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Liu P, Wu J, Ma W, Yang Y, Lv L, Cai J, Liu Z, He J, Shang Y, Li Z, Cao X. Molecular detection and characterization of Coxiella burnetii in aborted samples of livestock in China. Acta Trop 2024; 254:107163. [PMID: 38428630 DOI: 10.1016/j.actatropica.2024.107163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/14/2023] [Accepted: 02/27/2024] [Indexed: 03/03/2024]
Abstract
Coxiella burnetii is the causative agent of zoonotic Q fever. Animals are the natural reservoirs of C. burnetii, and domestic livestock represent the major sources of human infection. C. burnetii infection in pregnant females may causes abortion during late pregnancy, whereby massive shedding of C. burnetii with abortion products becomes aerosolized and persists in the environment. Therefore, monitoring and surveillance of this infection in livestock is important for the prevention of the C. burnetii transmission. Previous serological surveys have shown that C. burnetii infection is endemic in livestock in China. However, few data are available on the diagnosis of C. burnetii as a cause of abortion by molecular methods in livestock. To get a better understanding of the impact of C. burnetii infection on domestic livestock in China, a real-time PCR investigation was carried out on collected samples from different domestic livestock suffering abortion during 2021-2023. A total of 338 samples collected from eight herds of five livestock species were elected. The results showed that 223 (66 %) of the collected samples were positive for C. burnetii DNA using real-time PCR. For the aborted samples, 82 % (128/15) of sheep, 81 % (34/42) of goats, 44 % (15/34) of cattle, 69 % (18/26) of camels, and 50 % (17/34) of donkeys were positive for C. burnetii. Besides, 44 % (8/18) and 4 % (1/25) of asymptomatic individuals of sheep and donkey were also positive for C. burnetii. In addition, the positive samples were further confirmed by amplification and sequencing of the C. burnetii-specific isocitrate dehydrogenase (icd) gene. Phylogenetic analysis based on specific gene fragments of icd genes revealed that the obtained sequences in this study were clustered into two different groups associated with different origin of hosts and geographic regions. This is the first report confirming that C. burnetii exists in aborted samples of sheep, goats, cattle, donkeys and camels in China. Further studies are needed to fully elucidate the epidemiology of this pathogen in livestock as well as the potential risks to public health.
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Affiliation(s)
- Ping Liu
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Jinyan Wu
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Weimin Ma
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Yamin Yang
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Lv Lv
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Jiang Cai
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Zhijie Liu
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Jijun He
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Youjun Shang
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Zhaocai Li
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Xiaoan Cao
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
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Wang D, Zhang L, Cai Z, Liu Y. Diagnosis of Acute Q Fever in a Patient by Using Metagenomic Next-Generation Sequencing: A Case Report. Infect Drug Resist 2023; 16:1923-1930. [PMID: 37025192 PMCID: PMC10072143 DOI: 10.2147/idr.s405697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Background Q fever is a zoonotic disease caused by Coxiella burnetii infection, with domestic ruminants as the main source of infection and tick bites as one of the transmission vectors. The clinical manifestations of Q fever are varied and atypical. For the reason that C. burnetii is a strictly intracellular pathogen, it is difficult to be diagnosed by traditional culture methods. Additionally, serological and molecular diagnostic methods to assist in the diagnosis of Q fever are not routinely performed in most clinical laboratories. Therefore, early and rapid diagnosis of Q fever is a challenge. Case Presentation In the present study, a 34-year-old male patient presented with an acute onset and symptoms such as high fever, lethargy, pulmonary infection, and liver damage. In addition, he had a history of tick bites. Despite conducting relevant laboratory and radiological examinations, the etiology remained unknown. Subsequently, we detected the sequence reads of C. burnetii in a venous blood sample using metagenomic next-generation sequencing (mNGS), and the symptoms of patients were significantly improved after timely treatment with the special drug tetracycline. To our knowledge, this is the first report of Q fever associated with C. burnetii detected directly from venous blood sample in Wuhan, China. Conclusion Metagenomic next-generation sequencing is a new diagnostic technology that provides rapid and accurate detection of unexplained infections, including Q fever. Its application plays a crucial role in clinical diagnosis for identifying elusive pathogens.
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Affiliation(s)
- Dong Wang
- Department of Clinical Laboratory, Wuhan Asia General Hospital, Wuhan Asia General Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei Province, 430056, People’s Republic of China
| | - Litao Zhang
- Department of Clinical Laboratory, Wuhan Asia General Hospital, Wuhan Asia General Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei Province, 430056, People’s Republic of China
| | - Zhifang Cai
- Pulmonary and Critical Care Medicine, Hankou Hospital of Wuhan, Hankou Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei Province, 430012, People’s Republic of China
| | - Yumei Liu
- Pulmonary and Critical Care Medicine, Hankou Hospital of Wuhan, Hankou Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei Province, 430012, People’s Republic of China
- Correspondence: Yumei Liu, Email
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Evolution and emergence of mosquito-borne viruses of medical importance: towards a routine metagenomic surveillance approach. JOURNAL OF TROPICAL ECOLOGY 2023. [DOI: 10.1017/s0266467423000019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Abstract
During the last two decades, the world has witnessed the emergence and re-emergence of arthropod-borne viruses, better known as arboviruses. The close contact between sylvatic, rural and peri-urban vector species and humans has been mainly determined by the environment-modifying human activity. The resulting interactions have led to multiple dead-end host infections and have allowed sylvatic arboviruses to eventually adapt to new vectors and hosts, contributing to the establishment of urban transmission cycles of some viruses with enormous epidemiologic impact. The metagenomic next-generation sequencing (NGS) approach has allowed obtaining unbiased sequence information of millions of DNA and RNA molecules from clinical and environmental samples. Robust bioinformatics tools have enabled the assembly of individual sequence reads into contigs and scaffolds partially or completely representing the genomes of the microorganisms and viruses being present in biological samples of clinical relevance. In this review, we describe the different ecological scenarios for the emergence of viral diseases, the virus adaptation process required for the establishment of a new transmission cycle and the usefulness of NGS and computational methods for the discovery and routine genomic surveillance of mosquito-borne viruses in their ecosystems.
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Yang Y, Shi Q, Jin Q, Yang Z, Li W, Han J, Mao J, Zheng B. Case Report: Metagenomic Next-Generation Sequencing Clinches the Diagnosis of Acute Q Fever and Verified by Indirect Immunofluorescence Assay. Front Med (Lausanne) 2022; 9:846526. [PMID: 35721056 PMCID: PMC9204269 DOI: 10.3389/fmed.2022.846526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Q fever is a zoonotic infectious disease caused by Coxiella burnetii. The clinical symptoms of acute Q fever are usually atypical, and routine serological tests of C. burnetii are not readily available, making the diagnosis of Q fever a challenge. In this case, we report a male patient who had repeated fevers and was administered empirical anti-infective treatment, but the effect was poor. After conducting relevant laboratory and imagological examinations, the etiology has not yet been confirmed. Subsequently, metagenomic next-generation sequencing (mNGS) identified the sequence reads of C. burnetii from the patient's peripheral blood within 48 h, and then the diagnosis of acute Q fever was established. Moreover, the serological test of indirect immunofluorescence assay (IFA) of the C. burnetii antibody was further performed in the Centers for Disease Control, certifying the result of mNGS. The patient was ultimately treated with doxycycline and recovered well. mNGS is an unbiased and comprehensive method in infrequent or culture-negative pathogen identification. To our knowledge, this is the first case of acute Q fever identified by mNGS and confirmed by IFA in Taizhou, China. A further large-scale prospective clinical cohort study is worth carrying out to compare the diagnostic efficiency of mNGS with traditional serological methods and PCR in acute Q fever.
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Affiliation(s)
- Yide Yang
- Department of Infectious Diseases, Taizhou Municipal Hospital, Taizhou, China
| | - Qingmiao Shi
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Qian Jin
- Department of Infectious Diseases, Taizhou Municipal Hospital, Taizhou, China
| | - Zhangnv Yang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | | | - Jianfeng Han
- Sansure Biotech Inc. Medical Affairs Department, National Joint Local Engineering Research Center for Genetic Diagnosis of Infection Diseases and Tumours, Beijing, China
| | - Juanjuan Mao
- Department of Infectious Diseases, Taizhou Municipal Hospital, Taizhou, China
| | - Beiwen Zheng
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Xing F, Ye H, Deng C, Sun L, Yuan Y, Lu Q, Yang J, Lo SKF, Zhang R, Chen JHK, Chan JFW, Lau SKP, Woo PCY. Diverse and atypical manifestations of Q fever in a metropolitan city hospital: Emerging role of next-generation sequencing for laboratory diagnosis of Coxiella burnetii. PLoS Negl Trop Dis 2022; 16:e0010364. [PMID: 35442979 PMCID: PMC9060374 DOI: 10.1371/journal.pntd.0010364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/02/2022] [Accepted: 03/28/2022] [Indexed: 11/19/2022] Open
Abstract
Although Q fever has been widely reported in the rural areas of China, there is a paucity of data on the epidemiology and clinical characteristics of this disease in large metropolitan cities. In this study, we profile the epidemiology and clinical manifestations of Q fever from a tertiary hospital in Shenzhen, a Southern Chinese metropolitan city with a large immigrant population from other parts of China. A total of 14 patients were confirmed to have Q fever during a nine-year-and-six-month period, five of whom were retrospectively diagnosed during case review or incidentally picked up because of another research project on unexplained fever without localizing features. Some patients had the typical exposure histories and clinical features, while a few other patients had rare manifestations of Q fever, including one with heart failure and diffuse intracapillary proliferative glomerulonephritis, a patient presenting with a spontaneous bacterial peritonitis-like syndrome, and another one with concomitant Q fever and brucellosis. Using a combination of clinical manifestation, inflammatory marker levels, echocardiographic findings and serological or molecular test results, nine, three and two patients were diagnosed to have acute, chronic and convalescent Q fever, respectively. Seven, five and two patients were diagnosed to have Q fever by serological test, nested real-time PCR and next-generation sequencing respectively. Diverse and atypical manifestations are associated with Q fever. The incidence of Q fever is likely to be underestimated. Next-generation sequencing is becoming an important diagnostic modality for culture-negative infections, particularly those that the physicians fail to recognize clinically, such as Q fever. We describe the epidemiology and clinical manifestations of Q fever from a tertiary hospital in Shenzhen, a Southern Chinese metropolitan city in China. A total of 14 patients were confirmed to have Q fever during this study period. Notably, five of them were retrospectively diagnosed during case review or incidentally picked up because of another research project on patients with unexplained fever. Interestingly, some patients had rare manifestations of Q fever, such as heart failure and diffuse intracapillary proliferative glomerulonephritis and spontaneous bacterial peritonitis. One patient had concomitant Q fever and brucellosis. Half of the patients were diagnosed by traditional serological test, while the other half by PCR or next-generation sequencing. Clinicians should have a high index of suspicion of Q fever because of its diverse and atypical manifestations. The incidence of Q fever is likely to be underestimated. Next-generation sequencing is becoming increasingly important for diagnosis of culture-negative infections.
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Affiliation(s)
- Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Haiyan Ye
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Chaowen Deng
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Linlin Sun
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Yanfei Yuan
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Qianyun Lu
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Jin Yang
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Simon K. F. Lo
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Ruiping Zhang
- Department of Pathology, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
| | | | - Jasper F. W. Chan
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong—Shenzhen Hospital, Shenzhen, Guangdong, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Susanna K. P Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- * E-mail: (SKPL); (PCYW)
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- * E-mail: (SKPL); (PCYW)
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