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McDougall FK, Boardman WS, Speight N, Stephenson T, Funnell O, Smith I, Graham PL, Power ML. Carriage of antibiotic resistance genes to treatments for chlamydial disease in koalas ( Phascolarctos cinereus): A comparison of occurrence before and during catastrophic wildfires. One Health 2023; 17:100652. [PMID: 38024267 PMCID: PMC10665209 DOI: 10.1016/j.onehlt.2023.100652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Growing reports of diverse antibiotic resistance genes in wildlife species around the world symbolises the extent of this global One Health issue. The health of wildlife is threatened by antimicrobial resistance in situations where wildlife species develop disease and require antibiotics. Chlamydial disease is a key threat for koalas in Australia, with infected koalas frequently entering wildlife hospitals and requiring antibiotic therapy, typically with chloramphenicol or doxycycline. This study investigated the occurrence and diversity of target chloramphenicol and doxycycline resistance genes (cat and tet respectively) in koala urogenital and faecal microbiomes. DNA was extracted from 394 urogenital swabs and 91 faecal swabs collected from koalas in mainland Australia and on Kangaroo Island (KI) located 14 km off the mainland, before (n = 145) and during (n = 340) the 2019-2020 wildfires. PCR screening and DNA sequencing determined 9.9% of samples (95%CI: 7.5% to 12.9%) carried cat and/or tet genes, with the highest frequency in fire-affected KI koalas (16.8%) and the lowest in wild KI koalas sampled prior to fires (6.5%). The diversity of cat and tet was greater in fire-affected koalas (seven variants detected), compared to pre-fire koalas (two variants detected). Fire-affected koalas in care that received antibiotics had a significantly higher proportion (p < 0.05) of cat and/or tet genes (37.5%) compared to koalas that did not receive antibiotics (9.8%). Of the cat and/or tet positive mainland koalas, 50.0% were Chlamydia-positive by qPCR test. Chloramphenicol and doxycycline resistance genes in koala microbiomes may contribute to negative treatment outcomes for koalas receiving anti-chlamydial antibiotics. Thus a secondary outcome of wildfires is increased risk of acquisition of cat and tet genes in fire-affected koalas that enter care, potentially exacerbating the already significant threat of chlamydial disease on Australia's koalas. This study highlights the importance of considering impacts to wildlife health within the One Health approach to AMR and identifies a need for greater understanding of AMR ecology in wildlife.
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Affiliation(s)
- Fiona K. McDougall
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Wayne S.J. Boardman
- School of Animal and Veterinary Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Natasha Speight
- School of Animal and Veterinary Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Tamsyn Stephenson
- School of Animal and Veterinary Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Oliver Funnell
- Zoos South Australia, Frome Rd, Adelaide, SA 5001, Australia
| | - Ian Smith
- School of Animal and Veterinary Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Roseworthy, SA 5371, Australia
- Zoos South Australia, Frome Rd, Adelaide, SA 5001, Australia
| | - Petra L. Graham
- School of Mathematical and Physical Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Michelle L. Power
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia
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Pro-Inflammatory Oral Microbiota in Juvenile Spondyloarthritis: A Pilot Study. CHILDREN 2022; 9:children9111764. [DOI: 10.3390/children9111764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/01/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
Abstract
The role of the microbiota in the pathogenesis of arthritis is gaining increasing attention. While multiple studies have queried the intestinal microbiota, very few have analyzed the contents of the oral microbiota. In this pilot study, we obtained salivary and sub-gingival specimens from a cohort of six healthy controls and five children with well-controlled spondyloarthritis (SpA) and performed 16S sequencing on bacteria obtained from both habitats. The Quantitative Insight into Microbial Ecology tool suite was used to generate operational taxonomic units, Phyloseq was used for diversity analyses, and DeSeq2 was used to compare abundances while adjusting for multiple comparisons. A repeat specimen was obtained from one subject during a flare. Clustering based upon diagnosis was observed from both habitats, with decreased alpha diversity seen within the plaque obtained from the patients vs. controls. Among the differentially abundant taxa were statistically significantly increased plaque Fusobacterium and salivary Rothia mucilaginosa among the patients compared to the controls. Additionally, the abundance of plaque Fusobacterium increased in one patient at the time of a flare. Our data suggest that the oral cavity may harbor bacteria involved in the pathogenesis of spondyloarthritis; additional studies are warranted.
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Quigley BL, Timms P. Helping koalas battle disease - Recent advances in Chlamydia and koala retrovirus (KoRV) disease understanding and treatment in koalas. FEMS Microbiol Rev 2020; 44:583-605. [PMID: 32556174 PMCID: PMC8600735 DOI: 10.1093/femsre/fuaa024] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/14/2020] [Indexed: 12/31/2022] Open
Abstract
The iconic Australian marsupial, the koala (Phascolarctos cinereus), has suffered dramatic population declines as a result of habitat loss and fragmentation, disease, vehicle collision mortality, dog attacks, bushfires and climate change. In 2012, koalas were officially declared vulnerable by the Australian government and listed as a threatened species. In response, research into diseases affecting koalas has expanded rapidly. The two major pathogens affecting koalas are Chlamydia pecorum, leading to chlamydial disease and koala retrovirus (KoRV). In the last eight years, these pathogens and their diseases have received focused study regarding their sources, genetics, prevalence, disease presentation and transmission. This has led to vast improvements in pathogen detection and treatment, including the ongoing development of vaccines for each as a management and control strategy. This review will summarize and highlight the important advances made in understanding and combating C. pecorum and KoRV in koalas, since they were declared a threatened species. With complementary advances having also been made from the koala genome sequence and in our understanding of the koala immune system, we are primed to make a significant positive impact on koala health into the future.
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Affiliation(s)
- Bonnie L Quigley
- Genecology Research Centre, University of the Sunshine Coast,
90 Sippy Downs Drive, Sippy Downs, Queensland, 4556, Australia
| | - Peter Timms
- Genecology Research Centre, University of the Sunshine Coast,
90 Sippy Downs Drive, Sippy Downs, Queensland, 4556, Australia
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Hesseling J, Legione AR, Stevenson MA, McCowan CI, Pyman MF, Finochio C, Nguyen D, Roic CL, Thiris OL, Zhang AJ, van Schaik G, Coombe JE. Bovine digital dermatitis in Victoria, Australia. Aust Vet J 2019; 97:404-413. [PMID: 31286478 DOI: 10.1111/avj.12859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/24/2022]
Abstract
AIMS The objectives of this study were to estimate the prevalence of digital dermatitis (DD) in Victoria, Australia, and to investigate which organisms are consistent with typical DD lesions. The prevalence and causative pathogens of DD are not clear yet in Australia and this paper is one of the first to explore these questions in this country. METHODS Examination and sampling of limbs was undertaken at three knackeries in Victoria, Australia. Limbs were classified as normal (N), active DD-lesion (A), dried or chronic DD-lesion (D) or suspected case of DD (S). A total of 823 cows were examined. Six skin biopsies were taken at each knackery, from which DNA was extracted for diversity profiling. Histochemical staining of samples was performed on eight of the skin biopsies. RESULTS DD was detected in 29.8% of all cows. The prevalence of DD was significantly higher in dairy cows (32.2%) than in beef cows (10.8%). The differential abundance of Treponema-species was significantly increased in dried lesions, compared with the normal skin biopsies. Actinobacteria, Proteobacteria, Firmicutes and Tenericutes were found to be significantly different in abundance in the DD lesions compared with normal skin biopsies. Silver staining of samples showed only mild inflammation and in two samples organisms with morphology consistent with Spirochaetes were detected. CONCLUSIONS The calculated prevalence indicates that DD is present in Victoria, Australia. The results of diversity profiling showed that the presence of Treponema-species was significantly different between the samples of DD lesions and normal skin.
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Affiliation(s)
- J Hesseling
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - A R Legione
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - M A Stevenson
- Asia Pacific Centre for Animal Health, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - C I McCowan
- Agriculture Victoria, Veterinary Diagnostics, AgriBio, 5 Ring Road, Bundoora, Victoria, 3083, Australia
| | - M F Pyman
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - C Finochio
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - D Nguyen
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - C L Roic
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - O L Thiris
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - A J Zhang
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - G van Schaik
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - J E Coombe
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
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Exploration of antibiotic resistance risks in a veterinary teaching hospital with Oxford Nanopore long read sequencing. PLoS One 2019; 14:e0217600. [PMID: 31145757 PMCID: PMC6542553 DOI: 10.1371/journal.pone.0217600] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/14/2019] [Indexed: 11/19/2022] Open
Abstract
The Oxford Nanopore MinION DNA sequencing device can produce large amounts of long sequences, typically several kilobases, within a few hours. This long read capacity was exploited to detect antimicrobial resistance genes (ARGs) in a large veterinary teaching hospital environment, and to assess their taxonomic origin, genetic organisation and association with mobilisation markers concurrently. Samples were collected on eight occasions between November 2016 and May 2017 (inclusive) in a longitudinal study. Nanopore sequencing was performed on total DNA extracted from the samples after a minimal enrichment step in broth. Many ARGs present in the veterinary hospital environment could potentially confer resistance to antimicrobials widely used in treating infections of companion animals, including aminoglycosides, extended-spectrum beta-lactams, sulphonamides, macrolides, and tetracyclines. High-risk ARGs, defined here as single or multiple ARGs associated with pathogenic bacterial species or with mobile genetic elements, were shared between the intensive care unit (ICU) patient cages, a dedicated laundry trolley and a floor cleaning mop-bucket. By contrast, a floor surface from an office corridor without animal contact and located outside the veterinary hospital did not contain such high-risk ARGs. Relative abundances of high-risk ARGs and co-localisation of these genes on the same sequence read were higher in the laundry trolley and mop bucket samples, compared to the ICU cages, suggesting that amplification of ARGs is likely to occur in the collection points for hospital waste. These findings have prompted the implementation of targeted intervention measures in the veterinary hospital to mitigate the risks of transferring clinically important ARGs between sites and to improve biosecurity practices in the facility.
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Gonzalez E, Pitre FE, Brereton NJB. ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples. Environ Microbiol 2019; 21:2440-2468. [PMID: 30990927 PMCID: PMC6851558 DOI: 10.1111/1462-2920.14632] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/07/2019] [Accepted: 04/15/2019] [Indexed: 01/04/2023]
Abstract
Analysis of 16S ribosomal RNA (rRNA) gene amplification data for microbial barcoding can be inaccurate across complex environmental samples. A method, ANCHOR, is presented and designed for improved species‐level microbial identification using paired‐end sequences directly, multiple high‐complexity samples and multiple reference databases. A standard operating procedure (SOP) is reported alongside benchmarking against artificial, single sample and replicated mock data sets. The method is then directly tested using a real‐world data set from surface swabs of the International Space Station (ISS). Simple mock community analysis identified 100% of the expected species and 99% of expected gene copy variants (100% identical). A replicated mock community revealed similar or better numbers of expected species than MetaAmp, DADA2, Mothur and QIIME1. Analysis of the ISS microbiome identified 714 putative unique species/strains and differential abundance analysis distinguished significant differences between the Destiny module (U.S. laboratory) and Harmony module (sleeping quarters). Harmony was remarkably dominated by human gastrointestinal tract bacteria, similar to enclosed environments on earth; however, Destiny module bacteria also derived from nonhuman microbiome carriers present on the ISS, the laboratory's research animals. ANCHOR can help substantially improve sequence resolution of 16S rRNA gene amplification data within biologically replicated environmental experiments and integrated multidatabase annotation enhances interpretation of complex, nonreference microbiomes.
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Affiliation(s)
- Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, H3A 0G1, Canada.,Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada
| | - Frederic E Pitre
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.,Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - Nicholas J B Brereton
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
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Fabijan J, Caraguel C, Jelocnik M, Polkinghorne A, Boardman WSJ, Nishimoto E, Johnsson G, Molsher R, Woolford L, Timms P, Simmons G, Hemmatzadeh F, Trott DJ, Speight N. Chlamydia pecorum prevalence in South Australian koala (Phascolarctos cinereus) populations: Identification and modelling of a population free from infection. Sci Rep 2019; 9:6261. [PMID: 31000763 PMCID: PMC6472425 DOI: 10.1038/s41598-019-42702-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/02/2019] [Indexed: 11/21/2022] Open
Abstract
Chlamydia pecorum is an established and prevalent infection that produces severe clinical disease in many koala populations, contributing to dramatic population declines. In wild South Australian koala populations, C. pecorum occurrence and distribution is unknown. Here, C. pecorum-specific real-time quantitative PCR (qPCR) was applied to ocular and urogenital swabs from targeted surveys of wild koalas from the mainland Mount Lofty Ranges (MLR) (n = 75) and Kangaroo Island (KI) (n = 170) populations. Historical data from 13,081 KI koalas (1997–2018) provided additional evidence for assessing the absence of C. pecorum infection. In the MLR population, 46.7% (CI: 35.1–58.6%) of koalas were C. pecorum positive by qPCR but only 4% had grade 3 clinical disease. MLR koala fertility was significantly reduced by C. pecorum infection; all reproductively active females (n = 16) were C. pecorum negative, whereas 85.2% of inactive females (n = 23) were positive (P < 0.001). KI koalas were C. pecorum negative and the population was demonstrated to be free of C. pecorum infection with 95% confidence. C. pecorum is a real threat for the sustainability of the koala and KI is possibly the last isolated, large C. pecorum-free population remaining in Australia. These koalas could provide a safeguard against this serious disease threat to an iconic Australian species.
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Affiliation(s)
- Jessica Fabijan
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia.
| | - Charles Caraguel
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - Martina Jelocnik
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, 4558, Queensland, Australia
| | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, 4558, Queensland, Australia
| | - Wayne S J Boardman
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - Elisa Nishimoto
- Kangaroo Island Veterinary Clinic, Kingscote, 5223, South Australia, Australia
| | - Greg Johnsson
- Kangaroo Island Veterinary Clinic, Kingscote, 5223, South Australia, Australia
| | - Robyn Molsher
- Department for Environment and Water, Adelaide, 5000, South Australia, Australia
| | - Lucy Woolford
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, 4558, Queensland, Australia
| | - Greg Simmons
- School of Veterinary Sciences, The University of Queensland, Gatton, 4343, Queensland, Australia
| | - Farhid Hemmatzadeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - Darren J Trott
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - Natasha Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, South Australia, Australia
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Liu F, Lv L, Jiang H, Yan R, Dong S, Chen L, Wang W, Chen YQ. Alterations in the Urinary Microbiota Are Associated With Cesarean Delivery. Front Microbiol 2018; 9:2193. [PMID: 30258432 PMCID: PMC6143726 DOI: 10.3389/fmicb.2018.02193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022] Open
Abstract
Similar to the gut, the bladder contains urinary microbiota, and its bacterial composition and structure are determined by the individual’s health status. Cesarean section is a traumatic event for women and it is correlated with postpartum complications. To better understand the urinary microbiota alterations caused by cesarean section, 16S rDNA sequencing was used to assess urine specimens collected by transurethral catheterization from 30 healthy women undergoing cesarean section pre-delivery (PreD) and post-delivery (PostD). A significant increase in bacterial diversity and more detectable bacteria at the phylum, family, and genus levels was observed in the PostD group compared to the PreD group, indicating that cesarean delivery (a process that includes surgery and delivery) altered the bacterial community. Specifically, the phylum Firmicutes and its affiliated family Lactobacillaceae and genus Lactobacillus dramatically decreased in the PostD group, suggesting that beneficial bacteria decreased after cesarean section, and clinicians should be aware that this might increase the risk of complications. Concurrently, the phylum Proteobacteria and its affiliated bacteria Pseudomonadaceae and Pseudomonas increased in the PostD group compared to the PreD group. This indicates that pathogen growth increases after cesarean section, making it important for clinicians to combat these changes to protect women from infectious diseases. Interestingly, several metabolic pathways, such as metabolism of energy, cofactors and vitamins were strengthened in the PostD group, whereas membrane transport was lessened in this group. This suggests that women’s metabolic disorders might be cured by balancing urinary microbiota. In conclusion, the altered urinary microbiota between the PreD and PostD periods appears to provide insight into how to prevent postpartum metabolic disorders.
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Affiliation(s)
- Fengping Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Longxian Lv
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huiyong Jiang
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ren Yan
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shurong Dong
- Key Laboratory of Advanced Micro/Nano Electronic Devices and Smart Systems of Zhejiang, College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, China
| | - Liping Chen
- Intensive Unit, Affiliated Yancheng Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Wei Wang
- Department of Urology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yong Q Chen
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
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