recently in feedlot cattle and in pigs across a broader area of the continent. This study also found ST20 between 2009 and 2022 on three chicken farms and two turkey farms located in four Australian states. The sequences of 25 of these ST20 isolates were compared to 280 P. multocida genomes from 23 countries and to 94 ST20 Illumina datasets from Queensland that have been deposited in public databases. The ST20 isolates formed a single phylogenetic clade and were clustered into four sub-groups with highly similar genomes, possessing either LPS type 1 or type 3 loci. Various repertoires of mobile genetic elements were present in isolates from farmed, but not wild birds, suggesting complex histories of spill-over between avian populations and gene acquisition within farm environments. No major antimicrobial resistance was predicted in any of the ST20 isolates by the genomic analysis. The closest relative of these isolates was a ST394 bovine respiratory tract isolate from Queensland, which differed from ST20 by only one allele and carried beta-lactam and tetracycline resistance genes. These findings underline the importance of understanding the role of wild and commercial birds in the maintenance of fowl cholera, and of implementing regular epidemiological surveillance and biosecurity management programmes in wildlife, as well as free-range poultry farms.
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Affiliation(s)
- Joanne L Allen
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Rhys N Bushell
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, Victoria 3030 Australia
| | - Amir H Noormohammadi
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia; Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, Victoria 3030 Australia
| | - Andrew W Stent
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, Victoria 3030 Australia.
| | - Pam Whiteley
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, Victoria 3030 Australia; Wildlife Health Victoria: Surveillance, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, Victoria 3030 Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marc S Marenda
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia; Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, Victoria 3030 Australia
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11
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Obeng BM, Kelleher AD, Di Giallonardo F. Molecular epidemiology to aid virtual elimination of HIV transmission in Australia. Virus Res 2024; 341:199310. [PMID: 38185332 PMCID: PMC10825322 DOI: 10.1016/j.virusres.2024.199310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/09/2024]
Abstract
The Global UNAIDS 95/95/95 targets aim to increase the percentage of persons who know their HIV status, receive antiretroviral therapy, and have achieved viral suppression. Achieving these targets requires efforts to improve the public health response to increase access to care for those living with HIV, identify those yet undiagnosed with HIV early, and increase access to prevention for those most at risk of HIV acquisition. HIV infections in Australia are among the lowest globally having recorded significant declines in new diagnoses in the last decade. However, the HIV epidemic has changed with an increasing proportion of newly diagnosed infections among those born outside Australia observed in the last five years. Thus, the current prevention efforts are not enough to achieve the UNAIDS targets and virtual elimination across all population groups. We believe both are possible by including molecular epidemiology in the public health response. Molecular epidemiology methods have been crucial in the field of HIV prevention, particularly in demonstrating the efficacy of treatment as prevention. Cluster detection using molecular epidemiology can provide opportunities for the real-time detection of new outbreaks before they grow, and cluster detection programs are now part of the public health response in the USA and Canada. Here, we review what molecular epidemiology has taught us about HIV evolution and spread. We summarize how we can use this knowledge to improve public health measures by presenting case studies from the USA and Canada. We discuss the successes and challenges of current public health programs in Australia, and how we could use cluster detection as an add-on to identify gaps in current prevention measures easier and respond quicker to growing clusters. Lastly, we raise important ethical and legal challenges that need to be addressed when HIV genotypic data is used in combination with personal data.
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Affiliation(s)
- Billal M Obeng
- The Kirby Institute, University of New South Wales, Sydney, Australia
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12
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Li L, Li B, Wang J, Liu L, Li Y, Sun S, Yin S, Zhang L, Liu X, Xu X, Guo H. A novel recombination porcine epidemic diarrhea virus isolated from Gansu, China: Genetic characterization and pathogenicity. Vet Microbiol 2024; 290:109975. [PMID: 38183838 DOI: 10.1016/j.vetmic.2023.109975] [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: 10/10/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024]
Abstract
Porcine epidemic diarrhea virus (PEDV) is an acute and highly contagious porcine enteric coronavirus. It has caused serious economic losses of pig industry in China. Here we insolated a current PEDV field strain named GS2022, analyzed the characters of genetic variation and pathogenicity. The results demonstrated that the GS2022 strain was belong to a newly defined subgroup G2 d, forming an independent branch which mainly contains strains isolated in China from 2017 to 2023. Notably, there are multiple mutations and extensive N-glycosylation compared to CV777 strain and PT-P5 strain, therefore the structure of GS2022 strain is different from 6U7K and 7W6M. Animal pathogenicity test showed that GS2022 strain could cause severe clinical signs and the high level of virus shedding in 7-day-old piglets. But recovery of diarrhea after 5 days, and no pathological damage to important organs. Further study on 3-day-old piglets also indicated GS2022 strain have pathogenicity. In this study no piglets died, which make it possible for that GS2022 strain become a candidate vaccine. These results are helpful to understand the epidemiology, molecular characteristics, evolution, and antigenicity of PEDV circulating in China. It also provides reference for designing effective vaccines against PEDV.
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Affiliation(s)
- Linjie Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bingqing Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jin Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Lei Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Yi Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shiqi Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shuanghui Yin
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Liping Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xinsheng Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xingang Xu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
| | - Huichen Guo
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China.
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13
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Castro-Rodriguez B, León-Ordóñez K, Franco-Sotomayor G, Benítez-Medina JM, Jiménez-Pizarro N, Cárdenas-Franco G, Granda JC, Aguirre-Martínez JL, Orlando SA, Hermoso de Mendoza J, García-Bereguiain MÁ. Population structure of Mycobacterium tuberculosis in El Oro: A first insight into Ecuador-Peru tuberculosis transmission. J Infect Public Health 2024; 17:527-534. [PMID: 38310744 DOI: 10.1016/j.jiph.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/06/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) is a major public health concern in Ecuador and Peru, both settings of high burden of drug resistance TB. Molecular epidemiology tools are important to understand the transmission dynamics of Mycobacterium tuberculosis Complex (MTBC) and to track active transmission clusters of regional importance. This study is the first to address the transmission of TB between Peru and Ecuador through the population structure of MTBC lineages circulating in the Ecuadorian border province of "El Oro". METHODS A total number of 56 MTBC strains from this province for years 2012-2015 were included in the study and analyzed by 24-loci MIRU-VNTR and spoligotyping. RESULTS Genotyping revealed a high degree of diversity for MTBC in "El Oro", without active transmission clusters. MTBC L4 was predominant, with less than 2% of strains belonging to MTBC L2-Beijing. CONCLUSIONS These results may suggest that TB dynamics in this rural and semi-urban area would not be linked to highly transmitted strains like MTBC L2-Beijing from Peru, but related to TB relapse; although further studies with larger MTBC cultures collection from recent years are needed. Nevertheless, we recommend to reinforce TB surveillance programs in remote rural settings and border regions in Ecuador.
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Affiliation(s)
| | - Kerly León-Ordóñez
- One Health Research Group. Universidad de las Américas, Quito, Ecuador; Yachay Tech University, Urcuquí, Ecuador
| | - Greta Franco-Sotomayor
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador; Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | | | - Natalia Jiménez-Pizarro
- Departamento de Sanidad Animal. Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | | | - Juan Carlos Granda
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
| | | | - Solon Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador; Universidad Espíritu Santo, Guayaquil, Ecuador
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14
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Nakamizo T, Cologne J, Kishi T, Takahashi T, Inoue M, Ryukaku H, Hayashi T, Kusunoki Y, Fujiwara S, Ohishi W. Reliability, stability during long-term storage, and intra-individual variation of circulating levels of osteopontin, osteoprotegerin, vascular endothelial growth factor-A, and interleukin-17A. Eur J Med Res 2024; 29:133. [PMID: 38368424 PMCID: PMC10873926 DOI: 10.1186/s40001-024-01722-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 02/09/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND Studies in many populations have reported associations between circulating cytokine levels and various physiological or pathological conditions. However, the reliability of cytokine measurements in population studies, which measure cytokines in multiple assays over a prolonged period, has not been adequately examined; nor has stability during sample storage or intra-individual variation been assessed. METHODS We assessed (1) analytical reliability in short- and long-term repeated measurements; (2) stability and analytical reliability during long-term sample storage, and (3) variability within individuals over seasons, of four cytokines-osteopontin (OPN), osteoprotegerin (OPG), vascular endothelial growth factor-A (VEGF-A), and interleukin-17A (IL-17A). Measurements in plasma or serum samples were made with commercial kits according to standard procedures. Estimation was performed by fitting a random or mixed effects linear model on the log scale. RESULTS In repeated assays over a short period, OPN, OPG, and VEGF-A had acceptable reliability, with intra- and inter-assay coefficients of variation (CV) less than 0.11. Reliability of IL-17A was poor, with inter- and intra-assay CV 0.85 and 0.43, respectively. During long-term storage, OPG significantly decayed (- 33% per year; 95% confidence interval [- 54, - 3.7]), but not OPN or VEGF-A (- 0.3% or - 6.3% per year, respectively). Intra- and inter-assay CV over a long period were comparable to that in a short period except for a slight increase in inter-assay CV of VEGF-A. Within-individual variation was small for OPN and VEGF-A, with intra-class correlations (ICC) 0.68 and 0.83, respectively, but large for OPG (ICC 0.11). CONCLUSIONS We conclude that OPN and VEGF-A can be reliably measured in a large population, that IL-17A is suitable only for small experiments, and that OPG should be assessed with caution due to degradation during storage and intra-individual variation. The overall results of our study illustrate the need for validation under relevant conditions when measuring circulating cytokines in population studies.
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Affiliation(s)
| | | | - Takeshi Kishi
- Division of Clinical Laboratories, RERF, Hiroshima, Japan
| | - Tetsuya Takahashi
- Faculty of Rehabilitation, Hiroshima International University, Hiroshima, Japan
| | - Mayumi Inoue
- Division of Clinical Laboratories, RERF, Hiroshima, Japan
| | | | | | | | - Saeko Fujiwara
- Faculty of Pharmacy, Yasuda Women's University, Hiroshima, Japan
| | - Waka Ohishi
- Department of Clinical Studies, RERF, Hiroshima, Japan
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15
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Iman MN, Haslam DE, Liang L, Guo K, Joshipura K, Pérez CM, Clish C, Tucker KL, Manson JE, Bhupathiraju SN, Fukusaki E, Lasky-Su J, Putri SP. Multidisciplinary approach combining food metabolomics and epidemiology identifies meglutol as an important bioactive metabolite in tempe, an Indonesian fermented food. Food Chem 2024; 446:138744. [PMID: 38432131 DOI: 10.1016/j.foodchem.2024.138744] [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: 09/26/2023] [Revised: 02/09/2024] [Accepted: 02/10/2024] [Indexed: 03/05/2024]
Abstract
This study introduces a multidisciplinary approach to investigate bioactive food metabolites often overlooked due to their low concentrations. We integrated an in-house food metabolite library (n = 494), a human metabolite library (n = 891) from epidemiological studies, and metabolite pharmacological databases to screen for food metabolites with potential bioactivity. We identified six potential metabolites, including meglutol (3-hydroxy-3-methylglutarate), an understudied low-density lipoprotein (LDL)-lowering compound. We further focused on meglutol as a case study to showcase the range of characterizations achievable with this approach. Green pea tempe was identified to contain the highest meglutol concentration (21.8 ± 4.6 mg/100 g). Furthermore, we identified a significant cross-sectional association between plasma meglutol (per 1-standard deviation) and lower LDL cholesterol in two Hispanic adult cohorts (n = 1,628) (β [standard error]: -5.5 (1.6) mg/dl, P = 0.0005). These findings highlight how multidisciplinary metabolomics can serve as a systematic tool for discovering and enhancing bioactive metabolites in food, such as meglutol, with potential applications in personalized dietary approaches for disease prevention.
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Affiliation(s)
- Marvin N Iman
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan
| | - Danielle E Haslam
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kai Guo
- Center for Clinical Research and Health Promotion, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus, Puerto Rico, USA
| | - Kaumudi Joshipura
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Center for Clinical Research and Health Promotion, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus, Puerto Rico, USA
| | - Cynthia M Pérez
- Department of Biostatistics and Epidemiology, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus, Puerto Rico, USA
| | - Clary Clish
- Broad Institute of Massachusetts Institute of Technology and Harvard, USA
| | - Katherine L Tucker
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, USA
| | - JoAnn E Manson
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shilpa N Bhupathiraju
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Japan
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sastia P Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Japan.
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Onoja BA, Adamu AM, Anyang AS, Oragwa AO, Omeiza GK, Olabode OH, Horwood PF. Detection and genetic characterization of orf virus from sheep and goats in Nigeria. Trop Anim Health Prod 2024; 56:77. [PMID: 38351341 DOI: 10.1007/s11250-024-03893-4] [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: 05/08/2023] [Accepted: 01/05/2024] [Indexed: 02/16/2024]
Abstract
Orf is a contagious, viral epitheliotropic disease of small ruminants. We investigated the molecular epidemiology of orf virus (ORFV) in breeds of small ruminants to determine the evolutionary diversity in Nigeria. Out of 54 small ruminants screened, the number of animals that were positive for ORFV in the three locations were 25. The distribution of positive animals by location were FCT 45.0% (n = 9/20), Oyo State 42.9% (6/14), and Plateau State 50.0% (n = 10/20). ORFV sequences from this study clustered with viruses detected in Taiwan, Iran, USA, and France. Our findings highlight the risk of transmission across geographic boundaries in Nigeria and West Africa, and reinforces the need for increased surveillance to prevent and control spread. Comprehensive characterization of ORFV in small ruminants as well as in humans in Nigeria is required to better elucidate the epidemiological dynamics and the virus evolution.
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Affiliation(s)
- B A Onoja
- Department of Virology, University of Ibadan, Ibadan, 200005, Nigeria.
| | - A M Adamu
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
- Department of Veterinary Public Health and Preventive Medicine, University of Abuja, Abuja, 900105, Nigeria
| | - A S Anyang
- Department of Veterinary Public Health and Preventive Medicine, University of Abuja, Abuja, 900105, Nigeria
| | - A O Oragwa
- Department of Veterinary Microbiology and Pathology, University of Jos, Jos, 930003, Nigeria
| | - G K Omeiza
- Department of Veterinary Public Health and Preventive Medicine, University of Abuja, Abuja, 900105, Nigeria
| | - O H Olabode
- Department of Veterinary Microbiology, University of Abuja, Abuja, 900105, Nigeria
| | - P F Horwood
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
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Li J, Tang M, Liu Z, Wei Y, Xia F, Xia Y, Hu Y, Wang H, Zou M. Molecular characterization of extensively drug-resistant hypervirulent Pseudomonas aeruginosa isolates in China. Ann Clin Microbiol Antimicrob 2024; 23:13. [PMID: 38347529 PMCID: PMC10863134 DOI: 10.1186/s12941-024-00674-7] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/04/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Recently, extensively drug-resistant Pseudomonas aeruginosa (XDR-PA) isolates have been increasingly detected and posed great challenges to clinical anti-infection treatments. However, little is known about extensively resistant hypervirulent P. aeruginosa (XDR-hvPA). In this study, we investigate its epidemiological characteristics and provide important basis for preventing its dissemination. METHODS Clinical XDR-PA isolates were collected from January 2018 to January 2023 and identified using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry; antibiotic susceptibility testing was performed by broth microdilution method, and minimum inhibitory concentrations (MICs) were evaluated. Virulence was evaluated using the Galleria mellonella infection model; molecular characteristics, including resistance genes, virulence genes, and homology, were determined using whole-genome sequencing. RESULTS A total of 77 XDR-PA strains were collected; 47/77 strains were XDR-hvPA. Patients aged > 60 years showed a significantly higher detection rate of XDR-hvPA than of XDR-non-hvPA. Among the 47 XDR-hvPA strains, 24 strains carried a carbapenemase gene, including blaGES-1 (10/47), blaVIM-2 (6/47), blaGES-14 (4/47), blaIMP-45 (2/47), blaKPC-2 (1/47), and blaNDM-14 (1/47). ExoU, exoT, exoY, and exoS, important virulence factors of PA, were found in 31/47, 47/47, 46/47, and 29/47 strains, respectively. Notably, two XDR-hvPA simultaneously co-carried exoU and exoS. Six serotypes (O1, O4-O7, and O11) were detected; O11 (19/47), O7 (13/47), and O4 (9/47) were the most prevalent. In 2018-2020, O4 and O7 were the most prevalent serotypes; 2021 onward, O11 (16/26) was the most prevalent serotype. Fourteen types of ST were detected, mainly ST235 (14/47), ST1158 (13/47), and ST1800 (7/47). Five global epidemic ST235 XDR-hvPA carried blaGES and showed the MIC value of ceftazidime/avibactam reached the susceptibility breakpoint (8/4 mg/L). CONCLUSIONS The clinical detection rate of XDR-hvPA is unexpectedly high, particularly in patients aged > 60 years, who are seemingly more susceptible to contracting this infection. Clonal transmission of XDR-hvPA carrying blaGES, which belongs to the global epidemic ST235, was noted. Therefore, the monitoring of XDR-hvPA should be strengthened, particularly for elderly hospitalized patients, to prevent its spread.
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Affiliation(s)
- Jun Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Mengli Tang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zhaojun Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yuhan Wei
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Fengjun Xia
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yubing Xia
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yongmei Hu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Haichen Wang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Mingxiang Zou
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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Takeuchi C, Sato J, Yamamichi N, Kageyama-Yahara N, Sasaki A, Akahane T, Aoki R, Nakajima S, Ito M, Yamamichi M, Liu YY, Sakuma N, Takahashi Y, Sakaguchi Y, Tsuji Y, Sakurai K, Tomida S, Niimi K, Ushijima T, Fujishiro M. Marked intestinal trans-differentiation by autoimmune gastritis along with ectopic pancreatic and pulmonary trans-differentiation. J Gastroenterol 2024; 59:95-108. [PMID: 37962678 PMCID: PMC10810929 DOI: 10.1007/s00535-023-02055-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Autoimmune gastritis (AIG) is a prevalent chronic inflammatory disease with oncogenic potential that causes destruction of parietal cells and severe mucosal atrophy. We aimed to explore the distinctive gene expression profiles, activated signaling pathways, and their underlying mechanisms. METHODS A comprehensive gene expression analysis was conducted using biopsy specimens from AIG, Helicobacter pylori-associated gastritis (HPG), and non-inflammatory normal stomachs. Gastric cancer cell lines were cultured under acidic (pH 6.5) conditions to evaluate changes in gene expression. RESULTS Gastric mucosa with AIG had a unique gene expression profile compared with that with HPG and normal mucosa, such as extensively low expression of ATP4A and high expression of GAST and PAPPA2, which are involved in neuroendocrine tumorigenesis. Additionally, the mucosa with AIG and HPG showed the downregulation of stomach-specific genes and upregulation of small intestine-specific genes; however, intestinal trans-differentiation was much more prominent in AIG samples, likely in a CDX-dependent manner. Furthermore, AIG induced ectopic expression of pancreatic digestion-related genes, PNLIP, CEL, CTRB1, and CTRC; and a master regulator gene of the lung, NKX2-1/TTF1 with alveolar fluid secretion-related genes, SFTPB and SFTPC. Mechanistically, acidic conditions led to the downregulation of master regulator and stemness control genes of small intestine, suggesting that increased environmental pH may cause abnormal intestinal differentiation in the stomach. CONCLUSIONS AIG induces diverse trans-differentiation in the gastric mucosa, characterized by the transactivation of genes specific to the small intestine, pancreas, and lung. Increased environmental pH owing to AIG may cause abnormal differentiation of the gastric mucosa.
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Affiliation(s)
- Chihiro Takeuchi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Junichi Sato
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Nobutake Yamamichi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan.
- Center for Epidemiology and Preventive Medicine, The University of Tokyo Hospital, Tokyo, Japan.
| | - Natsuko Kageyama-Yahara
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Akiko Sasaki
- Department of Gastroenterology, Medicine Center, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Takemi Akahane
- Department of Gastroenterology, Nara Medical University, Nara, Japan
| | - Rika Aoki
- Tokushima Health Screening Center, Tokushima, Japan
| | - Shigemi Nakajima
- Department of General Medicine, Japan Community Healthcare Organization Shiga Hospital, Consortium for Community Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Masayoshi Ito
- Department of Gastroenterology, Yotsuya Medical Cube, Tokyo, Japan
| | - Mitsue Yamamichi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Yu-Yu Liu
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Nobuyuki Sakuma
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
- Center for Epidemiology and Preventive Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Yu Takahashi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Yoshiki Sakaguchi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Yosuke Tsuji
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Kouhei Sakurai
- Department of Pathology, Fujita Health University School of Medicine, Aichi, Japan
| | - Shuta Tomida
- Center for Comprehensive Genomic Medicine, Okayama University Hospital, Okayama, Japan
| | - Keiko Niimi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
- Center for Epidemiology and Preventive Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
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Lambert MÈ, Arsenault J, Côté JC, D'Allaire S. A descriptive study on spatial and temporal distributions of genetic clusters of porcine reproductive and respiratory syndrome virus infecting pig sites in Quebec, Canada, between 2010 and 2019. Porcine Health Manag 2024; 10:7. [PMID: 38273419 PMCID: PMC10809575 DOI: 10.1186/s40813-024-00357-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The wide diversity of porcine reproductive and respiratory syndrome virus (PRRSV) strains combined with incomplete heterologous cross-protection complicates the management of the disease at both the herd and the regional levels. The objectives of this study were to describe the spatial and temporal distribution of various PRRSV genetic clusters infecting pig sites in Quebec, Canada, and to compare PRRSV regional diversity of wild-type sequences over the years. MATERIALS AND METHODS A retrospective surveillance-based study was conducted on all pig sites which had PRRSV ORF5 sequences from field submissions transferred into the Laboratoire d'épidémiologie et de médecine porcine database from January 1, 2010 to December 31, 2019. A maximum likelihood phylogenetic tree inferred from multiple sequence alignment was used to identify genetic clusters. For each wild-type cluster gathering ≥ 15 sequences, the number of pig sites in which the cluster was detected per administrative region and per year were displayed on bubble charts and the spatiotemporal distribution of pig sites was illustrated using pie chart maps. A molecular analysis of variance was performed to compare PRRSV wild-type sequence diversity according to the administrative region for each year. RESULTS A total of 32 wild-type clusters gathering 1653 PRRSV2 sequences from 693 pig sites were described. Each cluster was detected on up to 132 pig sites and 7 administrative regions over the 10-year period. Annually, the mean (min-max) number of wild-type clusters detected in at least one pig site reached 24 (17-29). Some clusters remained localized on a few sites over time whereas others were widespread over the territory during a few or many years. For each year, regional differences were also observed in PRRSV diversity of wild-type sequences. CONCLUSIONS The differences observed in both the spatiotemporal distributions of PRRSV clusters and in the regional diversity of wild-type sequences highlight the importance of ongoing provincial surveillance to improve collective PRRS management strategies.
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Affiliation(s)
- Marie-Ève Lambert
- Laboratoire d'épidémiologie et de médecine porcine, Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, QC, Canada.
- Centre de recherche en infectiologie porcine et avicole - Fonds de recherche du Québec - Nature et technologies, Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, QC, Canada.
- Groupe de recherche sur les maladies infectieuses en production animale, Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, QC, Canada.
| | - Julie Arsenault
- Laboratoire d'épidémiologie et de médecine porcine, Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, QC, Canada
- Centre de recherche en infectiologie porcine et avicole - Fonds de recherche du Québec - Nature et technologies, Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, QC, Canada
| | - Jean-Charles Côté
- Laboratoire d'épidémiologie et de médecine porcine, Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, QC, Canada
- Centre de recherche en infectiologie porcine et avicole - Fonds de recherche du Québec - Nature et technologies, Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, QC, Canada
| | - Sylvie D'Allaire
- Laboratoire d'épidémiologie et de médecine porcine, Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, QC, Canada
- Centre de recherche en infectiologie porcine et avicole - Fonds de recherche du Québec - Nature et technologies, Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, QC, Canada
- Groupe de recherche sur les maladies infectieuses en production animale, Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, QC, Canada
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Ren X, Li P, Li X, Qian P. Epidemiological and genetic characteristics of foot-and-mouth disease virus in China from 2010 to 2022. Virology 2024; 589:109940. [PMID: 37984153 DOI: 10.1016/j.virol.2023.109940] [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: 07/05/2023] [Revised: 10/26/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023]
Abstract
Foot-and-mouth disease virus (FMDV) is a highly contagious picornavirus that can infect cloven-hoofed animals of significant agricultural importance. In China, foot-and-mouth disease (FMD) epidemics occur annually, resulting in localized outbreaks or sporadic epidemics that cause significant economic losses. This study summarized 123 cases of FMD reported in China between 2010 and 2022, using data from the official website of the Chinese Center for Animal Disease Control and Prevention. The epidemic situation and genetic characteristics of FMDV in China were studied through phylogenetic analysis, amino acid variation analysis of antigenic epitopes, and genetic recombination analysis. The findings provide important references for predicting the FMDV epidemic situation in China, developing vaccines, and effectively preventing and controlling FMD.
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Affiliation(s)
- Xujiao Ren
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Pengfei Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Xiangmin Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Ping Qian
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.
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Molini U, Coetzee LM, Christians V, Hemberger MY, Chiwome B, Amukwaya M, Khaiseb S, Cattoli G, Dundon WG, Franzo G. High detection frequency and genetic diversity of porcine circovirus 3 (PCV-3) in Namibian backyard farms and warthogs. Acta Trop 2024; 249:107085. [PMID: 38016512 DOI: 10.1016/j.actatropica.2023.107085] [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: 08/01/2023] [Revised: 11/02/2023] [Accepted: 11/25/2023] [Indexed: 11/30/2023]
Abstract
Since its first identification in 2015, porcine circovirus 3 (PCV-3) has been reported worldwide with a high frequency and in the presence of several clinical conditions, although its impact on pig health and productivity is still debated. Data on the presence of PCV-3 in Africa are, however, limited. A previous study performed on commercial pigs in Namibia failed to identify the pathogen. In the present study, the viral circulation in backyard farms, characterised by lower biosecurity measures and frequent animal exchange between farms, was assessed. The susceptibility of warthogs to PCV-3 infection and their potential epidemiological role were also evaluated. Tonsils from 77 pigs from backyard piggeries and 55 warthogs were collected in different regions of Namibia and tested by PCR. Positive samples were sequenced and compared to PCV-3 strains circulating globally. Forty-two out of 77 pigs (54.54 %) and 12 out of 55 warthogs (21.82 %) tested positive, demonstrating the presence of PCV-3 in the country and suggesting that the high biosecurity measures implemented in the commercial farms that previously tested negative for PCV-3 probably prevented viral introduction. The partial ORF2 gene was successfully sequenced in samples from 27 pigs and 6 warthogs. Genetically, the identified strains were part of 3 distinct groups which included both backyard pigs and warthogs from different regions of Namibia. There is also evidence for the occurrence of multiple introduction events most likely from Asian countries, either directly into Namibia or through other African countries. Considering the strict Namibian regulations on live animal importation, understanding the source of viral introduction is challenging, although semen importation or the habit of feeding backyard pigs with human food waste might have played a role. Pig exchanges between farms for breeding purposes or wildlife movements could also have been involved in PCV-3 dispersal within Namibia. Despite the significant advances in the field, further studies should be undertaken to properly understand PCV-3 epidemiology in Namibia and its impact on pig productivity and wildlife health.
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Affiliation(s)
- Umberto Molini
- Faculty of Health Sciences and Veterinary Medicine, School of Veterinary Medicine, Neudamm Campus, University of Namibia, Private Bag 13301, Windhoek 9000, Namibia
| | - Lauren M Coetzee
- Central Veterinary Laboratory (CVL), 24 Goethe Street, Private Bag 18137, Windhoek 9000, Namibia; Faculty of Veterinary Medicine, University of Teramo, Teramo 64100, Italy
| | - Vernon Christians
- Faculty of Health Sciences and Veterinary Medicine, School of Veterinary Medicine, Neudamm Campus, University of Namibia, Private Bag 13301, Windhoek 9000, Namibia
| | - Maria Y Hemberger
- Faculty of Health Sciences and Veterinary Medicine, School of Veterinary Medicine, Neudamm Campus, University of Namibia, Private Bag 13301, Windhoek 9000, Namibia
| | - Bernard Chiwome
- Faculty of Health Sciences and Veterinary Medicine, School of Veterinary Medicine, Neudamm Campus, University of Namibia, Private Bag 13301, Windhoek 9000, Namibia
| | - Maria Amukwaya
- Faculty of Health Sciences and Veterinary Medicine, School of Veterinary Medicine, Neudamm Campus, University of Namibia, Private Bag 13301, Windhoek 9000, Namibia
| | - Siegfried Khaiseb
- Central Veterinary Laboratory (CVL), 24 Goethe Street, Private Bag 18137, Windhoek 9000, Namibia
| | - Giovanni Cattoli
- Department of Nuclear Sciences and Applications, Joint FAO/IAEA Division, Animal Production and Health Laboratory, Animal Production and Health Section, International Atomic Energy Agency, P.O. Box 100, Vienna 1400, Austria
| | - William G Dundon
- Department of Nuclear Sciences and Applications, Joint FAO/IAEA Division, Animal Production and Health Laboratory, Animal Production and Health Section, International Atomic Energy Agency, P.O. Box 100, Vienna 1400, Austria
| | - Giovanni Franzo
- Department. of Animal Medicine, Production and Health, University of Padova, viale dell'Università 16, Legnaro 35020, Italy.
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Sharma M, Dwivedi P, Joshi V, Singh P. Novel mutations found in Mycobacterium leprae DNA repair gene nth from central India. J Infect Chemother 2023:S1341-321X(23)00315-X. [PMID: 38141720 DOI: 10.1016/j.jiac.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/02/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
INTRODUCTION The importance of DNA repair enzymes in maintaining genomic integrity is highlighted by the hypothesis that DNA damage by reactive oxygen/nitrogen species produced inside the host cell is essential for the mutagenesis process. Endonuclease III (Nth), formamidopyrimide (Fpg) and endonuclease VIII (Nei) DNA glycosylases are essential components of the bacterial base excision repair process. Mycobacterium leprae lost both fpg/nei genes during the reductive evolution event and only has the nth (ML2301) gene. This study aims to characterize the mutations in the nth gene of M. leprae strains and explore its correlation with drug-resistance. METHOD A total of 91 M. leprae positive DNA samples extracted from skin biopsy samples of newly diagnosed leprosy patients from NSCB Hospital Jabalpur were assessed for the nth gene as well as drug resistance-associated loci of the rpoB, gyrA and folP1 genes through PCR followed by Sanger sequencing. RESULTS Of these 91 patients, a total of two insertion frameshift mutations, two synonymous and seven nonsynonymous mutations were found in nth in seven samples. Sixteen samples were found to be resistant to ofloxacin and one was found to be dapsone resistant as per the known DRDR mutations. No mutations were found in the rpoB region. Interestingly, none of the nth mutations were identified in the drug-resistant associated samples. CONCLUSION The in-silico structural analysis of the non-synonymous mutations in the Nth predicted five of them were to be deleterious. Our results suggest that the mutations in the nth gene may be potential markers for phylogenetic and epidemiological studies.
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Affiliation(s)
- Mukul Sharma
- ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Purna Dwivedi
- ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India; The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Vandana Joshi
- ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India; School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Pushpendra Singh
- ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India.
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Tokoro M, Mizuno T, Bi X, Lacante S, Jiang C, Makunja R. Molecular screening of Entamoeba spp. ( E. histolytica, E. dispar, E. coli, and E. hartmanni) and Giardia intestinalis using PCR and sequencing. MethodsX 2023; 11:102361. [PMID: 37744888 PMCID: PMC10511480 DOI: 10.1016/j.mex.2023.102361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 09/01/2023] [Indexed: 09/26/2023] Open
Abstract
A wide range of intestinal protozoan parasites inhabit the human gut. To establish a more comprehensive molecular screening, we designed PCR-sequencing screening methods for Entamoeba spp., including commensal species, and Giardia intestinalis, and performed such methods using 174 stool samples collected from Kenyan children. The prevalences of the target species were as follows: E. histolytica (2/174, 1.1%), E. dispar (20/174, 11.5%), E. coli (107/174, 61.5%), E. hartmanni (77/174, 44.3%), and G. intestinalis (54/174, 31.0%). PCR amplicons specific to G. intestinalis was differentiated to assemblages A (8/174, 4.6%) and B (46/174, 26.4%). PCR specificity for Entamoeba spp. was quite high, except for some cross-reactions between E. hartmanni detection primers and G. intestinalis, although the false-positive amplicons were discernible by the band size. The 18S rRNA PCR primers that was designed by Monis et al. in 1999 for G. intestinalis, have specificity issue, therefore amplicon sequencing was essential not only to determine assemblage classifications but also to confirm the positive results by eliminating potential non-specific reactions. The detection sensitivity of both the Entamoeba universal PCR and the G. intestinalis PCR was more than 100 copies of the target loci, which is sufficient for detecting a single trophozoite or cyst of both species.
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Affiliation(s)
- M. Tokoro
- Department of Global Infectious Diseases, Graduate School of Medical Sciences, Kanazawa University, Japan
| | - T. Mizuno
- Department of Global Infectious Diseases, Graduate School of Medical Sciences, Kanazawa University, Japan
| | - X. Bi
- Department of Global Infectious Diseases, Graduate School of Medical Sciences, Kanazawa University, Japan
| | - S.A. Lacante
- Department of Global Infectious Diseases, Graduate School of Medical Sciences, Kanazawa University, Japan
| | - C. Jiang
- Department of Global Infectious Diseases, Graduate School of Medical Sciences, Kanazawa University, Japan
| | - R.N. Makunja
- Department of Global Infectious Diseases, Graduate School of Medical Sciences, Kanazawa University, Japan
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Takai S, Suzuki Y, Sasaki Y, Kakuda T, Ribeiro MG, Makrai L, Witkowski L, Cohen N, Sekizaki T. Short review: Geographical distribution of equine-associated pVAPA plasmids in Rhodococcus equi in the world. Vet Microbiol 2023; 287:109919. [PMID: 38000208 DOI: 10.1016/j.vetmic.2023.109919] [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: 07/11/2023] [Revised: 10/25/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023]
Abstract
Virulent Rhodococcus equi strains expressing virulence-associated 15-17 kDa protein (VapA) and having a large virulence plasmid (pVAPA) of 85-90 kb containing vapA gene are pathogenic for horses. In the last two decades, following pVAPA, two host-associated virulence plasmid types of R. equi have been discovered: a circular plasmid, pVAPB, associated with porcine isolates in 1995, and a recently detected linear plasmid, pVAPN, related to bovine and caprine isolates. Molecular epidemiological studies of R. equi infection in foals on horse-breeding farms in Japan and many countries around the world have been conducted in the last three decades, and the epidemiological studies using restriction enzyme digestion patterns of plasmid DNAs from virulent isolates have shown 14 distinct pVAPA subtypes and their geographical preference. This short review summarizes previous reports regarding equine-associated pVAPA subtypes in the world and discusses their geographic distribution from the standpoint of horse movements.
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Affiliation(s)
- Shinji Takai
- Department of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan.
| | - Yasunori Suzuki
- Department of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan
| | - Yukako Sasaki
- Department of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan
| | - Tsutomu Kakuda
- Department of Animal Hygiene, School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan
| | - Márcio Garcia Ribeiro
- Department of Veterinary Hygiene and Public Health, School of Veterinary Medicine and Animal Sciences, UNESP-São Paulo State University, Botucatu, SP, Brazil
| | - László Makrai
- Department of Microbiology and Infectious Diseases, Faculty of Veterinary Science, Szent István University, Hungária krt. 23-25, H-1143 Budapest, Hungary
| | - Lucjan Witkowski
- Laboratory of Veterinary Epidemiology and Economics, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-776, Warsaw, Poland
| | - Noah Cohen
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Tsutomu Sekizaki
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Chiou CS, Chen BH, Lauderdale TL, Hong YP, Teng RH, Liao YS, Wang YW, Chang JH, Liang SY, Tsao CS, Wei HL. Epidemiological trends and antimicrobial resistance in Salmonella enterica serovar Typhimurium clones in Taiwan between 2004 and 2019. J Glob Antimicrob Resist 2023; 35:128-136. [PMID: 37709137 DOI: 10.1016/j.jgar.2023.09.005] [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: 07/13/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/16/2023] Open
Abstract
OBJECTIVES We investigated the temporal trends of Salmonella enterica serovar Typhimurium (S. Typhimurium) clones in Taiwan from 2004 to 2019, focusing on antimicrobial resistance (AMR), resistance genetic determinants, and plasmid types. METHODS Salmonella isolates were characterized using pulsed-field gel electrophoresis (PFGE), whole-genome sequencing, and antimicrobial susceptibility testing. Clones were defined using PFGE clustering and the hierarchical cgMLST clustering (HierCC) assignments. RESULTS Seven major S. Typhimurium clones, HC100_2, 13, 41, 305, 310, 501, and 46261, accounted for 97.6% (8079/8275) of human isolates in Taiwan. Each clone displayed a unique AMR profile, resistance genetic determinants, and plasmid types. Four highly resistant clones (HC100_2, 41, 305, and 310) exhibited multiple resistance in 86.5% to 96.1% of isolates. HC100_305 and HC100_2 were pandemic multidrug-resistant clones, characterized by resistance to ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline (ACSSuT) and ASSuT, respectively. The prevalence of the ACSSuT clone decreased from 68.7% of S. Typhimurium isolates in 2004 to 1.7% in 2019, while the ASSuT clone emerged in 2007 and became the largest clone after 2010. Several plasmids, including IncHI2-IncHI2A, IncC, IncFIB(K), and IncI1-1(α), carried multiple resistance genes or were associated with the carriage of mph(A), blaCMY-2, and blaDHA-1. CONCLUSIONS Between 2004 and 2019, Taiwan experienced the emergence, prevalence, and subsequent decline of several highly resistant S. Typhimurium clones. The clones defined using the HierCC approach have global comparability. The increasing resistance to third-generation cephalosporins, cephamycins, ciprofloxacin, and azithromycin in recent years poses a significant medical concern.
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Affiliation(s)
- Chien-Shun Chiou
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Taichung, Taiwan.
| | - Bo-Han Chen
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Taichung, Taiwan
| | - Tsai-Ling Lauderdale
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan, Taiwan
| | - Yu-Ping Hong
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Taichung, Taiwan
| | - Ru-Hsiou Teng
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Taichung, Taiwan
| | - Ying-Shu Liao
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Taichung, Taiwan
| | - You-Wun Wang
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Taichung, Taiwan
| | - Jui-Hsien Chang
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Taichung, Taiwan
| | - Shiu-Yun Liang
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Taichung, Taiwan
| | - Chi-Sen Tsao
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Taichung, Taiwan
| | - Hsiao Lun Wei
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Taichung, Taiwan
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Wu D, Wang J, Zhang Y, Wang Q, Liu Q, Shao S. Characterization and pathogenicity analysis of a newly isolated strain of infectious hematopoietic necrosis virus. Microb Pathog 2023; 185:106443. [PMID: 37949305 DOI: 10.1016/j.micpath.2023.106443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/25/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023]
Abstract
Rainbow trout is one of the fastest-growing aquaculture species and infectious hematopoietic necrosis virus (IHNV) is endemic throughout almost all rainbow trout farms in China nowadays. In this study, IHNV GS21 was identified as the causative pathogen, which resulted in massive mortality of rainbow trout occurring in northwest China. GS21 isolate was propagated in Chinook salmon embryonic cell line (CHSE-214) and induced apparent cytopathic effects (CPE) at 3 days post-infection (dpi). Phylogenetic analysis revealed that GS21 isolate was clustered with other reported Chinese isolates within the J genogroup. Moreover, the complete cDNA sequence of GS21 isolate was obtained and it possesses more than 98 % of ANI values and 89 % of DDH values with other Chinese IHNV isolates. The detailed sequence analysis of G gene revealed the distinct amino acid substitutions of G230, G252, G270, and I277 in GS21 isolate. Furthermore, the artificially infected rainbow trout exhibited similar clinical disease symptoms as natural infection did. The cumulative mortality infected by GS21 isolate of 104 PFU/mL reached 93 % at approximately 13.5 °C. Additionally, viral loads in tissues increased first and declined then as well as the expression of immune-associated genes. Collectively, our results characterized a novel IHNV GS21 isolate that can lead to massive mortality in juvenile rainbow trout and provided a basis to define the pathogenic characteristics and evolutionary relationship of IHNV and host immune response against IHNV infection.
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Affiliation(s)
- Di Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jing Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuanxing Zhang
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China; Laboratory of Aquatic Animal Diseases of MOA, Shanghai, 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China; Laboratory of Aquatic Animal Diseases of MOA, Shanghai, 200237, China
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China; Laboratory of Aquatic Animal Diseases of MOA, Shanghai, 200237, China
| | - Shuai Shao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China; Laboratory of Aquatic Animal Diseases of MOA, Shanghai, 200237, China.
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Dorji T, Dorji K, Wangchuk T, Pelki T, Gyeltshen S. Genetic diversity and evolutionary patterns of SARS-CoV-2 among the Bhutanese population during the pandemic. Osong Public Health Res Perspect 2023; 14:494-507. [PMID: 38204428 PMCID: PMC10788421 DOI: 10.24171/j.phrp.2023.0209] [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: 07/26/2023] [Revised: 10/12/2023] [Accepted: 11/08/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic, caused by a dynamic virus, has had a profound global impact. Despite declining global COVID-19 cases and mortality rates, the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants remains a major concern. This study provides a comprehensive analysis of the genomic sequences of SARS-CoV-2 within the Bhutanese population during the pandemic. The primary aim was to elucidate the molecular epidemiology and evolutionary patterns of SARS-CoV-2 in Bhutan, with a particular focus on genetic variations and lineage dynamics. METHODS Whole-genome sequences of SARS-CoV-2 collected from Bhutan between May 2020 and February 2023 (n=135) were retrieved from the Global Initiative on Sharing All Influenza Database. RESULTS The SARS-CoV-2 variants in Bhutan were predominantly classified within the Nextstrain clade 20A (31.1%), followed by clade 21L (20%) and clade 22D (15.6%). We identified 26 Pangolin lineages with variations in their spatial and temporal distribution. Bayesian time-scaled phylogenetic analysis estimated the time to the most recent common ancestor as February 15, 2020, with a substitution rate of 0.97×10-3 substitutions per site per year. Notably, the spike glycoprotein displayed the highest mutation frequency among major viral proteins, with 116 distinct mutations, including D614G. The Bhutanese isolates also featured mutations such as E484K, K417N, and S477N in the spike protein, which have implications for altered viral properties. CONCLUSION This is the first study to describe the genetic diversity of SARS-CoV-2 circulating in Bhutan during the pandemic, and this data can inform public health policies and strategies for preventing future outbreaks in Bhutan.
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Affiliation(s)
- Tshering Dorji
- Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Kunzang Dorji
- Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Tandin Wangchuk
- Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Tshering Pelki
- Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Sonam Gyeltshen
- Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
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Kadaikunnan S, Alharbi N. Colistin-induced structural and biochemical changes in carbapenem-resistant Acinetobacter baumannii isolated from the hospital environment. J Infect Public Health 2023; 16 Suppl 1:26-32. [PMID: 37980240 DOI: 10.1016/j.jiph.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND Acinetobacter baumannii is an emerging multidrug-resistant bacterium and is considered as one of the important causes of nosocomial infections. OBJECTIVES The main objectives are to determine the drug-resistant pattern of beta-lactamase-producing A. baumannii, colistin-induced structural and biochemical changes. METHODS A. baumannii strains were isolated from the restrooms using the selective media, viz., restroom door, restroom floor, washing area, and restroom tap. A total of 120 samples were collected from all four sampling sites. These strains and their drug-resistance patterns were identified. Then carbapenem-resistance was analyzed and the occurrence of the drug-resistant gene (blaOXA-23) was determined. Colistin was applied at various concentrations (20 - 100 µg/mL) and the molecular mechanism of A. baumannii was analysed. RESULTS The bacterial population was high on doors (53 ± 2 CFU/mL), followed by restroom tap (19 ± 1 CFU/mL), restroom floor (14 ± 3 CFU/mL), and washing area (3 ± 0 CFU/mL), respectively. A total of 343 A. baumannii strains were isolated from the 120 samples obtained for one year from the restroom. The isolated bacteria showed resistance to selected carbapenems, with 100% isolates being resistant to imipenem, followed by cefotaxime (1.4 ± 0.2% susceptibility). More blaOXA-23 gene carrying strains were isolated from restroom tap(89 ± 2.1%) than other sources. Colistin exhibited bactericidal activity against drug-resistant A. baumannii. Treating A. baumannii strain with 100 µg/mL colistin induced cell membrane roughness in vitro. Scanning Electron Microscopy (SEM) analysis revealed moderate cell shrinkage after treatment with colistin. Bacterial cells treated with hydrogen peroxide or colistin for 30 min induced the production of hydroxyl radicals. The bacterial lysis increased fluorescence and hydroxyl radicals, and released cellular protein and sugars. CONCLUSIONS The isolated A. baumannii was resistant to imipenem and showed susceptibility to colistin. Colistin disrupted cell membrane in drug-resistant A. baumannii in vitro. The regular screening for drug-resistance among A. baumannii strains can help monitor the outbreak of A. baumannii and manage control measures.
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Affiliation(s)
- Shine Kadaikunnan
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - NaiyfS Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia.
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Rabotnick MH, Ehlinger J, Haidari A, Goodrich JM. Prenatal exposures to endocrine disrupting chemicals: The role of multi-omics in understanding toxicity. Mol Cell Endocrinol 2023; 578:112046. [PMID: 37598796 PMCID: PMC10592024 DOI: 10.1016/j.mce.2023.112046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/22/2023]
Abstract
Endocrine disrupting chemicals (EDCs) are a diverse group of toxicants detected in populations globally. Prenatal EDC exposures impact birth and childhood outcomes. EDCs work through persistent changes at the molecular, cellular, and organ level. Molecular and biochemical signals or 'omics' can be measured at various functional levels - including the epigenome, transcriptome, proteome, metabolome, and the microbiome. In this narrative review, we introduce each omics and give examples of associations with prenatal EDC exposures. There is substantial research on epigenomic modifications in offspring exposed to EDCs during gestation, and a growing number of studies evaluating the transcriptome, proteome, metabolome, or microbiome in response to these exposures. Multi-omics, integrating data across omics layers, may improve understanding of disrupted function pathways related to early life exposures. We highlight several data integration methods to consider in multi-omics studies. Information from multi-omics can improve understanding of the biological processes and mechanisms underlying prenatal EDC toxicity.
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Affiliation(s)
- Margaret H Rabotnick
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Jessa Ehlinger
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Ariana Haidari
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
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Rose R, Feehan A, Lain BN, Ashcraft D, Nolan DJ, Velez-Climent L, Huston C, LaFleur T, Rosenthal S, Fogel GB, Miele L, Pankey G, Garcia-Diaz J, Lamers SL. Whole-genome sequencing of carbapenem-resistant Enterobacterales isolates in southeast Louisiana reveals persistent genetic clusters spanning multiple locations. J Infect Public Health 2023; 16:1911-1917. [PMID: 37866269 DOI: 10.1016/j.jiph.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 10/02/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND We investigated 51 g-negative carbapenem-resistant Enterobacterales (CRE) isolates collected from 22 patients over a five-year period from six health care institutions in the Ochsner Health network in southeast Louisiana. METHODS Short genomic reads were generated using Illumina sequencing and assembled for each isolate. Isolates were classified as Enterobacter spp. (n = 20), Klebsiella spp. (n = 30), and Escherichia coli (n = 1) and grouped into 19 different multi-locus sequence types (MLST). Species and patient-specific core genomes were constructed representing ∼50% of the chromosomal genome. RESULTS We identified two sets of patients with genetically related infections; in both cases, the related isolates were collected > 6 months apart, and in one case, the isolates were collected in different locations. On the other hand, we identified four sets of patients with isolates of the same species collected within 21 days from the same location; however, none had genetically related infections. Genes associated with resistance to carbapenem drugs (blaKPC and/or blaCTX-M-15) were found in 76% of the isolates. We found three blaKPC variants (blaKPC-2, blaKPC-3, and blaKPC-4) associated with four different Enterobacter MLST variants, and two blaKPC variants (blaKPC-2, blaKPC-3) associated with seven different Klebsiella MLST variants. CONCLUSIONS Molecular surveillance is increasingly becoming a powerful tool to understand bacterial spread in both community and clinical settings. This study provides evidence that genetically related infections in clinical settings do not necessarily reflect temporal associations, and vice versa. Our results also highlight the regional genomic and resistance diversity within related bacterial lineages.
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Affiliation(s)
- Rebecca Rose
- BioInfoExperts, LLC, Thibodaux, LA, USA; FoxSeq, LLC, Thibodaux, LA, USA.
| | - Amy Feehan
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | - Deborah Ashcraft
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | | | | | | | | | | | - Lucio Miele
- Translational Science and Genetics at LSU Health Science Center, New Orleans, LA, USA
| | - George Pankey
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Julia Garcia-Diaz
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Susanna L Lamers
- BioInfoExperts, LLC, Thibodaux, LA, USA; FoxSeq, LLC, Thibodaux, LA, USA
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Umar S, Yang R, Wang X, Liu Y, Ke P, Qin S. Molecular epidemiology and characteristics of respiratory syncytial virus among hospitalized children in Guangzhou, China. Virol J 2023; 20:272. [PMID: 37993935 PMCID: PMC10666375 DOI: 10.1186/s12985-023-02227-4] [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: 08/28/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Human respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection and hospitalization, especially in children. Highly mutagenic nature and antigenic diversity enable the RSV to successfully survive in human population. We conducted a molecular epidemiological study during 2017-2021 to investigate the prevalence and genetic characteristics of RSV. METHODS A total of 6499 nasopharyngeal (NP) swabs were collected from hospitalized children at Department of Pediatrics, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, Guangdong, China. All NP swab specimens were preliminary screened for common respiratory viruses and then tested for RSV using specific PCR assays. Partial G genes of RSV were amplified for phylogenetic analysis and genetic characterization. RESULTS The overall detection rate for common respiratory viruses was 16.12% (1048/6499). Among those, 405 specimens (6.20%, 405/6499) were found positive for RSV. The monthly distribution of RSV and other respiratory viruses was variable, and the highest incidence was recorded in Autumn and Winter. Based on the sequencing of hypervariable region of G gene, 93 RSV sequences were sub-grouped into RSV-A (56, 60.2%) and RSV-B (37, 39.8%). There was no coinfection of RSV-A and RSV-B in the tested samples. Phylogenetic analysis revealed that RSV-A and RSV-B strains belonged to ON1 and BA9 genotypes respectively, indicating predominance of these genotypes in Guangzhou. Several substitutions were observed which may likely change the antigenicity and pathogenicity of RSV. Multiple glycosylation sites were noticed, demonstrating high selection pressure on these genotypes. CONCLUSION This study illustrated useful information about epidemiology, genetic characteristics, and circulating genotypes of RSV in Guangzhou China. Regular monitoring of the circulating strains of RSV in different parts of China could assist in the development of more effective vaccines and preventive measures.
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Affiliation(s)
- Sajid Umar
- Global Health Research Center, Duke Kunshan University, Kunshan, China
- Division of Natural and Applied Sciences (DNAS), Duke Kunshan University, Kunshan, China
| | - Rongyuan Yang
- Key Laboratory for Infectious Disease, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xinye Wang
- School of Biomedical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Yuntao Liu
- Emergency Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peifeng Ke
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111 Dade Road, Yuexiu District, Guangzhou, China.
| | - Sheng Qin
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111 Dade Road, Yuexiu District, Guangzhou, China.
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Decker NS, Johnson T, Vey JA, Le Cornet C, Behrens S, Obi N, Kaaks R, Chang-Claude J, Fortner RT. Circulating oxysterols and prognosis among women with a breast cancer diagnosis: results from the MARIE patient cohort. BMC Med 2023; 21:438. [PMID: 37964298 PMCID: PMC10648629 DOI: 10.1186/s12916-023-03152-7] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Breast cancer is the most commonly diagnosed cancer in women worldwide, and underlying mechanistic pathways associated with breast cancer-specific and non-breast cancer-related deaths are of importance. Emerging evidence suggests a role of oxysterols, derivates of cholesterol, in multiple chronic diseases including breast cancer and coronary artery diseases. However, associations between oxysterols and survival have been minimally studied in women diagnosed with breast cancer. In this large breast cancer patient cohort, we evaluated associations between a panel of circulating oxysterols and mortality and recurrence outcomes. METHODS Concentrations of 13 circulating oxysterols representing different pathways of cholesterol metabolism were quantified using liquid-chromatography mass-spectrometry. Associations between baseline levels of oxysterols and cause-specific mortality outcomes and recurrence following a breast cancer diagnosis were assessed in 2282 women from the MARIE study over a median follow-up time of 11 years. We calculated hazard ratios (HR) and 95% confidence intervals (CI) using multivariable Cox proportional hazard models and competing risks models. RESULTS We observed no associations for circulating oxysterols and breast cancer-specific outcomes. Higher levels of six oxysterols were associated with an increased risk of cardiovascular disease death, including 24S-hydroxycholesterol (alternative bile acid pathway, HRlog2 = 1.73 (1.02, 2.93)), lanosterol (cholesterol biosynthesis pathway, HRlog2 = 1.95 (1.34, 2.83)), 7-ketocholesterol (HRlog2 = 1.26 (1.03, 1.55)), 5α,6α-epoxycholesterol (HRlog2 = 1.34 (1.02-1.77)), and 5a,6β-dihydroxycholestanol (HRlog2 = 1.34 (1.03, 1.76)). After adjusting for multiple comparisons, none of the associations were statistically significant. CONCLUSION We provide first evidence on a range of circulating oxysterols and mortality following a breast cancer diagnosis, contributing to a better understanding of associations between different pathways of cholesterol metabolism and prognosis in women with a breast cancer diagnosis. The findings of this study suggest circulating oxysterols may be associated with cardiovascular mortality among women diagnosed with breast cancer. Further studies are needed to evaluate these oxysterols as potential markers of risk for cardiovascular mortality among women with a breast cancer diagnosis as well as their clinical potential.
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Affiliation(s)
- Nina Sophia Decker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Theron Johnson
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Johannes A Vey
- Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
| | - Charlotte Le Cornet
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Nadia Obi
- Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- University Cancer Center Hamburg, Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Renée Turzanski Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Department of Research, Cancer Registry of Norway, Ullernchausseen 64, 0379, Oslo, Norway.
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Yan X, He S, Liu Y, Han B, Zhang N, Deng H, Wang Y, Liu M. Molecular identification and phylogenetic analysis of gastrointestinal nematodes in different populations of Kazakh sheep. Exp Parasitol 2023; 254:108625. [PMID: 37769836 DOI: 10.1016/j.exppara.2023.108625] [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: 12/09/2022] [Revised: 08/26/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Gastrointestinal nematode (GIN) infection in sheep has been recognized globally as a major problem challenging animal health and production. The objective of this study is to use a molecular diagnosis of the prevalence for gastrointestinal nematode (GIN) dominant species of Kazakh sheep and its hybrid (Kazakh × Texel). The internal transcribed spacer 2 (ITS-2) sequences of ribosomal DNA (rDNA) were used as the target sequence. In the study, three dominant species of nematodes, namely Haemonchus contortus, Trichostrongylus spp., and Teladorsagia (Ostertagia) circumcincta from the Kazakh sheep and the F1 and F2 generations of Texel × Kazakh sheep hybrids were subjected to molecular identification and phylogenetic analysis. The fecal and single larva genomic DNA were extracted and amplified by PCR using specific primers to determine the infection rate of the three nematode species. In addition, the PCR products were sequenced and analyzed using bioinformatics methods to construct a phylogenetic tree. The results showed that all the three species had their ITS-2 specific amplified. According to the sequence homology analysis of PCR products, the results showed a high homology (above 98.5% homology) with H. contortus, Trichostrongylus spp., T. circumcincta ITS-2 sequences in GenBank. Phylogenetic analysis showed that the ITS-2 sequences of the three species were on the same branch as the ITS-2 sequences of the same species in NCBI. And on different branches from those of the ITS-2 sequences of different families, genera and species. Sequences carried out on three species from different samples showed a close relationship and little genetic difference in phylogenetic tree. The infection rates based on fecal DNA were 35.59, 25.55, and 11.24% for H. contortus, Trichostrongylus spp., and T. circumcincta, respectively. While the infection rates based on larva DNA, were 24.07, 18.89, and 13.26% for H. contortus, Trichostrongylus spp., and T. circumcincta, respectively. The seasonal prevalence of the three dominant species in spring was significantly higher than that in autumn and winter. And there was no significant difference between Kazakh, F1 and F2 sheep considering the infection rate of the studied three species of nematodes. This study provides valuable molecular approaches for epidemiological surveillance and for assisting in the control of Nematodirus infection in sheep.
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Affiliation(s)
- Xiaofei Yan
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Sangang He
- Institute of Biotechnology, Xinjiang Academy of Animal Science, Key Laboratory of Genetic Breeding and Reproduction of Herbivorous Livestock of Ministry of Agriculture, Xinjiang Key Laboratory of Animal Biotechnology, Urumqi, Xinjiang Province, China
| | - Yiyong Liu
- Animal Husbandry, Terminus of Ili Kazakh Autonomous Prefecture, Yining, Xinjiang Province, China
| | - Bing Han
- Institute of Biotechnology, Xinjiang Academy of Animal Science, Key Laboratory of Genetic Breeding and Reproduction of Herbivorous Livestock of Ministry of Agriculture, Xinjiang Key Laboratory of Animal Biotechnology, Urumqi, Xinjiang Province, China
| | - Ning Zhang
- Institute of Biotechnology, Xinjiang Academy of Animal Science, Key Laboratory of Genetic Breeding and Reproduction of Herbivorous Livestock of Ministry of Agriculture, Xinjiang Key Laboratory of Animal Biotechnology, Urumqi, Xinjiang Province, China
| | - Haifeng Deng
- Zhaosu Horse Farm, Ili Kazakh Autonomous Prefecture, Zhaosu, Xinjiang Province, China
| | - Yuqi Wang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Mingjun Liu
- Institute of Biotechnology, Xinjiang Academy of Animal Science, Key Laboratory of Genetic Breeding and Reproduction of Herbivorous Livestock of Ministry of Agriculture, Xinjiang Key Laboratory of Animal Biotechnology, Urumqi, Xinjiang Province, China.
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Bauer BU, Knittler MR, Andrack J, Berens C, Campe A, Christiansen B, Fasemore AM, Fischer SF, Ganter M, Körner S, Makert GR, Matthiesen S, Mertens-Scholz K, Rinkel S, Runge M, Schulze-Luehrmann J, Ulbert S, Winter F, Frangoulidis D, Lührmann A. Interdisciplinary studies on Coxiella burnetii: From molecular to cellular, to host, to one health research. Int J Med Microbiol 2023; 313:151590. [PMID: 38056089 DOI: 10.1016/j.ijmm.2023.151590] [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: 07/03/2023] [Revised: 10/19/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
The Q-GAPS (Q fever GermAn interdisciplinary Program for reSearch) consortium was launched in 2017 as a German consortium of more than 20 scientists with exceptional expertise, competence, and substantial knowledge in the field of the Q fever pathogen Coxiella (C.) burnetii. C. burnetii exemplifies as a zoonotic pathogen the challenges of zoonotic disease control and prophylaxis in human, animal, and environmental settings in a One Health approach. An interdisciplinary approach to studying the pathogen is essential to address unresolved questions about the epidemiology, immunology, pathogenesis, surveillance, and control of C. burnetii. In more than five years, Q-GAPS has provided new insights into pathogenicity and interaction with host defense mechanisms. The consortium has also investigated vaccine efficacy and application in animal reservoirs and identified expanded phenotypic and genotypic characteristics of C. burnetii and their epidemiological significance. In addition, conceptual principles for controlling, surveilling, and preventing zoonotic Q fever infections were developed and prepared for specific target groups. All findings have been continuously integrated into a Web-based, interactive, freely accessible knowledge and information platform (www.q-gaps.de), which also contains Q fever guidelines to support public health institutions in controlling and preventing Q fever. In this review, we will summarize our results and show an example of how an interdisciplinary consortium provides knowledge and better tools to control a zoonotic pathogen at the national level.
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Affiliation(s)
- Benjamin U Bauer
- Clinic for Swine and Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Michael R Knittler
- Friedrich-Loeffler-Institut, Institute of Immunology, Greifswald - Insel Riems, Germany
| | - Jennifer Andrack
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Christian Berens
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Amely Campe
- Department of Biometry, Epidemiology and Information Processing, (IBEI), WHO Collaborating Centre for Research and Training for Health at the Human-Animal-Environment Interface, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Bahne Christiansen
- Friedrich-Loeffler-Institut, Institute of Immunology, Greifswald - Insel Riems, Germany
| | - Akinyemi M Fasemore
- Bundeswehr Institute of Microbiology, Munich, Germany; University of Würzburg, Würzburg, Germany; ZB MED - Information Centre for Life Science, Cologne, Germany
| | - Silke F Fischer
- Landesgesundheitsamt Baden-Württemberg, Ministerium für Soziales, Gesundheit und Integration, Stuttgart, Germany
| | - Martin Ganter
- Clinic for Swine and Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Sophia Körner
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany; Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany
| | - Gustavo R Makert
- Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany
| | - Svea Matthiesen
- Friedrich-Loeffler-Institut, Institute of Immunology, Greifswald - Insel Riems, Germany
| | - Katja Mertens-Scholz
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Sven Rinkel
- Institut für Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Martin Runge
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Food and Veterinary Institute Braunschweig/Hannover, Hannover, Germany
| | - Jan Schulze-Luehrmann
- Institut für Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Sebastian Ulbert
- Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany
| | - Fenja Winter
- Department of Biometry, Epidemiology and Information Processing, (IBEI), WHO Collaborating Centre for Research and Training for Health at the Human-Animal-Environment Interface, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Dimitrios Frangoulidis
- Bundeswehr Institute of Microbiology, Munich, Germany; Bundeswehr Medical Service Headquarters VI-2, Medical Intelligence & Information, Munich, Germany
| | - Anja Lührmann
- Institut für Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany.
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Moraga-Fernández A, Muñoz-Hernández C, Sánchez-Sánchez M, Fernández de Mera IG, de la Fuente J. Exploring the diversity of tick-borne pathogens: The case of bacteria (Anaplasma, Rickettsia, Coxiella and Borrelia) protozoa (Babesia and Theileria) and viruses (Orthonairovirus, tick-borne encephalitis virus and louping ill virus) in the European continent. Vet Microbiol 2023; 286:109892. [PMID: 37866329 DOI: 10.1016/j.vetmic.2023.109892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 10/04/2023] [Accepted: 10/13/2023] [Indexed: 10/24/2023]
Abstract
Ticks are the main vectors for the transmission of bacterial, protist and viral pathogens in Europe affecting wildlife and domestic animals. However, some of them are zoonotic and can cause serious, sometimes fatal, problems in human health. A systematic review in PubMed/MEDLINE database was conducted to determine the spatial distribution and host and tick species ranges of a selection of tick-borne bacteria (Anaplasma spp., Borrelia spp., Coxiella spp., and Rickettsia spp.), protists (Babesia spp. and Theileria spp.), and viruses (Orthonairovirus, and flaviviruses tick-borne encephalitis virus and louping ill virus) on the European continent in a five-year period (November 2017 - November 2022). Only studies using PCR methods were selected, retrieving a total of 429 articles. Overall, up to 85 species of the selected tick-borne pathogens were reported from 36 European countries, and Anaplasma spp. was described in 37% (159/429) of the articles, followed by Babesia spp. (34%, 148/429), Borrelia spp. (34%, 147/429), Rickettsia spp. (33%, 142/429), Theileria spp. (11%, 47/429), tick-borne flaviviruses (9%, 37/429), Orthonairovirus (7%, 28/429) and Coxiella spp. (5%, 20/429). Host and tick ranges included 97 and 50 species, respectively. The highest tick-borne pathogen diversity was detected in domestic animals, and 12 species were shared between humans, wildlife, and domestic hosts, highlighting the following zoonotic species: Anaplasma phagocytophilum, Babesia divergens, Babesia microti, Borrelia afzelii, Borrelia burgdorferi s.s., Borrelia garinii, Borrelia miyamotoi, Crimean-Congo hemorrhagic fever virus, Coxiella burnetii, Rickettsia monacensis and tick-borne encephalitis virus. These results contribute to the implementation of effective interventions for the surveillance and control of tick-borne diseases.
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Affiliation(s)
- Alberto Moraga-Fernández
- Health and Biotechnology Research Group (SaBio). Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Clara Muñoz-Hernández
- Health and Biotechnology Research Group (SaBio). Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain; Department of Animal Health, Faculty of Veterinary Sciences, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain.
| | - Marta Sánchez-Sánchez
- Health and Biotechnology Research Group (SaBio). Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Isabel G Fernández de Mera
- Health and Biotechnology Research Group (SaBio). Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - José de la Fuente
- Health and Biotechnology Research Group (SaBio). Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain; Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
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Shi Y, Liu Y, Wu Y, Hu S, Sun B. Molecular epidemiology and recombination of enterovirus D68 in China. Infect Genet Evol 2023; 115:105512. [PMID: 37827347 DOI: 10.1016/j.meegid.2023.105512] [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: 08/10/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
Enterovirus D68 (EV-D68), a member of Enterovirus genus of the Picornaviridae family, mainly causes respiratory system-related diseases as well as neurological complications in some patients. At present, there is no effective vaccine or treatment for the virus. The aim of this research was to systematically analyse the molecular epidemiology, recombination and changes in the epitope of EV-D68 in China from 2008 to 2022. Through phylogenetic analysis based on VP1 sequences, it was found that there was limited information about EV-D68 infection before 2011 and that EV-D68 infection was dominated by the A2 gene subtype from 2011 to 2013 and the B3 genotype from 2014 to 2018, during which A2 and B3 were coprevalent and alternately prevalent. We also constructed a phylogenetic tree using the EV-D68 full-length genome sequences, and the genotype of each sequence was consistent with that of the VP1 sequence evolutionary tree. Recombination analysis showed that MH341715 underwent intertypic recombination with the A2 genotype MH341729 at the 5' untranslated region (5'UTR) and that P1-P3 underwent recombination with the B3 genotype MH341712. The capsid protein VP1 is one of the most important structural proteins. In VP1, the BC-loop (89-105 amino acids) and DE-loop (140-152 amino acids) are the most variable domains on the surface of the virus and are associated with epitopes. In this study, it was found that the dominant amino acid composition of the BC-loop and DE-loop continued to change with the epidemic of the virus; the amino acid composition also differed in different regions of the same genotypes. The ongoing genomic and molecular epidemiology of EV-D68 remains important for predicting emergence of new viruses and preventing major outbreaks of respiratory diseases.
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Affiliation(s)
- Yingying Shi
- Department of Immunology, School of Medicine, Jianghan University, Wuhan, Hubei 430056, China
| | - Yongjuan Liu
- Department of Central Laboratory, the Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, Jiangsu 222002, China
| | - Yanli Wu
- Department of Immunology, School of Medicine, Jianghan University, Wuhan, Hubei 430056, China
| | - Song Hu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Binlian Sun
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China.
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Cui Y, Zhang C, Jia Q, Gong X, Tan Y, Hua X, Jian W, Yang S, Hayer K, Raja Idris RK, Zhang Y, Wu Y, Tu Z. An epidemiological surveillance study (2021-2022): detection of a high diversity of Clostridioides difficile isolates in one tertiary hospital in Chongqing, Southwest China. BMC Infect Dis 2023; 23:703. [PMID: 37858038 PMCID: PMC10588108 DOI: 10.1186/s12879-023-08666-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Clostridioides difficile is a bacterium that causes antibiotic-associated infectious diarrhea and pseudomembranous enterocolitis. The impact of C. difficile infection (CDI) in China has gained significant attention in recent years. However, little epidemiological data are available from Chongqing, a city located in Southwest China. This study aimed to investigate the epidemiological pattern of CDI and explore the drug resistance of C. difficile isolates in Chongqing. METHODS A case-control study was conducted to investigate the clinical infection characteristics and susceptibility factors of C. difficile. The features of the C. difficile isolates were evaluated by testing for toxin genes and using multi-locus sequence typing (MLST). The susceptibility of strains to nine antibiotics was determined using agar dilution technique. RESULTS Out of 2084 diarrhea patients, 90 were tested positive for the isolation of toxigenic C. difficile strains, resulting in a CDI prevalence rate of 4.32%. Tetracycline, cephalosporins, hepatobiliary disease, and gastrointestinal disorders were identified as independent risk factors for CDI incidence. The 90 strains were classified into 21 sequence types (ST), with ST3 being the most frequent (n = 25, 27.78%), followed by ST2 (n = 10, 11.11%) and ST37 (n = 9, 10%). Three different toxin types were identified: 69 (76.67%) were A+B+CDT-, 12 (13.33%) were A-B+CDT-, and 9 (10%) were A+B+CDT+. Although substantial resistance to erythromycin (73.33%), moxifloxacin (62.22%), and clindamycin (82.22%), none of the isolates exhibited resistance to vancomycin, tigecycline, or metronidazole. Furthermore, different toxin types displayed varying anti-microbial characteristics. CONCLUSIONS The strains identified in Chongqing, Southwest China, exhibited high genetic diversity. Enhance full awareness of high-risk patients with HA-CDI infection, particularly those with gastrointestinal and hepatocellular diseases, and emphasize caution in the use of tetracycline and capecitabine. These findings suggest that a potential epidemic of CDI may occur in the future, emphasizing the need for timely monitoring.
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Affiliation(s)
- Yihong Cui
- Department of Pathogen Biology, College of Basic Medical Science, Chongqing Medical University, 400016, Chongqing, China
| | - Chuanming Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Qianying Jia
- Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Xue Gong
- Department of Pathogen Biology, College of Basic Medical Science, Chongqing Medical University, 400016, Chongqing, China
| | - Yu Tan
- Department of Pathogen Biology, College of Basic Medical Science, Chongqing Medical University, 400016, Chongqing, China
| | - Xinping Hua
- Department of Pathogen Biology, College of Basic Medical Science, Chongqing Medical University, 400016, Chongqing, China
| | - Wenwen Jian
- Department of Pathogen Biology, College of Basic Medical Science, Chongqing Medical University, 400016, Chongqing, China
| | - Shenglin Yang
- Department of Pathogen Biology, College of Basic Medical Science, Chongqing Medical University, 400016, Chongqing, China
| | - Kim Hayer
- Leicester Medical School, University of Leicester, LE1 7RH, Leicester, UK
| | | | - Yi Zhang
- International Medical College, Chongqing Medical University, 400016, Chongqing, China
| | - Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, National Insti for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, 102206, Beijing, China
| | - Zeng Tu
- Department of Pathogen Biology, College of Basic Medical Science, Chongqing Medical University, 400016, Chongqing, China.
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Hong H, Tang C, Liu Y, Jiang H, Fang T, Xu G. HIV-1 drug resistance and genetic transmission network among newly diagnosed people living with HIV/AIDS in Ningbo, China between 2018 and 2021. Virol J 2023; 20:233. [PMID: 37833806 PMCID: PMC10576354 DOI: 10.1186/s12985-023-02193-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND As the HIV epidemic continues to grow, transmitted drug resistance(TDR) and determining relationship of HIV transmission are major barriers to reduce the risk of HIV transmissions.This study aimed to examine the molecular epidemiology and TDR and evaluated the transmission pattern among newly diagnosed people living with HIV/AIDS(PLWHA) in Ningbo city, which could contribute to the development of targeted precision interventions. METHODS Consecutive cross-sectional surveys were conducted in Ningbo City between January 2018 and December 2021. The HIV-1 pol gene region was amplified and sequenced for drug resistance and genetic transmission network analysis. TDR was determined using the Stanford University HIV Drug Resistance Database. Genetic transmission network was visualized using Cytoscape with the genetic distance threshold of 0.013. RESULTS A total of 1006 sequences were sequenced successfully, of which 61 (6.1%) showed evidence of TDR. The most common mutations were K103N (2.3%), E138A/G/Q (1.7%) and V179D/E (1.2%). 12 HIV-1 genotypes were identified, with CRF07_BC being the major genotype (43.3%, 332/767), followed by CRF01_AE (33.7%, 339/1006). 444 (44.1%) pol sequences formed 856 links within 120 transmission clusters in the network. An increasing trend in clustering rate between 2018 and 2021(χ2 = 9.546, P = 0.023) was observed. The odds of older age (≥ 60 years:OR = 2.038, 95%CI = 1.072 ~ 3.872, compared to < 25 years), HIV-1 genotypes (CRF07_BC: OR = 2.147, 95%CI = 1.582 ~ 2.914; CRF55_01B:OR = 2.217, 95%CI = 1.201 ~ 4.091, compared to CRF01_AE) were significantly related to clustering. Compared with CRF01_AE, CRF07_BC were prone to form larger clusters. The largest cluster with CRF07_BC was increased from 15 cases in 2018 to 83 cases in 2021. CONCLUSIONS This study revealed distribution of HIV-1 genotypes, and genetic transmission network were diverse and complex in Ningbo city. The prevalence of TDR was moderate, and NVP and EFV were high-level NNRTI resistance. Individuals aged ≥ 60 years old were more easily detected in the networks and CRF07_BC were prone to form rapid growth and larger clusters. These date suggested that surveillance and comprehensive intervention should be designed for key rapid growth clusters to reduce the potential risk factors of HIV-1 transmission.
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Affiliation(s)
- Hang Hong
- School of Public health, Health Science Center, Ningbo University, Ningbo, Zhengjiang, 315211, China
| | - Chunlan Tang
- School of Public health, Health Science Center, Ningbo University, Ningbo, Zhengjiang, 315211, China
| | - Yuhui Liu
- Ningbo Center for Disease Control and Prevention, Ningbo, Zhengjiang, 315010, China
| | - Haibo Jiang
- Ningbo Center for Disease Control and Prevention, Ningbo, Zhengjiang, 315010, China
| | - Ting Fang
- School of Public health, Health Science Center, Ningbo University, Ningbo, Zhengjiang, 315211, China
| | - Guozhang Xu
- School of Public health, Health Science Center, Ningbo University, Ningbo, Zhengjiang, 315211, China.
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Jiménez-Avalos G, Soto-Obando A, Solis M, Gilman RH, Cama V, Gonzalez AE, García HH, Sheen P, Requena D, Zimic M. Assembly and phylogeographical analysis of novel Taenia solium mitochondrial genomes suggest stratification within the African-American genotype. Parasit Vectors 2023; 16:349. [PMID: 37803424 PMCID: PMC10559519 DOI: 10.1186/s13071-023-05958-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/30/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Taenia solium is a parasite of public health concern, causing human taeniasis and cysticercosis. Two main genotypes have been identified: Asian and African-American. Although characterizing T. solium genotypes is crucial to understanding the genetic epidemiology of its diseases, not much is known about the differences between T. solium mitochondrial genomes from different genotypes. Also, little is known about whether genotypes are further subdivided. Therefore, this study aimed to identify a set of point mutations distributed throughout the T. solium mitochondrial genome that differentiate the African-American from the Asian genotype. Another objective was to identify whether T. solium main genotypes are further stratified. METHODS One Mexican and two Peruvian T. solium mitochondrial genomes were assembled using reads available in the NCBI Sequence Read Archive and the reference genome from China as a template. Mutations with respect to the Chinese reference were identified by multiple genome alignment. Jensen-Shannon and Grantham scores were computed for mutations in protein-coding genes to evaluate whether they affected protein function. Phylogenies by Bayesian inference and haplotype networks were constructed using cytochrome c oxidase subunit 1 and cytochrome b from these genomes and other isolates to infer phylogeographical relationships. RESULTS A set of 31 novel non-synonymous point mutations present in all genomes of the African-American genotype were identified. These mutations were distributed across the mitochondrial genome, differentiating the African-American from the Asian genotype. All occurred in non-conserved protein positions. Furthermore, the analysis suggested a stratification of the African-American genotypes into an East African and a West African sublineage. CONCLUSIONS A novel set of 31 non-synonymous mutations differentiating the main T. solium genotypes was identified. None of these seem to be causing differences in mitochondrial protein function between parasites of the two genotypes. Furthermore, two sublineages within the African-American genotype are proposed for the first time. The presence of the East African sublineage in the Americas suggests an underestimated connection between East African and Latin American countries that might have arisen in the major slave trade between Portuguese Mozambique and the Americas. The results obtained here help to complete the molecular epidemiology of the parasite.
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Affiliation(s)
- Gabriel Jiménez-Avalos
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería. Universidad Peruana Cayetano Heredia, Lima, Perú
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Alina Soto-Obando
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Maria Solis
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Robert H Gilman
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, USA
| | - Vitaliano Cama
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, USA
| | - Armando E Gonzalez
- Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Hector H García
- Departamento de Microbiología, Universidad Peruana Cayetano Heredia, Lima, Perú
- Cysticercosis Unit, Instituto Nacional de Ciencias Neurológicas, Lima, Perú
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - David Requena
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería. Universidad Peruana Cayetano Heredia, Lima, Perú.
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, USA.
- Bioinformatics Group in Multi-Omics and Immunology, New York, NY, 10065, USA.
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería. Universidad Peruana Cayetano Heredia, Lima, Perú.
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de Alba P, Garro C, Florin-Christensen M, Schnittger L. Prevalence, risk factors and molecular epidemiology of neonatal cryptosporidiosis in calves: The Argentine perspective. Curr Res Parasitol Vector Borne Dis 2023; 4:100147. [PMID: 37941927 PMCID: PMC10628544 DOI: 10.1016/j.crpvbd.2023.100147] [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] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/20/2023] [Accepted: 09/24/2023] [Indexed: 11/10/2023]
Abstract
Cryptosporidium spp. are enteroparasitic protozoans that cause cryptosporidiosis in newborn calves. Clinical signs of the infection are diarrhoea and dehydration leading to decreased productivity and economic losses in cattle farms around the world. Additionally, cryptosporidiosis is a relevant zoonotic disease since the ingestion of oocysts can be fatal for children under five years of age, the elderly, and/or immunocompromised adults. This review aims to integrate existing knowledge on the epidemiological situation of calf cryptosporidiosis and associated risk factors in Argentina. In addition, the GP60 subtype diversity of the pathogen was analysed and related with the global distribution of corresponding GP60 subtypes. Depending on the study region and applied diagnostics, prevalence among calves up to 20 days of age varied between 25.2% and 42.5%, while a prevalence of 16.3-25.5% was observed at the age of 1-90 days. So far, molecular studies have determined exclusively Cryptosporidium parvum in preweaned calves. In addition, C. parvum infection was reported as the major cause of calf diarrhoea, followed by rotavirus A (RVA), while enteropathogens such as coronavirus, Escherichiacoli, and Salmonella sp. played a negligible role. Calf age of 20 days or less, incidence of diarrhoea, poorly drained soils, and large farm size were identified as risk factors for C. parvum-infection in Argentina. A total of nine GP60 subtypes (IIaAxxG1R1, xx = 16 to 24) were identified, showing a stepwise increase of the trinucleotide motif TCA, and including the zoonotic subtypes IIaA16G1R1, IIaA17G1R1, IIaA18G1R1, IIaA19G1R1, and IIaA20G1R1. We found that an increase in the A16→A24 trinucleotide repeat was accompanied by a gradual decrease in the global distribution of GP60 alleles, strongly suggesting that IIaA16G1R1 represents the primordial allelic variant of this group. Since identified GP60 alleles have a similar genetic background, we hypothesize that the continuous trinucleotide repeat array has been generated by stepwise repeat expansion of A16. The information gathered and integrated in this study contributes to an improved understanding of the epidemiological characteristics of bovine cryptosporidiosis in and beyond Argentina, which in turn can help to develop control strategies for this parasitosis of veterinary and medical relevance.
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Affiliation(s)
- Paloma de Alba
- Instituto de Patobiología Veterinaria, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), INTA-Castelar, Los Reseros y Nicolas Repetto s/n, Hurlingham, 1686, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
| | - Carlos Garro
- Instituto de Patobiología Veterinaria, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), INTA-Castelar, Los Reseros y Nicolas Repetto s/n, Hurlingham, 1686, Argentina
| | - Monica Florin-Christensen
- Instituto de Patobiología Veterinaria, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), INTA-Castelar, Los Reseros y Nicolas Repetto s/n, Hurlingham, 1686, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
| | - Leonhard Schnittger
- Instituto de Patobiología Veterinaria, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), INTA-Castelar, Los Reseros y Nicolas Repetto s/n, Hurlingham, 1686, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
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Pierangeli A, Piralla A, Uceda Renteria S, Giacomel G, Lunghi G, Pagani E, Giacobazzi E, Vian E, Biscaro V, Piccirilli G, Lazzarotto T, Menzo S, Ferreri ML, Novazzi F, Petrarca L, Licari A, Ferrari G, Oliveto G, Antonelli G, Binda S, Galli C, Pellegrinelli L, Pariani E, Baldanti F. Multicenter epidemiological investigation and genetic characterization of respiratory syncytial virus and metapneumovirus infections in the pre-pandemic 2018-2019 season in northern and central Italy. Clin Exp Med 2023; 23:2725-2737. [PMID: 36522554 PMCID: PMC9754777 DOI: 10.1007/s10238-022-00973-3] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) cause a high burden of disease, particularly in children and the elderly. With the aim to add knowledge on RSV and HMPV infections in Italy, a prospective, multicenter study was conducted by eight centers of the Working Group on Respiratory Virus Infections (GLIViRe), from December 2018-April 2019. Weekly distribution and patients' demographic and clinical data were compared in 1300 RSV and 222 HMPV-positive cases. Phylogenetic analysis of the G-glycoprotein coding region was performed to characterize circulating strains. RSV positivity ranged from 6.4% in outpatients of all ages to 31.7% in hospitalized children; HMPV positivity was 4-1.2% with no age-association. RSV season peaked in February and ended in mid-April: HMPV circulation was higher when RSV decreased in early spring. RSV was more frequent in infants, whereas HMPV infected comparatively more elderly adults; despite, their clinical course was similar. RSV-B cases were two-thirds of the total and had similar clinical severity compared to RSV-A. Phylogenetic analysis showed the circulation of RSV-A ON1 variants and the predominance of RSV-B genotype BA10. HMPV genotype A2c was the prevalent one and presented insertions of different lengths in G. This first multicenter Italian report on seasonality, age-specific distribution, and clinical presentation of RSV and HMPV demonstrated their substantial disease burden in young patients but also in the elderly. These data may provide the basis for a national respiratory virus surveillance network.
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Affiliation(s)
- Alessandra Pierangeli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University of Rome, V.Le Porta Tiburtina, 28; 00185, Rome, Italy
| | - Antonio Piralla
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Sara Uceda Renteria
- Virology Unit, Clinical Laboratory, Foundation IRCCS Ca’ Granda Ospedale Maggiore, Milan, Italy
| | - Giovanni Giacomel
- Virology Unit, Clinical Laboratory, Foundation IRCCS Ca’ Granda Ospedale Maggiore, Milan, Italy
| | - Giovanna Lunghi
- Virology Unit, Clinical Laboratory, Foundation IRCCS Ca’ Granda Ospedale Maggiore, Milan, Italy
| | - Elisabetta Pagani
- Laboratorio Aziendale Di Microbiologia E Virologia, Hospital of Bolzano (SABES-ASDAA), Bolzano, Italy
| | - Elisabetta Giacobazzi
- Laboratorio Aziendale Di Microbiologia E Virologia, Hospital of Bolzano (SABES-ASDAA), Bolzano, Italy
| | - Elisa Vian
- Microbiology Unit, Hospital of Treviso (AULSS2), Treviso, Italy
| | - Valeria Biscaro
- Microbiology Unit, Hospital of Treviso (AULSS2), Treviso, Italy
| | - Giulia Piccirilli
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria, Bologna, Italy
| | - Tiziana Lazzarotto
- Section of Microbiology, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Università Politecnica Delle Marche, Ancona, Italy
| | - Monica Lucia Ferreri
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti Di Ancona, Ancona, Italy
| | - Federica Novazzi
- Ospedale Di Circolo E Fondazione Macchi, ASST Sette Laghi, Varese, Italy
| | - Laura Petrarca
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Amelia Licari
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Guglielmo Ferrari
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giuseppe Oliveto
- Virology Laboratory, Department of Molecular Medicine, Sapienza University of Rome, V.Le Porta Tiburtina, 28; 00185, Rome, Italy
| | - Guido Antonelli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University of Rome, V.Le Porta Tiburtina, 28; 00185, Rome, Italy
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Fausto Baldanti
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
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Metrailer MC, Hoang TTH, Jiranantasak T, Luong T, Hoa LM, Ngoc DB, Pham QT, Pham VK, Hung TTM, Huong VTL, Pham TL, Ponciano JM, Hamerlinck G, Dang DA, Norris MH, Blackburn JK. Spatial and phylogenetic patterns reveal hidden infection sources of Bacillus anthracis in an anthrax outbreak in Son La province, Vietnam. Infect Genet Evol 2023; 114:105496. [PMID: 37678701 DOI: 10.1016/j.meegid.2023.105496] [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: 06/03/2023] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Bacillus anthracis, the bacterial cause of anthrax, is a zoonosis affecting livestock and wildlife often spilling over into humans. In Vietnam, anthrax has been nationally reportable since 2015 with cases occurring annually, mostly in the northern provinces. In April 2022, an outbreak was reported in Son La province following the butchering of a water buffalo, Bubalus bubalis. A total of 137 humans from three villages were likely exposed to contaminated meat from the animal. Early epidemiological investigations suggested a single animal was involved in all exposures. Five B. anthracis isolates were recovered from human clinical cases along with one from the buffalo hide, another from associated maggots, and one from soil at the carcass site. The isolates were whole genome sequenced, allowing global, regional, and local molecular epidemiological analyses of the outbreak strains. All recovered B. anthracis belong to the A.Br.001/002 lineage based on canonical single nucleotide polymorphism analysis (canSNP). Although not previously identified in Vietnam, this lineage has been identified in the nearby countries of China, India, Indonesia, Thailand, as well as Australia. A twenty-five marker multi-locus variable number tandem repeat analysis (MLVA-25) was used to investigate the relationship between human, soil, and buffalo strains. Locally, four MLVA-25 genotypes were identified from the eight isolates. This level of genetic diversity is unusual for the limited geography and timing of cases and differs from past literature using MLVA-25. The coupled spatial and phylogenetic data suggest this outbreak originated from multiple, likely undetected, animal sources. These findings were further supported by local news reports that identified at least two additional buffalo deaths beyond the initial animal sampled in response to the human cases. Future outbreak response should include intensive surveillance for additional animal cases and additional molecular epidemiological traceback to identify pathogen sources.
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Affiliation(s)
- Morgan C Metrailer
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | | | - Treenate Jiranantasak
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Tan Luong
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Luong Minh Hoa
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Do Bich Ngoc
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Quang Thai Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Van Khang Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | | | | | | | | | | | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Michael H Norris
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Jason K Blackburn
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
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Ito Y, Tanimoto K, Chiba N, Otsuka M, Ota M, Yoshida M, Hashimoto Y, Nomura T, Tomita H. Molecular epidemiological analyses of Clostridioides difficile isolates in a university hospital in Japan. Heliyon 2023; 9:e20167. [PMID: 37800060 PMCID: PMC10550568 DOI: 10.1016/j.heliyon.2023.e20167] [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: 12/05/2022] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 10/07/2023] Open
Abstract
Background We performed molecular epidemiological analyses of Clostridioides difficile isolates in a university hospital in Japan to reveal the risk of C. difficile infection. Methods Cultured isolates from 919 stool samples from 869 patients obtained from July 2015 to August 2016 were subjected to toxin gene detection, ribotyping, multilocus sequence typing, antimicrobial susceptibility testing, and quantitative real-time polymerase chain reaction testing for C. difficile toxin gene expression. Results Of the 919 stool samples from 869 patients, C. difficile was isolated from 153 samples (16.6%), of which 49 (32%) and 104 (68%) were from patients with and without C. difficile infection, respectively. Analyses showed genetic diversity, with ST8 and ST17 strains of healthcare-associated infections, some of which caused C. difficile infections. There was no significant difference in the transcription levels of C. difficile toxin genes between isolates from patients with and without C. difficile infection. Conclusions Major Japanese clonal strains, ST8 and ST17, have been in the hospital environment for a long time and cause healthcare-associated C. difficile infections. The C. difficile toxin genes were transcribed in the isolates from both patients with and without C. difficile infection but were no significant relationship with the development of C. difficile infection.
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Affiliation(s)
- Yukitaka Ito
- Division of Clinical Microbiology Laboratory, Toho University Ohashi Medical Center, Tokyo, Japan
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Koichi Tanimoto
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Naoko Chiba
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Masanobu Otsuka
- Division of Clinical Microbiology Laboratory, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Masato Ota
- Division of Clinical Microbiology Laboratory, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Mieko Yoshida
- Division of Clinical Microbiology Laboratory, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Takahiro Nomura
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Gunma, Japan
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Furtado LFV, de Miranda RRC, Tennessen JA, Blouin MS, Rabelo ÉML. Molecular variability of the Ancylostoma secreted Protein-2 (Aca-asp-2) gene from Ancylostoma caninum contributes to expand information on population genetic studies of hookworms. Exp Parasitol 2023; 253:108590. [PMID: 37544398 DOI: 10.1016/j.exppara.2023.108590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Hookworm infection is a major public health problem in many regions of the world. Given the high levels of host morbidity and even mortality of the host caused by these infections, it is crucial to understand the genetic structure of hookworm populations. This understanding can provide insights into the ecology, transmission patterns, mechanisms of drug resistance, and the development of vaccines and immunotherapeutic strategies. Previously, we examined presumably neutral molecular markers, such as microsatellites and COI (Cytochrome C oxidase subunit 1) in Brazilian populations of Ancylostoma caninum. Here we analyze the molecular variability of a genomic fragment of the Aca-asp-2 (Ancylostoma secreted protein-2) gene from Ancylostoma caninum. This gene is a highly expressed and activated following the infection of the L3 larvae in the host. We obtained individuals of A. caninum from five different geographic locations in Brazil, sequenced and analyzed parts of the gene. The results revealed extensive polymorphism at this fragment, especially in the intronic region, indicating low selective pressure acting on these sequences. However, we also observed irregular distributions of nucleotides and polymorphisms in the coding region of this gene, resulting in the identification of 27 alleles. The data presented here contribute to expanding the understanding of population genetic studies of hookworms.
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Affiliation(s)
- Luis Fernando Viana Furtado
- Universidade Federal de Minas Gerais, Faculdade de Farmácia, Departamento de Análises Clínicas e Toxicológicas, Avenida Presidente Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
| | - Rodrigo Rodrigues Cambraia de Miranda
- Universidade Federal de Uberlândia, Instituto de Ciências Biomédicas, Avenida Maranhão, 1783, Umuarama, CEP 38405-318, Uberlândia, Minas Gerais, Brazil
| | | | | | - Élida Mara Leite Rabelo
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Parasitologia, Avenida Presidente Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
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Gonçalves MM, Marcão A, Sousa C, Nogueira C, Ferreira F, Fonseca H, Rocha H, Vilarinho L. Portuguese Neonatal Screening Programme: A Retrospective Cohort Study of 18 Years of MS/MS. Endocr Metab Immune Disord Drug Targets 2023; 23:EMIDDT-EPUB-134549. [PMID: 37711117 DOI: 10.2174/1871530323666230914114505] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023]
Abstract
INTRODUCTION The Portuguese Neonatal Screening Programme (PNSP) identifies patients with rare diseases through nationwide screening. Currently, 27 diseases are diagnosed, amongst which are 24 Inborn Errors of Metabolism (IEM), covering approximately 100% of neonates (1). In 2004, the national laboratory implemented a new screening method, tandem mass spectrometry (MS/MS) to test for amino acids and acylcarnitines. This new protocol revolutionized the PNSP and allowed for the analysis of an increased number of IEM, with clear improvements in treatment timings and clinical outcomes (2). METHODS From 2004 to 2022, 1 764 830 neonates were screened with MS/MS technology. Those who displayed biochemical profiles indicating an IEM were subjected to molecular characterization via genomic DNA extraction, PCR amplification, and direct Sanger sequencing method of dried blood spot samples. RESULTS/CASE REPORT A cohort of 681 newborns were diagnosed with an IEM. MCAD deficiency is the most frequent, with 233 confirmed diagnoses, showing predominantly c.985A>G (p.K329E) mutation of the ACADM gene in homozygosity. Approximately 1/3 of the 33 confirmed cases of Glutaric Aciduria type I present homozygous for the c.1204C>T (p.Arg402Trp) mutation in GCDH. Around 60% of cases of MAT II/III deficiency display the dominant mutation of the MAT1A gene, c.791G>A (p.Arg264His). These genetic profiles and others were determined as diagnostic confirmation for 24 of the IEM screened. CONCLUSION This data shows the molecular epidemiology of patients with confirmed IEM diagnosis identified by neonatal screening. Some diseases out of the scope of the PNSP were also detected as a differential diagnosis after biochemical suspicion in the dried blood spot sample. The retrospective analysis of the PNSP allows for an overview of 18 years of achievements accomplished by the national screening for IEM since MS/MS was implemented. For some pathologies with low incidence, it's difficult to trace a discernible pattern. However, presenting de novo mutations for these diseases might provide insights on how to approach different phenotypes. The aim of this work is to establish the molecular epidemiology of metabolic diseases screened.
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Affiliation(s)
| | - Ana Marcão
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Oporto, Portugal
| | - Carmen Sousa
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Oporto, Portugal
| | - Célia Nogueira
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Oporto, Portugal
| | - Filipa Ferreira
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Oporto, Portugal
| | - Helena Fonseca
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Oporto, Portugal
| | - Hugo Rocha
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Oporto, Portugal
| | - Laura Vilarinho
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Oporto, Portugal
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Wan Y, Ganner M, Mumin Z, Ready D, Moore G, Potterill I, Paranthaman K, Jauneikaite E, Patel B, Harley A, Getino M, Brown CS, Demirjian A, Pichon B. Whole-genome sequencing reveals widespread presence of Staphylococcus capitis NRCS-A clone in neonatal units across the United Kingdom. J Infect 2023; 87:210-219. [PMID: 37394013 DOI: 10.1016/j.jinf.2023.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 06/13/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023]
Abstract
OBJECTIVE Increased incidence of neonatal Staphylococcus capitis bacteraemia in summer 2020, London, raised suspicion of widespread multidrug-resistant clone NRCS-A. We set out to investigate the molecular epidemiology of this clone in neonatal units (NNUs) across the UK. METHODS We conducted whole-genome sequencing (WGS) on presumptive S. capitis NRCS-A isolates collected from infants admitted to nationwide NNUs and from environmental sampling in two distinct NNUs in 2021. Previously published S. capitis genomes were added for comparison. Genetic clusters of NRCS-A isolates were defined based on core-genome single-nucleotide polymorphisms. RESULTS We analysed WGS data of 838 S. capitis isolates and identified 750 NRCS-A isolates. We discovered a possible UK-specific NRCS-A lineage consisting of 611 isolates collected between 2005 and 2021. We determined 28 genetic clusters of NRCS-A isolates, which covered all geographical regions in the UK, and isolates of 19 genetic clusters were found in ≥2 regions, suggesting inter-regional spread. Within the NRCS-A clone, strong genetic relatedness was identified between contemporary clinical and incubator-associated fomite isolates and between clinical isolates associated with inter-hospital infant transfer. CONCLUSIONS This WGS-based study confirms the dispersion of S. capitis NRCS-A clone amongst NNUs across the UK and urges research on improving clinical management of neonatal S. capitis infection.
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Affiliation(s)
- Yu Wan
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK.
| | - Mark Ganner
- Reference Services Division, National Infection Service, UK Health Security Agency, London, UK
| | - Zaynab Mumin
- Reference Services Division, National Infection Service, UK Health Security Agency, London, UK
| | - Derren Ready
- UK Health Security Agency, Field Service South West, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluation at University of Bristol, Bristol, UK
| | - Ginny Moore
- Research and Evaluation, UK Health Security Agency, Porton Down, Salisbury, UK
| | - Isabelle Potterill
- Reference Services Division, National Infection Service, UK Health Security Agency, London, UK
| | | | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK; Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Bharat Patel
- Public Health Laboratory London, Science Group, UK Health Security Agency, London, UK
| | - Alessandra Harley
- Reference Services Division, National Infection Service, UK Health Security Agency, London, UK
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
| | - Colin S Brown
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
| | - Alicia Demirjian
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK; Paediatric Infectious Diseases and Immunology, Evelina London Children's Hospital, London, UK; Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Bruno Pichon
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
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Correa LP, da Costa Farias F, Dos Santos Barile KA, Palmeira MK, de Melo Amaral CE. Human T-lymphotropic virus 2 (HTLV-2) prevalence of blood donors in the state of Pará, Brazil. Braz J Microbiol 2023; 54:1745-1750. [PMID: 37454039 PMCID: PMC10484891 DOI: 10.1007/s42770-023-01067-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023] Open
Abstract
INTRODUCTION The present study had the objective to describe the molecular prevalence and epidemiological aspects of the human T-lymphotropic virus 2 (HTLV-2) infection in the blood donor population of the Pará state. METHODS The present study is a descriptive, retrospective, and cross-sectional review of epidemiological, serological, and molecular data on inapt blood donors in the State Center for Hematology and Hemotherapy from January 2015 to December 2021. The data were digitalized to create a database using the Statistical Package for Social Sciences program. The prevalence of HTLV-2 was calculated based on the total number of donations during the study period. Descriptive frequency was used to analyze the qualitative data. RESULTS A total of 665,568 blood donations were made. Out of these, 1884 (0.2%) samples presented serological detection to HTLV and further were evaluated using molecular confirmatory tests. Out of these, 36 samples were positive for HTLV-2 using qPCR Taqman assay based on pol gene region (0.005%). The HTLV-2 was found to be more prevalent in women (63.9%); aged between 39 and 59 years (55.6%); residents of the metropolitan region of Belém (80.6%); with self-declared race as brown (80.6%); individuals who had completed high school (58.6%); and first-time donors (58.3%) CONCLUSION: The present study identified the presence of HTLV-2 (1 HTLV-2 case/20,000 donations; 0.005%) in the specific population of blood donors in Pará state. These findings can contribute to the existing literature on the subject both for specific population groups under study and for understanding the prevalence of HTLV-2 in the general population.
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Affiliation(s)
- Lucas Pinheiro Correa
- Centro Universitário Metropolitano da Amazônia (UNIFAMAZ), Rua de Óbidos 179, apto. 1001, Belém, PA, 66020-446, Brazil.
| | - Fatyene da Costa Farias
- Centro Universitário Metropolitano da Amazônia (UNIFAMAZ), Rua de Óbidos 179, apto. 1001, Belém, PA, 66020-446, Brazil
| | - Katarine Antonia Dos Santos Barile
- Centro Universitário Metropolitano da Amazônia (UNIFAMAZ), Rua de Óbidos 179, apto. 1001, Belém, PA, 66020-446, Brazil
- Fundação Centro de Hemoterapia e Hematologia do Pará (HEMOPA), Belém, Pará, Brazil
| | - Maurício Koury Palmeira
- Centro Universitário Metropolitano da Amazônia (UNIFAMAZ), Rua de Óbidos 179, apto. 1001, Belém, PA, 66020-446, Brazil
- Fundação Centro de Hemoterapia e Hematologia do Pará (HEMOPA), Belém, Pará, Brazil
| | - Carlos Eduardo de Melo Amaral
- Centro Universitário Metropolitano da Amazônia (UNIFAMAZ), Rua de Óbidos 179, apto. 1001, Belém, PA, 66020-446, Brazil
- Fundação Centro de Hemoterapia e Hematologia do Pará (HEMOPA), Belém, Pará, Brazil
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Abdelsalam MA, Felefel W, Fadl S, Bessat M. Molecular prevalence and associated infection risk factors of tick-borne protozoan and rickettsial blood pathogens in small ruminants. BMC Vet Res 2023; 19:138. [PMID: 37653481 PMCID: PMC10469425 DOI: 10.1186/s12917-023-03702-4] [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] [Received: 11/19/2022] [Accepted: 08/22/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Tick-borne blood pathogens cause highly pathogenic diseases, which are associated with substantial economic losses in ruminants. Despite this, epidemiological research on these pathogens remains neglected in many countries. This study initiated a regional epidemiological survey that included the detection of molecular prevalence, associated risk factors, and gene sequencing, combined with phylogenetic analysis, targeting the two main tick-borne blood protozoan and rickettsial pathogens of Babesia, Theileria, and Anaplasma that infect small ruminants. One hundred blood samples were collected from 76 sheep and 24 goats. RESULTS Microscopic examination of Giemsa-stained blood films revealed that 73% of the samples were infected with at least one species of the three blood pathogenic organisms. Molecular diagnosis based on the 18 S rRNA for Babesia and Theileria species and the major surface protein 4 (msp4) for Anaplasma species, revealed that 43% of the small ruminants were infected with at least one of these pathogens. The animal's sex was the most significant associated risk factor, with 49.4% of female animals infected compared with only 4% of male animals (P < 0.05). The open breeding system recorded the highest infection rate for tick-borne blood pathogens. Homology-based and phylogenetic analyses indicated that the specific isolate species were Babesia ovis (B. ovis), Theileria ovis (T. ovis), and Anaplasma ovis (A. ovis), with sequences showing significant identities with isolates from sheep, goats, and other animal species, and geographically diverse countries in Africa, Asia, and Europe, in addition to Egypt. CONCLUSION This was the first molecular evidence of B. ovis, T. ovis, and A. ovis infections in sheep and goat populations in the North Coast region of Egypt. More extensive studies are required to develop an epidemiological map of blood pathogenic organisms, while more effective control strategies are required to reduce the burden of tick-borne pathogens on small ruminants.
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Affiliation(s)
- Mennat-Allah Abdelsalam
- Department of Parasitology, Faculty of Veterinary Medicine, Matrouh University, Matrouh, Egypt.
| | - Wael Felefel
- Department of Parasitology, Faculty of Veterinary Medicine, Matrouh University, Matrouh, Egypt
| | - Sabreen Fadl
- Department of Biochemistry, Faculty of Veterinary Medicine, Matrouh University, Matrouh, Egypt
| | - Mohamed Bessat
- Department of Parasitology, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
- Faculty of Veterinary Medicine, King Salman International University KSIU, Ras Sudr, South Sinai, Egypt
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Lin HH, Li JW, Yang TY, Lee CY, Jain SH, Lin SY, Lu PL. Emergence of a predominant sequence type ST7363 and the increasing trend of resistance to cefixime and ceftriaxone in Neisseria gonorrhoeae in Southern Taiwan, 2019-2021. J Microbiol Immunol Infect 2023; 56:833-841. [PMID: 37002111 DOI: 10.1016/j.jmii.2023.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 07/07/2022] [Revised: 02/22/2023] [Accepted: 03/12/2023] [Indexed: 03/30/2023]
Abstract
BACKGROUND/PURPOSE Multi-drug resistance and the presence of epidemic lineages of Neisseria gonorrhoeae locally and globally were important clinical and public health issues. We aimed to investigate the molecular epidemiology and the antimicrobial susceptibility profiles of N. gonorrhoeae in Southern Taiwan. METHODS Between 2019 and 2021, adult patients who had suspected gonorrhea and attended a urology clinic in southern Taiwan were recruited to participate in this study. Clinical data from medical records and a questionnaire, antimicrobial susceptibility testing using a disk diffusion test in accordance with the guidelines by the Clinical and Laboratory Standards Institute, and Multi-locus sequence typing (MLST) were analyzed. RESULTS A total of 500 patients participated in the surveillance study. Among them, 232 N. gonorrhoeae isolates were identified, but only 164 isolates were recovered for further research. ST7363 (n = 83, 50.61%) was found to be the predominant sequence type, followed by ST1583 (n = 24, 14.63%), ST1588 (n = 13, 7.93%), and ST7827 (n = 12, 7.32%). 100% resistance to penicillin and 99.4% non-susceptible rate of ciprofloxacin were observed. The azithromycin resistant rate being 15.24% and the cefixime non-susceptible rate being 17.07% were alarming, both with decreasing trends in susceptibilities during 2019-2021. The 25 azithromycin resistant isolates were mainly belonged to ST7363 (n = 12) and ST7827 (n = 3). Seven (4.2%) isolates were ceftriaxone non-susceptible. Among them, four were assigned to be ST 7827 and three belonged to ST7363. CONCLUSION We observed the emergence of a predominant sequence type ST7363 in southern Taiwan. Compared with previous Taiwan studies, the increasing trend of resistance to cefixime and ceftriaxone necessitates clinicians' alertness for clinical treatment response of the extended spectrum cephalosporins and the further surveillance monitor.
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Affiliation(s)
- Hsuan-Han Lin
- School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of General Medicine, Department of Medical Education, Shin Kong Wu Ho-Su Memorial Hospital, Taiwan
| | - Jia-Wen Li
- Fengshan Li Jiawen Urology Clinic, Kaohsiung, Taiwan
| | - Tsung-Ying Yang
- Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Medical Laboratory Science, I-Shou University, Taiwan
| | - Chun-Yuan Lee
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; M.Sc. Program in Tropical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Shu-Huei Jain
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shang-Yi Lin
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Po-Liang Lu
- Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Taiwan.
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50
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Monge A, Romero M, Groopman JD, McGlynn KA, Santiago-Ruiz L, Villalpando-Hernández S, Mannan R, Burke SM, Remes-Troche JM, Lajous M. Aflatoxin exposure in adults in southern and eastern Mexico in 2018: A descriptive study. Int J Hyg Environ Health 2023; 253:114249. [PMID: 37672956 PMCID: PMC10538954 DOI: 10.1016/j.ijheh.2023.114249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/08/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023]
Abstract
OBJECTIVE To estimate the frequency of detection and levels of aflatoxin B1-lysine adduct (AFB1-lys), an important hepatocellular carcinoma (HCC) risk factor, in eastern and southern Mexico. MATERIALS AND METHODS We determined serum AFB1-lys using mass spectrometry in a representative sample of 952 adults (weighted n = 7,493,354) from five states (Campeche, Chiapas, Tamaulipas, Veracruz and Yucatán) in 2018. We calculated overall and subgroup-specific frequency of detection and 95% confidence intervals (95%CI) and median AFB1-lys levels and quartiles. RESULTS The overall frequency of detection of AFB1-lys was 91.9% (95%CI 88.6, 94.3). The median AFB1-lys level was 0.172 pg/μL (Q1-Q3, 0.060-0.582). Levels differed geographically (median pg/μL, 0.361 for Veracruz and 0.061 for Yucatan) and were higher among men and older individuals. Levels were almost three times higher in rural relative to urban areas (0.317 vs. 0.123 pg/μL). We observed higher AFB1-lys exposure in lower socioeconomic status (SES) level populations. CONCLUSION AFB1-lys frequency of detection was very high and exposure levels were highest in Veracruz, men, rural areas, and among persons of lower SES. Understanding modifiable HCC risk factors in populations with unique epidemiological patterns could inform preventative interventions.
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Affiliation(s)
- Adriana Monge
- Center for Research on Population Health, National Institute of Public Health, Cuernavaca, Mexico
| | - Martín Romero
- Center for Research on Evaluation and Surveys, National Institute of Public Health, Cuernavaca, Mexico
| | - John D Groopman
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | - Luis Santiago-Ruiz
- Center for Research on Population Health, National Institute of Public Health, Cuernavaca, Mexico
| | | | - Reima Mannan
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Sean M Burke
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | - Martín Lajous
- Center for Research on Population Health, National Institute of Public Health, Cuernavaca, Mexico; Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, USA.
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