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Qin X, Huang J, Liang J, Gong E, Wang W, Lv Y, Hou L, Song J, Sun Y, Wen B, Xu J, Qin T. A novel variant of Chlamydia psittaci causing human psittacosis in China. Int J Infect Dis 2024:107180. [PMID: 39059574 DOI: 10.1016/j.ijid.2024.107180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/12/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024] Open
Abstract
From January 2022 to November 2022, sporadic psittacosis occurred in Lishui city, China. The patients presented with fever, cough, and pulmonary infiltration. Their clinical symptoms were not relieved after receiving cephalosporin, penicillin, beta-lactamase inhibitors, and quinolones. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid samples from the patients revealed Chlamydia psittaci infection. Then, three C. psittaci strains were isolated from the patients. Their whole genome sequences (WGSs) were obtained, and a core genome multilocus sequence typing (cgMLST) method was developed to study the population structure of C. psittaci. Using the constructed cgMLST method, 72 WGSs were divided into four related groups and ten sub-clusters. The Lishui strains formed a unique population of C. psittaci, which might represent a new variant of C. psittaci. In vitro antimicrobial susceptibility testing suggested that the Lishui strains were sensitive to tetracycline, macrolides, and quinolones, and no drug-resistance was observed.
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Affiliation(s)
- Xincheng Qin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jinwei Huang
- Department of Respiratory and Critical Care Medicine, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang province, China
| | - Junrong Liang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Enhui Gong
- Department of Respiratory and Critical Care Medicine, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang province, China
| | - Wen Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuankai Lv
- Department of Respiratory and Critical Care Medicine, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang province, China
| | - Ling Hou
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jingdong Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yamin Sun
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Research Institute of Public Health, Nankai University, Tianjin, China
| | - Bohai Wen
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jianguo Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tian Qin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China..
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Herrmann B, Aaziz R, Kaden R, Riedel HM, Spörndly-Nees E, Sandelin LL, Laroucau K. SNP-based high-resolution typing of Chlamydia psittaci from humans and wild birds in Sweden: circulation of the Mat116 genotype reveals the transmission mode to humans. Microbes Infect 2024; 26:105251. [PMID: 37952689 DOI: 10.1016/j.micinf.2023.105251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/29/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
The incidence of Chlamydia psittaci respiratory tract infections in humans has increased in Sweden in recent years. This study aimed to identify the transmission route by genotyping C. psittaci from infected humans and birds. 42 human C. psittaci samples and 5 samples from C. psittaci-infected birds were collected. Genotyping was performed using ompA sequencing, Multi-locus sequence typing, and/or SNP-based high-resolution melting-PCR. Epidemiological data was also collected, and a phylogenetic analysis was conducted. Analysis of ompA provided limited resolution, while the SNP-based PCR analysis successfully detected the Mat116 genotype in 3/5 passerine birds and in 26/29 human cases, indicating a high prevalence of this genotype in the human population. These cases were associated with contact with wild birds, mainly through bird feeding during winter or other outdoor exposure. Human cases caused by other genotypes (psittacine and pigeon) were less common and were linked to exposure to caged birds or pigeons. The SNP-genotype Mat116 is rare, but predominated in this study. The use of SNP-based PCR provided a better understanding of the C. psittaci transmission from birds to humans compared to ompA analysis. In Sweden, human psittacosis appears mainly to be transmitted from garden birds during bird feeding in the winter season.
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Affiliation(s)
- Björn Herrmann
- Department of Clinical Microbiology, Uppsala University Hospital, SE-751 85 Uppsala, Sweden; Department of Medical Sciences, Clinical Microbiology, Uppsala University, SE-751 85 Uppsala, Sweden.
| | - Rachid Aaziz
- Anses, Laboratory for Animal Health, Bacterial Zoonosis Unit, Paris-Est University, F-94706 Maisons-Alfort, France
| | - Rene Kaden
- Department of Clinical Microbiology, Uppsala University Hospital, SE-751 85 Uppsala, Sweden; Science for Life Laboratory, Clinical Genomics Uppsala, SE-751 85 Uppsala, Sweden
| | - Hilde M Riedel
- Department of Clinical Microbiology, Uppsala University Hospital, SE-751 85 Uppsala, Sweden; Department of Medical Sciences, Clinical Microbiology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Ellinor Spörndly-Nees
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), SE-751 89 Uppsala, Sweden
| | - Lisa Labbé Sandelin
- Department of Communicable Diseases and Disease Control, Region Kalmar County, SE- 391 26 Kalmar, Sweden; Department of Biology and Environmental Science, Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Karine Laroucau
- Anses, Laboratory for Animal Health, Bacterial Zoonosis Unit, Paris-Est University, F-94706 Maisons-Alfort, France
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Szymańska-Czerwińska M, Zaręba-Marchewka K, Niemczuk K. New insight on chlamydiae. J Vet Res 2023; 67:559-565. [PMID: 38130448 PMCID: PMC10730554 DOI: 10.2478/jvetres-2023-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
This article provides an overview of the current knowledge on chlamydiae, which are intracellular bacteria belonging to the Chlamydiaceae family. Whole-genome sequencing leads to great increases in the available data about Chlamydia spp. Recently, novel chlamydial taxons in various hosts living in different environments have been recognised. New species and taxons with Candidatus status have been recorded mainly in birds and reptiles. Chlamydia gallinacea is an emerging infectious agent in poultry with indirectly confirmed zoonotic potential. Recently, a new group of avian C. abortus strains with worldwide distribution in various wild bird families has been described. The definition of C. abortus species became outdated with the discovery of these strains and has been amended. It now includes two subgroups, mammalian and avian, the latter including all isolates hitherto referred to as atypical C. psittaci or C. psittaci/C. abortus intermediates.
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Affiliation(s)
- Monika Szymańska-Czerwińska
- Department of Cattle and Sheep Diseases, Puławy, Poland
- Laboratory of Serological Diagnosis, National Veterinary Research Institute, 24-100Puławy, Poland
| | | | - Krzysztof Niemczuk
- Department of Cattle and Sheep Diseases, Puławy, Poland
- Laboratory of Serological Diagnosis, National Veterinary Research Institute, 24-100Puławy, Poland
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Kasimov V, White RT, Jelocnik M. Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows ( Corvus orru) shed light on possible reservoir hosts and evolutionary pathways. Microb Genom 2023; 9. [PMID: 37991482 DOI: 10.1099/mgen.0.001134] [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] [Indexed: 11/23/2023] Open
Abstract
Chlamydia abortus, an obligate intracellular bacterium, is a major causative agent of reproductive loss in ruminants, with zoonotic potential. Though this pathogen is primarily known to infect livestock, recent studies have detected and isolated genetically distinct avian strains of C. abortus from wild birds globally. Before this study, only five avian C. abortus genomes were publicly available. Therefore, we performed culture-independent probe-based whole-genome sequencing on clinical swabs positive for avian C. abortus obtained from Australian Torresian crows (Corvus orru) in 2019 and 2020. We successfully obtained draft genomes for three avian C. abortus strains (C1, C2 and C3), each comprising draft chromosomes with lengths of 1 115 667, 1 120 231 and 1 082 115 bp, and associated 7 553 bp plasmids, with a genome completeness exceeding 92 %. Molecular characterization revealed that these three strains comprise a novel sequence type (ST333), whilst phylogenetic analyses placed all three strains in a cluster with other avian C. abortus genomes. Interestingly, these three strains share a distant genomic relation (2693 single nucleotide variants) with the reference strain 15-58d/44 (ST152), isolated from a Eurasian magpie (Pica pica) in Poland, highlighting the need for more publicly available genomes. Broad comparative analyses with other avian C. abortus genomes revealed that the three draft genomes contain conserved Chlamydia genomic features, including genes coding for type III secretion system and polymorphic membrane proteins, and potential virulence factors such as the large chlamydial cytotoxin, warranting further studies. This research provides the first avian C. abortus draft genomes from Australian birds, highlighting Torresian crows as novel reservoir hosts for these potential pathogens, and demonstrates a practical methodology for sequencing novel Chlamydia genomes without relying on traditional cell culture.
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Affiliation(s)
- Vasilli Kasimov
- University of the Sunshine Coast, School of Science, Engineering and Technology, Sippy Downs, Sunshine Coast, QLD 4556, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Sunshine Coast, QLD 4557, Australia
| | - Rhys T White
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Martina Jelocnik
- University of the Sunshine Coast, School of Science, Engineering and Technology, Sippy Downs, Sunshine Coast, QLD 4556, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Sunshine Coast, QLD 4557, Australia
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Kasimov V, White RT, Foxwell J, Jenkins C, Gedye K, Pannekoek Y, Jelocnik M. Whole-genome sequencing of Chlamydia psittaci from Australasian avian hosts: A genomics approach to a pathogen that still ruffles feathers. Microb Genom 2023; 9:mgen001072. [PMID: 37486739 PMCID: PMC10438822 DOI: 10.1099/mgen.0.001072] [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: 04/19/2023] [Accepted: 06/26/2023] [Indexed: 07/25/2023] Open
Abstract
Chlamydia psittaci is a globally distributed veterinary pathogen with zoonotic potential. Although C. psittaci infections have been reported in various hosts, isolation and culture of Chlamydia is challenging, hampering efforts to produce contemporary global C. psittaci genomes. This is particularly evident in the lack of avian C. psittaci genomes from Australia and New Zealand. In this study, we used culture-independent probe-based whole-genome sequencing to expand the global C. psittaci genome catalogue. Here, we provide new C. psittaci genomes from two pigeons, six psittacines, and novel hosts such as the Australian bustard (Ardeotis australis) and sooty shearwater (Ardenna grisea) from Australia and New Zealand. We also evaluated C. psittaci genetic diversity using multilocus sequence typing (MLST) and major outer membrane protein (ompA) genotyping on additional C. psittaci-positive samples from various captive avian hosts and field isolates from Australasia. We showed that the first C. psittaci genomes sequenced from New Zealand parrots and pigeons belong to the clonal sequence type (ST)24 and diverse 'pigeon-type' ST27 clade, respectively. Australian parrot-derived strains also clustered in the ST24 group, whereas the novel ST332 strain from the Australian bustard clustered in a genetically diverse clade of strains from a fulmar, parrot, and livestock. MLST and ompA genotyping revealed ST24/ompA genotype A in wild and captive parrots and a sooty shearwater, whilst 'pigeon-types' (ST27/35 and ompA genotypes B/E) were found in pigeons and other atypical hosts, such as captive parrots, a little blue penguin/Kororā (Eudyptula minor) and a zebra finch (Taeniopygia guttata castanotis) from Australia and New Zealand. This study provides new insights into the global phylogenomic diversity of C. psittaci and further demonstrates the multi-host generalist capacity of this pathogen.
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Affiliation(s)
- Vasilli Kasimov
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia
| | - Rhys T. White
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, Brisbane, Queensland 4072, Australia
- The University of Queensland, Australian Centre for Ecogenomics, Brisbane, Queensland 4072, Australia
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Jonathan Foxwell
- Animal Health Laboratory, Ministry for Primary Industries, 66 Ward Street, Upper Hutt 5018, New Zealand
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia
| | - Kristene Gedye
- Massey University, School of Veterinary Science, Palmerston North 4442, New Zealand
| | - Yvonne Pannekoek
- University of Amsterdam, Amsterdam UMC, Department of Medical Microbiology and Infection Prevention, Amsterdam 1105, Netherlands
| | - Martina Jelocnik
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia
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