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Hilt EE, Ferrieri P. Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes (Basel) 2022; 13:genes13091566. [PMID: 36140733 PMCID: PMC9498426 DOI: 10.3390/genes13091566] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.
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Yang S, Hemarajata P, Hilt EE, Price TK, Garner OB, Green NM. Investigation of SARS-CoV-2 Epsilon Variant and Hospitalization Status by Genomic Surveillance in a Single Large Health System During the 2020-2021 Winter Surge in Southern California. Am J Clin Pathol 2022; 157:649-652. [PMID: 34875004 PMCID: PMC8689746 DOI: 10.1093/ajcp/aqab203] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/27/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES This study aimed to assess whether the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Epsilon variant (B.1.429/427) is more virulent, leading to more hospitalization and more severe disease requiring intensive care unit (ICU) admission. METHODS SARS-CoV-2 genomic surveillance was performed on respiratory samples from 231 unique patients, collected at a single large health system in Southern California between November 2020 and March 2021 during the winter surge. RESULTS The frequencies of the Epsilon variant among outpatients, hospitalized patients, and ICU patients were indifferent. CONCLUSIONS Our study suggests that the Epsilon variant is not associated with increased hospitalization and ICU admission.
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Affiliation(s)
- Shangxin Yang
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | | | - Evann E Hilt
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Travis K Price
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Omai B Garner
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Nicole M Green
- Los Angeles Department of Public Health, Downey, CA, USA
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3
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Guo L, Boocock J, Hilt EE, Chandrasekaran S, Zhang Y, Munugala C, Sathe L, Alexander N, Arboleda VA, Flint J, Eskin E, Luo C, Yang S, Garner OB, Yin Y, Bloom JS, Kruglyak L. Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA. BMC Genomics 2022; 23:260. [PMID: 35379194 PMCID: PMC8978495 DOI: 10.1186/s12864-022-08488-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 03/15/2022] [Indexed: 11/10/2022] Open
Abstract
Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide insights to contain or prevent viral transmission. Investigation of the transmission history requires efficient sequencing methods and analytic strategies, which can be generally useful in the study of viral outbreaks. Methods The County of Los Angeles (hereafter, LA County) sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history, we carried out surveillance viral genome sequencing to determine 142 viral genomes from unique patients seeking care at the University of California, Los Angeles (UCLA) Health System. 86 of these genomes were from samples collected before April 19, 2020. Results We found that the early outbreak in LA County, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a USA-specific strain, B.1.43, which was found predominantly in California and Washington State. While samples from LA County carried the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carried additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus were effective at preventing transmission, but might have been undermined by the many introductions of SARS-CoV-2 into the region. Conclusion Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health response. Our results reinforce the critical need for the USA to have coordinated inter-state responses to the pandemic. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08488-7.
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Affiliation(s)
- Longhua Guo
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA.,Howard Hughes Medical Institute, HHMI, Chevy Chase, USA.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA.,Howard Hughes Medical Institute, HHMI, Chevy Chase, USA.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Evann E Hilt
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Sukantha Chandrasekaran
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Yi Zhang
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Chetan Munugala
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Laila Sathe
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Noah Alexander
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Jonathan Flint
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA.,Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Eleazar Eskin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA.,Department of Computer Science, Samueli School of Engineering, UCLA, Los Angeles, USA.,Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Chongyuan Luo
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Shangxin Yang
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Omai B Garner
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Yi Yin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA.
| | - Joshua S Bloom
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA. .,Howard Hughes Medical Institute, HHMI, Chevy Chase, USA. .,Octant, Inc, Los Angeles, USA.
| | - Leonid Kruglyak
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, USA. .,Howard Hughes Medical Institute, HHMI, Chevy Chase, USA. .,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, USA.
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4
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Price TK, Mirasol R, Ward KW, Dayo AJ, Hilt EE, Chandrasekaran S, Garner OB, de St Maurice A, Yang S. Genomic Characterizations of Clade III Lineage of Candida auris, California, USA. Emerg Infect Dis 2021; 27:1223-1227. [PMID: 33755003 PMCID: PMC8007294 DOI: 10.3201/eid2704.204361] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Candida auris is an emerging multidrug-resistant yeast. We describe an ongoing C. auris outbreak that began in October 2019 in Los Angeles, California, USA. We used genomic analysis to determine that isolates from 5 of 6 patients belonged to clade III; 4 isolates were closely related.
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5
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Bloom JS, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EM, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Sina Booeshaghi A, Brandenberg OF, Guo L, Boocock J, Hochman M, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, Oland G, Choe BJ, Chandrasekaran S, Hilt EE, Butte MJ, Damoiseaux R, Kravit C, Cooper AR, Yin Y, Pachter L, Garner OB, Flint J, Eskin E, Luo C, Kosuri S, Kruglyak L, Arboleda VA. Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples. Nat Biomed Eng 2021; 5:657-665. [PMID: 34211145 PMCID: PMC10810734 DOI: 10.1038/s41551-021-00754-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/20/2021] [Indexed: 02/02/2023]
Abstract
Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay, which we named SwabSeq, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives, and that reduces the requirements for automation, purification and sample-to-sample normalization. We used SwabSeq to perform 80,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests, in less than two months with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens.
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Affiliation(s)
- Joshua S Bloom
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Octant Inc., Emeryville, CA, USA.
| | - Laila Sathe
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Chetan Munugala
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | | | | | | | | | | | - Dawn Marquette
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Stephania Kay
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Mark Lucas
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - TreQuan Love
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Oliver F Brandenberg
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Longhua Guo
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | | | - Isabella Lin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Nathan LaPierre
- Department of Computer Science, Samueli School of Engineering, UCLA, Los Angeles, CA, USA
| | - Duke Hong
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Yi Zhang
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Gabriel Oland
- Department of Surgery, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Bianca Judy Choe
- Department of Emergency Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sukantha Chandrasekaran
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Evann E Hilt
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Manish J Butte
- Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology & Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Robert Damoiseaux
- California NanoSystems Institute, UCLA, Los Angeles, CA, USA
- Department of Bioengineering, Samueli School of Engineering, UCLA, Los Angeles, CA, USA
- Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Clifford Kravit
- Department of Digital Technology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Yi Yin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Lior Pachter
- Division of Biology and Bioengineering, Department of Computing and Mathematical Sciences, Caltech, Pasadena, CA, USA
| | - Omai B Garner
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jonathan Flint
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Eleazar Eskin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computer Science, Samueli School of Engineering, UCLA, Los Angeles, CA, USA
| | - Chongyuan Luo
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sriram Kosuri
- Octant Inc., Emeryville, CA, USA.
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA.
| | - Leonid Kruglyak
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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6
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Hilt EE, Boocock J, Trejo M, Le CQ, Guo L, Zhang Y, Sathe L, Arboleda VA, Yin Y, Bloom JS, Wang PC, Elmore JG, Kruglyak L, Shrestha L, Bakhash SAM, Lin M, Xie H, Huang ML, Roychoudhury P, Greninger A, Chandrasekaran S, Yang S, Garner OB. Retrospective Detection of SARS-CoV-2 in Symptomatic Patients prior to Widespread Diagnostic Testing in Southern California. Clin Infect Dis 2021; 74:271-277. [PMID: 33939799 PMCID: PMC8135745 DOI: 10.1093/cid/ciab360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Indexed: 01/15/2023] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused one of the worst pandemics in recent history. Few reports have revealed that SARS-CoV-2 was spreading in the United States as early as the end of January. In this study, we aimed to determine if SARS-CoV-2 had been circulating in the Los Angeles (LA) area at a time when access to diagnostic testing for coronavirus disease 2019 (COVID-19) was severely limited. Methods We used a pooling strategy to look for SARS-CoV-2 in remnant respiratory samples submitted for regular respiratory pathogen testing from symptomatic patients from November 2019 to early March 2020. We then performed sequencing on the positive samples. Results We detected SARS-CoV-2 in 7 specimens from 6 patients, dating back to mid-January. The earliest positive patient, with a sample collected on January 13, 2020 had no relevant travel history but did have a sibling with similar symptoms. Sequencing of these SARS-CoV-2 genomes revealed that the virus was introduced into the LA area from both domestic and international sources as early as January. Conclusions We present strong evidence of community spread of SARS-CoV-2 in the LA area well before widespread diagnostic testing was being performed in early 2020. These genomic data demonstrate that SARS-CoV-2 was being introduced into Los Angeles County from both international and domestic sources in January 2020.
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Affiliation(s)
- Evann E Hilt
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, California, USA.,Howard Hughes Medical Institute, David Geffen School of Medicine, UCLA, California, USA
| | - Marisol Trejo
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| | - Catherine Q Le
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| | - Longhua Guo
- Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, California, USA.,Howard Hughes Medical Institute, David Geffen School of Medicine, UCLA, California, USA
| | - Yi Zhang
- Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA
| | - Laila Sathe
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| | - Valerie A Arboleda
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA.,Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA
| | - Yi Yin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA
| | - Joshua S Bloom
- Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, California, USA
| | - Pin-Chieh Wang
- Department of Medicine, David Geffen School of Medicine, UCLA, California, USA
| | - Joann G Elmore
- Department of Medicine, David Geffen School of Medicine, UCLA, California, USA
| | - Leonid Kruglyak
- Department of Human Genetics, David Geffen School of Medicine, UCLA, California, USA.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, California, USA.,Howard Hughes Medical Institute, David Geffen School of Medicine, UCLA, California, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Shah A Mohamed Bakhash
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Michelle Lin
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Alexander Greninger
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Sukantha Chandrasekaran
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| | - Shangxin Yang
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
| | - Omai B Garner
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), California, USA
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7
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Bloom JS, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EM, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Booeshaghi AS, Brandenberg OF, Guo L, Boocock J, Hochman M, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, Oland G, Choe BJ, Chandrasekaran S, Hilt EE, Butte MJ, Damoiseaux R, Kravit C, Cooper AR, Yin Y, Pachter L, Garner OB, Flint J, Eskin E, Luo C, Kosuri S, Kruglyak L, Arboleda VA. Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing. medRxiv 2021. [PMID: 32909008 PMCID: PMC7480060 DOI: 10.1101/2020.08.04.20167874] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission1,2. Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. After setting up SwabSeq in a high-complexity CLIA laboratory, we performed more than 80,000 tests for COVID-19 in less than two months, confirming in a real world setting that SwabSeq inexpensively delivers highly sensitive and specific results at scale, with a turn-around of less than 24 hours. Our clinical laboratory uses SwabSeq to test both nasal and saliva samples without RNA extraction, while maintaining analytical sensitivity comparable to or better than traditional RT-qPCR tests. Moving forward, SwabSeq can rapidly scale up testing to mitigate devastating spread of novel pathogens.
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Affiliation(s)
- Joshua S Bloom
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Octant, Inc
| | - Laila Sathe
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Chetan Munugala
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI
| | | | | | | | | | | | | | | | - Dawn Marquette
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Stephania Kay
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Mark Lucas
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - TreQuan Love
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | | | - Oliver F Brandenberg
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA
| | - Longhua Guo
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA
| | | | | | - Isabella Lin
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Nathan LaPierre
- Department of Computer Science, Samueli School of Engineering, UCLA
| | - Duke Hong
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Yi Zhang
- Department of Human Genetics, David Geffen School of Medicine, UCLA
| | - Gabriel Oland
- Department of Surgery, David Geffen School of Medicine, UCLA
| | - Bianca Judy Choe
- Department of Emergency Medicine, David Geffen School of Medicine, UCLA
| | | | - Evann E Hilt
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Manish J Butte
- Department of Pediatrics, David Geffen School of Medicine, UCLA.,Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, UCLA
| | - Robert Damoiseaux
- California NanoSystems Institute, UCLA.,Department of Bioengineering, Samueli School of Engineering, UCLA.,David Geffen School of Medicine, Research Information Technology
| | - Clifford Kravit
- David Geffen School of Medicine, Research Information Technology
| | | | - Yi Yin
- Department of Human Genetics, David Geffen School of Medicine, UCLA
| | - Lior Pachter
- Division of Biology and Bioengineering & Department of Computing and Mathematical Sciences, Caltech
| | - Omai B Garner
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Jonathan Flint
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA
| | - Eleazar Eskin
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Department of Computer Science, Samueli School of Engineering, UCLA.,Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Chongyuan Luo
- Department of Human Genetics, David Geffen School of Medicine, UCLA
| | - Sriram Kosuri
- Octant, Inc.,Department of Chemistry and Biochemistry, UCLA
| | - Leonid Kruglyak
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
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8
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Price TK, Lin H, Gao X, Thomas-White KJ, Hilt EE, Mueller ER, Wolfe AJ, Dong Q, Brubaker L. Bladder bacterial diversity differs in continent and incontinent women: a cross-sectional study. Am J Obstet Gynecol 2020; 223:729.e1-729.e10. [PMID: 32380174 DOI: 10.1016/j.ajog.2020.04.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 01/03/2020] [Revised: 04/15/2020] [Accepted: 04/23/2020] [Indexed: 01/21/2023]
Abstract
BACKGROUND Since the discovery of the bladder microbiome (urobiome), interest has grown in learning whether urobiome characteristics have a role in clinical phenotyping and provide opportunities for novel therapeutic approaches for women with common forms of urinary incontinence. OBJECTIVE This study aimed to test the hypothesis that the bladder urobiome differs among women in the control cohort and women affected by urinary incontinence by assessing associations between urinary incontinence status and the cultured urobiome. STUDY DESIGN With institutional review board oversight, urine specimens from 309 adult women were collected through transurethral catheterization. These women were categorized into 3 cohorts (continent control, stress urinary incontinence [SUI], and urgency urinary incontinence [UUI]) based on their responses to the validated Pelvic Floor Distress Inventory (PFDI) questionnaire. Among 309 women, 150 were in the continent control cohort, 50 were in the SUI cohort, and 109 were in the UUI cohort. Symptom severity was assessed by subscale scoring with the Urinary Distress Inventory (UDI), subscale of the Pelvic Floor Distress Inventory. Microbes were assessed by expanded quantitative urine culture protocol, which detects the most common bladder microbes (bacteria and yeast). Microbes were identified to the species level by matrix-assisted laser desorption and ionization time-of-flight mass spectrometry. Alpha diversity indices were calculated for culture-positive samples and compared across the 3 cohorts. The correlations of UDI scores, alpha diversity indices, and species abundance were estimated. RESULTS Participants had a mean age of 53 years (range 22-90); most were whites (65%). Women with urinary incontinence were slightly older (control, 47; SUI, 54; UUI, 61). By design, UDI symptom scores differed (control, 8.43 [10.1]; SUI, 97.95 [55.36]; UUI, 93.71 [49.12]; P<.001). Among 309 participants, 216 (70%) had expanded quantitative urine culture-detected bacteria; furthermore, the urinary incontinence cohorts had a higher detection frequency than the control cohort (control, 57%; SUI, 86%; UUI, 81%; P<.001). In addition, the most frequently detected species among the cohorts were as follows: continent control, Lactobacillus iners (12.7%), Streptococcus anginosus (12.7%), L crispatus (10.7%), and L gasseri (10%); SUI, S anginosus (26%), L iners (18%), Staphylococcus epidermidis (18%), and L jensenii (16%); and UUI, S anginosus (30.3%), L gasseri (22%), Aerococcus urinae (18.3%), and Gardnerella vaginalis (17.4%). However, only Actinotignum schaalii (formerly Actinobaculum schaalii), A urinae, A sanguinicola, and Corynebacterium lipophile group were found at significantly higher mean abundances in 1 of the urinary incontinence cohorts when compared with the control cohort (Wilcoxon rank sum test; P<.02), and no individual genus differed significantly between the 2 urinary incontinence cohorts. Both urinary incontinence cohorts had increased alpha diversity similar to continent control cohort with indices of species richness, but not evenness, strongly associated with urinary incontinence. CONCLUSION In adult women, the composition of the culturable bladder urobiome is associated with urinary incontinence, regardless of common incontinence subtype. Detection of more unique living microbes was associated with worsening incontinence symptom severity. Culturable species richness was significantly greater in the urinary incontinence cohorts than in the continent control cohort.
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Affiliation(s)
- Travis K Price
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL; Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Huaiying Lin
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL
| | - Xiang Gao
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL
| | - Krystal J Thomas-White
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
| | - Evann E Hilt
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL; Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Elizabeth R Mueller
- Departments of Obstetrics and Gynecology and Urology, Loyola University Medical Center, Maywood, IL
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL
| | - Qunfeng Dong
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL
| | - Linda Brubaker
- Division of Female Pelvic Medicine and Reconstructive Surgery, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA.
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9
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Thomas-White K, Taege S, Limeira R, Brincat C, Joyce C, Hilt EE, Mac-Daniel L, Radek KA, Brubaker L, Mueller ER, Wolfe AJ. Vaginal estrogen therapy is associated with increased Lactobacillus in the urine of postmenopausal women with overactive bladder symptoms. Am J Obstet Gynecol 2020; 223:727.e1-727.e11. [PMID: 32791124 DOI: 10.1016/j.ajog.2020.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 01/30/2020] [Revised: 07/23/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Previous work has shown that the vaginal microbiome decreases in Lactobacillus predominance and becomes more diverse after menopause. It has also been shown that estrogen therapy restores Lactobacillus dominance in the vagina and that topical estrogen is associated with overactive bladder symptom improvement. We now know that the bladder contains a unique microbiome and that increased bladder microbiome diversity is associated with overactive bladder. However, there is no understanding of how quickly each pelvic floor microbiome responds to estrogen or if those changes are associated with symptom improvement. OBJECTIVE This study aimed to determine if estrogen treatment of postmenopausal women with overactive bladder decreases urobiome diversity. STUDY DESIGN We analyzed data from postmenopausal participants in 2 trials (NCT02524769 and NCT02835846) who chose vaginal estrogen as the primary overactive bladder treatment and used 0.5 g of conjugated estrogen (Premarin cream; Pfizer, New York City, NY) twice weekly for 12 weeks. Baseline and 12-week follow-up data included the Overactive Bladder questionnaire, and participants provided urine samples via catheter, vaginal swabs, perineal swabs, and voided urine samples. Microbes were detected by an enhanced culture protocol. Linear mixed models were used to estimate microbiome changes over time. Urinary antimicrobial peptide activity was assessed by a bacterial growth inhibition assay and correlated with relative abundance of members of the urobiome. RESULTS In this study, 12 weeks of estrogen treatment resulted in decreased microbial diversity within the vagina (Shannon, P=.047; Richness, P=.043) but not in the other niches. A significant increase in Lactobacillus was detected in the bladder (P=.037) but not in the vagina (P=.33), perineum (P=.56), or voided urine (P=.28). The change in Lactobacillus levels in the bladder was associated with modest changes in urgency incontinence symptoms (P=.02). The relative abundance of the genus Corynebacterium correlated positively with urinary antimicrobial peptide activity after estrogen treatment. CONCLUSION Estrogen therapy may change the microbiome of different pelvic floor niches. The vagina begins to decrease in diversity, and the bladder experiences a significant increase in Lactobacillus levels; the latter is correlated with a modest improvement in the symptom severity subscale of the Overactive Bladder questionnaire.
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Affiliation(s)
- Krystal Thomas-White
- Departments of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
| | - Susanne Taege
- Obstetrics and Gynecology and Urology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL; Mount Carmel Medical Group, Mount Carmel Urogynecology and Pelvic Floor, Westerville, OH
| | - Roberto Limeira
- Departments of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL; Loyola Genomics Facility, Loyola University Chicago, Maywood, IL
| | - Cynthia Brincat
- Obstetrics and Gynecology and Urology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL; Department of Obstetrics and Gynecology, Rush University Medical Center, Chicago, IL
| | - Cara Joyce
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL
| | - Evann E Hilt
- Departments of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL; Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA
| | - Laura Mac-Daniel
- Surgery, Stritch School of Medicine, Loyola University Chicago, Maywood, IL
| | - Katherine A Radek
- Departments of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL; Surgery, Stritch School of Medicine, Loyola University Chicago, Maywood, IL
| | - Linda Brubaker
- Obstetrics and Gynecology and Urology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL; Division of Female Pelvic Medicine and Reconstructive Surgery, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, San Diego, CA
| | - Elizabeth R Mueller
- Obstetrics and Gynecology and Urology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL
| | - Alan J Wolfe
- Departments of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL; Loyola Genomics Facility, Loyola University Chicago, Maywood, IL.
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Hilt EE, Fitzwater SP, Ward K, de St Maurice A, Chandrasekaran S, Garner OB, Yang S. Carbapenem Resistant Aeromonas hydrophila Carrying bla cphA7 Isolated From Two Solid Organ Transplant Patients. Front Cell Infect Microbiol 2020; 10:563482. [PMID: 33194801 PMCID: PMC7649429 DOI: 10.3389/fcimb.2020.563482] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 05/18/2020] [Accepted: 09/23/2020] [Indexed: 11/30/2022] Open
Abstract
Aeromonas hydrophila resides in a variety of aquatic environments. Infections with A. hydrophila mainly occur after contact with fresh or brackish water. Nosocomial infections with A. hydrophila can also occur. A. hydrophila infections can be difficult to treat due to both intrinsic and acquired antimicrobial resistance (AMR) mechanisms. In 2018–19, we isolated multi-drug resistant (MDR) A. hyrodphila from two solid organ transplant patients with intra-abdominal infections. We aimed to characterize their AMR mechanisms and to determine their genetic relatedness to aid epidemiological investigation. We performed whole genome sequencing (WGS) using Illumina MiSeq and Nanopore MinIon on 3 A. hydrophila isolates, with one isolate from Patient A (blood) and two isolates from Patient B (abdominal and T-tube fluid, isolated 2 weeks apart). Phenotypic assays included: Broth Microdilution (BMD), Modified Hodge Test (MHT), Modified Carbapenem Inactivation Method (mCIM), and EDTA Carbapenem Inactivation Method (eCIM). Data analyses were performed using CLCbio and Geneious. AMR genomic analysis revealed that all three isolates possess chromosomally encoded genes including blaOXA−12(oxacillinase), blacepS(AmpC), and blacphA7(metallo-beta-lactamase). All isolates tested strongly positive by MHT and mCIM, but only Patient B's second isolate (after 2 weeks of meropenem treatment) tested positive by eCIM. More intriguingly, Patient B's first isolate (before meropenem treatment) tested falsely susceptible to carbapenems by BMD, suggesting blacphA7 gene was not expressed constitutively. Phylogenetic analysis showed the two isolates from Patient B were highly similar with only 1 SNP difference. The isolate from Patient A only differed from Patient B's isolates by 35 and 36 SNPs, respectively, suggesting close genetic relatedness. Further epidemiological investigation is undergoing. We report the first cases of CphA-mediated carbapenem resistant A. hydrophila in the U.S. It is concerning that 1 out of 3 isolates tested falsely susceptible to carbapenems by BMD despite clear carbapenemase production shown by strongly positive MHT and mCIM. In both cases, meropenem was initially used to treat the patients. Clinicians and microbiologists in the US should be aware of the emerging MDR Aeromonas nosocomial infections and the potential false carbapenem susceptible results due to CphA-type carbapenemase, which may be induced during treatment.
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Affiliation(s)
- Evann E Hilt
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Sean Patrick Fitzwater
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kevin Ward
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Annabelle de St Maurice
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Sukantha Chandrasekaran
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Omai B Garner
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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11
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Chen J, Hilt EE, Li F, Wu H, Jiang Z, Zhang Q, Wang J, Wang Y, Li Z, Tang J, Yang S. Epidemiological and Genomic Analysis of SARS-CoV-2 in 10 Patients From a Mid-Sized City Outside of Hubei, China in the Early Phase of the COVID-19 Outbreak. Front Public Health 2020; 8:567621. [PMID: 33072702 PMCID: PMC7531217 DOI: 10.3389/fpubh.2020.567621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/30/2020] [Accepted: 08/14/2020] [Indexed: 12/28/2022] Open
Abstract
A novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing Coronavirus Disease 2019 (COVID-19) pandemic. In this study, we performed a comprehensive epidemiological and genomic analysis of SARS-CoV-2 genomes from 10 patients in Shaoxing (Zhejiang Province), a mid-sized city outside of the epicenter Hubei province, China, during the early stage of the outbreak (late January to early February, 2020). We obtained viral genomes with >99% coverage and a mean depth of 296X demonstrating that viral genomic analysis is feasible via metagenomics sequencing directly on nasopharyngeal samples with SARS-CoV-2 Real-time PCR Ct values <28. We found that a cluster of four patients with travel history to Hubei shared the exact same virus with patients from Wuhan, Taiwan, Belgium, and Australia, highlighting how quickly this virus spread to the globe. The virus from another cluster of two family members living together without travel history but with a sick contact of a confirmed case from another city outside of Hubei accumulated significantly more mutations (9 SNPs vs. average 4 SNPs), suggesting a complex and dynamic nature of this outbreak. Our findings add to the growing knowledge of the epidemiological and genomic characteristics of SARS-CoV-2 and offers a glimpse into the early phase of this viral infection outside of Hubei, China.
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Affiliation(s)
- Jinkun Chen
- Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Evann E Hilt
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Fan Li
- Three Coin Analytics, Inc., Pleasanton, CA, United States
| | - Huan Wu
- IngeniGen XunMinKang Biotechnology Inc., Shaoxing, China
| | - Zhuojing Jiang
- Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Qinchao Zhang
- Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Jiling Wang
- Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Yifang Wang
- IngeniGen XunMinKang Biotechnology Inc., Shaoxing, China
| | - Ziqin Li
- Zhejiang-California International Nanosystems Institute, Zhejiang University, Hangzhou, China
| | - Jialiang Tang
- Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Zhejiang-California International Nanosystems Institute, Zhejiang University, Hangzhou, China
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12
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Larkin PMK, Lawson KL, Contreras DA, Le CQ, Trejo M, Realegeno S, Hilt EE, Chandrasekaran S, Garner OB, Fishbein GA, Yang S. Amplicon-Based Next-Generation Sequencing for Detection of Fungi in Formalin-Fixed, Paraffin-Embedded Tissues: Correlation with Histopathology and Clinical Applications. J Mol Diagn 2020; 22:1287-1293. [PMID: 32738297 DOI: 10.1016/j.jmoldx.2020.06.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/26/2020] [Indexed: 01/13/2023] Open
Abstract
Invasive fungal infections are increasing in prevalence because of an expanding population of immunocompromised individuals. To reduce morbidity and mortality, it is critical to accurately identify fungal pathogens to guide treatment. Current methods rely on histopathology, fungal culture, and serology, which are often insufficient for diagnosis. Herein, we describe the use of a laboratory-developed internal transcribed spacer-targeted amplicon-based next-generation sequencing (NGS) assay for the identification of fungal etiology in fungal stain-positive formalin-fixed, paraffin-embedded tissues by using Illumina MiSeq. A total of 44 specimens from 35 patients were included in this study, with varying degrees of fungal burden from multiple anatomic sites. NGS identified 20 unique species across the 54 total organisms detected, including 40 molds, 10 yeasts, and 4 dimorphic fungi. The histopathologic morphology and the organisms suspected by surgical pathologist were compared with the organisms identified by NGS, with 100% (44/44) and 93.2% (41/44) concordance, respectively. In contrast, fungal culture only provided an identification in 27.3% (12/44) of specimens. We demonstrated that NGS is a powerful method for accurate and unbiased fungal identification in formalin-fixed, paraffin-embedded tissues. A retrospective evaluation of the clinical utility of the NGS results also suggests this technology can potentially improve both the speed and the accuracy of diagnosis for invasive fungal infections.
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Affiliation(s)
- Paige M K Larkin
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Katy L Lawson
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Deisy A Contreras
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Catherine Q Le
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Marisol Trejo
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Susan Realegeno
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Evann E Hilt
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Sukantha Chandrasekaran
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Omai B Garner
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Gregory A Fishbein
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California.
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13
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Price TK, Hilt EE, Thomas-White K, Mueller ER, Wolfe AJ, Brubaker L. The urobiome of continent adult women: a cross-sectional study. BJOG 2019; 127:193-201. [PMID: 31469215 DOI: 10.1111/1471-0528.15920] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2019] [Indexed: 01/30/2023]
Abstract
OBJECTIVE To characterise the bladder microbiota of continent adult women. DESIGN Cross-sectional study of adult women who contributed catheterised urine samples, completed validated symptom questionnaires, and provided demographic data. SETTING US academic medical centre. POPULATION Well-characterised continent adult women. METHODS Participants contributed symptoms questionnaires, demographic data, and catheterised urine samples that were analysed by enhanced urine culture methodology and 16S rRNA gene sequencing. MAIN OUTCOME MEASURES Associations between demographics and microbial community state structures (urotypes, defined by the dominant taxon of each specimen). RESULTS The bladder microbiota (urobiome) of a control group of 224 continent women were characterised, demonstrating variability in terms of urotype. The most common urotype was Lactobacillus (19%), which did not differ with any demographic. In contrast, the Gardnerella (P < 0.001) and Escherichia (P = 0.005) urotypes were more common in younger and older women, respectively. CONCLUSIONS For urobiome research, enhanced culture methods and/or DNA sequencing are the preferred techniques for bacterial detection. The interpretation of clinical tests, such as the standard urine culture, should incorporate the knowledge that some women have Gardnerella or Escherichia urotypes without evidence of any clinical disorder. Clinical care strategies should preserve or restore the beneficial effects of the native urobiome, as disruption of that microbial community could result in unintended vulnerability to uropathogen invasion or opportunistic pathogen overgrowth. Longitudinal studies of urobiome responses to therapies should be encouraged. TWEETABLE ABSTRACT In continent adult women bladder microbiome composition differs by age, with relevance for clinical practice.
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Affiliation(s)
- T K Price
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - E E Hilt
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - K Thomas-White
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - E R Mueller
- Departments of Obstetrics & Gynecology and Urology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - A J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - L Brubaker
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, 92093, USA
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14
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Thomas-White K, Forster SC, Kumar N, Van Kuiken M, Putonti C, Stares MD, Hilt EE, Price TK, Wolfe AJ, Lawley TD. Culturing of female bladder bacteria reveals an interconnected urogenital microbiota. Nat Commun 2018; 9:1557. [PMID: 29674608 PMCID: PMC5908796 DOI: 10.1038/s41467-018-03968-5] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/26/2018] [Indexed: 12/12/2022] Open
Abstract
Metagenomic analyses have indicated that the female bladder harbors an indigenous microbiota. However, there are few cultured reference strains with sequenced genomes available for functional and experimental analyses. Here we isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women. This culture collection spans 78 species, representing approximately two thirds of the bacterial diversity within the sampled bladders, including Proteobacteria, Actinobacteria, and Firmicutes. Detailed genomic and functional comparison of the bladder microbiota to the gastrointestinal and vaginal microbiotas demonstrates similar vaginal and bladder microbiota, with functional capacities that are distinct from those observed in the gastrointestinal microbiota. Whole-genome phylogenetic analysis of bacterial strains isolated from the vagina and bladder in the same women identifies highly similar Escherichia coli, Streptococcus anginosus, Lactobacillus iners, and Lactobacillus crispatus, suggesting an interlinked female urogenital microbiota that is not only limited to pathogens but is also characteristic of health-associated commensals. The female bladder seems to harbor a poorly characterized indigenous microbiota. Here, the authors isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women, generating a culture collection representing two thirds of the bacterial diversity within the samples.
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Affiliation(s)
- Krystal Thomas-White
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Michelle Van Kuiken
- Department of Urology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA.,Department of Computer Science, Loyola University Chicago, Chicago, IL, 60660, USA.,Bioinformatics Program, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Mark D Stares
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Evann E Hilt
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Travis K Price
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.
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15
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Jacobs KM, Thomas-White KJ, Hilt EE, Wolfe AJ, Waters TP. Microorganisms Identified in the Maternal Bladder: Discovery of the Maternal Bladder Microbiota. AJP Rep 2017; 7:e188-e196. [PMID: 28970961 PMCID: PMC5621969 DOI: 10.1055/s-0037-1606860] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/15/2017] [Indexed: 01/08/2023] Open
Abstract
Objective The objective of this study was to characterize the bladder microbiota in pregnancy. Methods A prospective observational study of 51 pregnant women, admitted to a tertiary care hospital, who underwent straight catheterization urine collection or transurethral Foley catheter placement. 16S rRNA gene sequencing and enhanced quantitative urine culture assessed the maternal bladder microbiota with comparisons made to standard urine culture results. Results Enhanced quantitative urine culture and 16S rRNA gene sequencing detected bacteria in the majority of participants. Lactobacillus and Gardnerella were the most commonly detected microbes. In contrast, standard urine culture had a 100% false-negative rate and failed to detect several known or emerging urinary pathogens. Conclusion There are live bacteria in the bladders of most pregnant women. This challenges the definition of asymptomatic bacteriuria.
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Affiliation(s)
- Kristin M. Jacobs
- Department of Obstetrics and Gynecology, Loyola University Medical Center, Maywood, Illinois
| | - Krystal J. Thomas-White
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois
| | - Evann E. Hilt
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois
| | - Thaddeus P. Waters
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Loyola University Medical Center, Maywood, Illinois
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16
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Malki K, Shapiro JW, Price TK, Hilt EE, Thomas-White K, Sircar T, Rosenfeld AB, Kuffel G, Zilliox MJ, Wolfe AJ, Putonti C. Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome. PLoS One 2016; 11:e0166757. [PMID: 27861551 PMCID: PMC5115800 DOI: 10.1371/journal.pone.0166757] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 10/19/2016] [Indexed: 01/21/2023] Open
Abstract
Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates from the bladder reveal a large pangenome, as well as evidence of high frequency horizontal gene transfer. Prophage gene sequences were found to be abundant amongst the strains isolated from the bladder, as well as amongst publicly available Gardnerella genomes from the vagina and endometrium, motivating an in depth examination of these sequences. Amongst the 39 Gardnerella strains examined here, there were more than 400 annotated prophage gene sequences that we could cluster into 95 homologous groups; 49 of these groups were unique to a single strain. While many of these prophages exhibited no sequence similarity to any lytic phage genome, estimation of the rate of phage acquisition suggests both vertical and horizontal acquisition. Furthermore, bioinformatic evidence indicates that prophage acquisition is ongoing within both vaginal and bladder Gardnerella populations. The abundance of prophage sequences within the strains examined here suggests that phages could play an important role in the species’ evolutionary history and in its interactions within the complex communities found in the female urinary and reproductive tracts.
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Affiliation(s)
- Kema Malki
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Jason W. Shapiro
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Travis K. Price
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Evann E. Hilt
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Krystal Thomas-White
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Trina Sircar
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Amy B. Rosenfeld
- Center for Biomedical Informatics, Loyola Genomics Facility, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Gina Kuffel
- Center for Biomedical Informatics, Loyola Genomics Facility, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Michael J. Zilliox
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Computer Science, Loyola University Chicago, Chicago, Illinois, United States of America
- * E-mail:
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Price TK, Mehrtash A, Kalesinskas L, Malki K, Hilt EE, Putonti C, Wolfe AJ. Genome sequences and annotation of two urinary isolates of E. coli. Stand Genomic Sci 2016; 11:79. [PMID: 27777649 PMCID: PMC5060011 DOI: 10.1186/s40793-016-0202-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 05/13/2016] [Accepted: 10/04/2016] [Indexed: 11/10/2022] Open
Abstract
The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result most often from colonization of the bladder by uropathogenic E. coli strains. In contrast, a poorly defined condition called asymptomatic bacteriuria results from colonization of the bladder with E. coli strains without symptoms. As part of an on-going attempt to identify and characterize the newly discovered female urinary microbiota, we report the genome sequences and annotation of two urinary isolates of E. coli: one (E78) was isolated from a female patient who self-reported cystitis; the other (E75) was isolated from a female patient who reported that she did not have symptoms of cystitis. Whereas strain E75 is most closely related to an avian extraintestinal pathogen, strain E78 is a member of a clade that includes extraintestinal strains often found in the human bladder. Both genomes are uncommonly rich in prophages.
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Affiliation(s)
- Travis K Price
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, 2160 South First Avenue, Maywood, IL 60153 USA
| | - Arya Mehrtash
- Bioinformatics Program, Loyola University Chicago, Chicago, IL USA
| | - Laurynas Kalesinskas
- Bioinformatics Program, Loyola University Chicago, Chicago, IL USA ; Department of Biology, Loyola University Chicago, Chicago, IL USA
| | - Kema Malki
- Department of Biology, Loyola University Chicago, Chicago, IL USA
| | - Evann E Hilt
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, 2160 South First Avenue, Maywood, IL 60153 USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL USA ; Department of Biology, Loyola University Chicago, Chicago, IL USA ; Department of Computer Science, Loyola University Chicago, Chicago, IL USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, 2160 South First Avenue, Maywood, IL 60153 USA
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Barr-Beare E, Saxena V, Hilt EE, Thomas-White K, Schober M, Li B, Becknell B, Hains DS, Wolfe AJ, Schwaderer AL. The Interaction between Enterobacteriaceae and Calcium Oxalate Deposits. PLoS One 2015; 10:e0139575. [PMID: 26448465 PMCID: PMC4598009 DOI: 10.1371/journal.pone.0139575] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/15/2015] [Indexed: 12/11/2022] Open
Abstract
Background The role of calcium oxalate crystals and deposits in UTI pathogenesis has not been established. The objectives of this study were to identify bacteria present in pediatric urolithiasis and, using in vitro and in vivo models, to determine the relevance of calcium oxalate deposits during experimental pyelonephritis. Methods Pediatric kidney stones and urine were collected and both cultured and sequenced for bacteria. Bacterial adhesion to calcium oxalate was compared. Murine kidney calcium oxalate deposits were induced by intraperitoneal glyoxalate injection and kidneys were transurethrally inoculated with uropathogenic Escherichia coli to induce pyelonephritis Results E. coli of the family Enterobacteriaceae was identified in patients by calcium oxalate stone culture. Additionally Enterobacteriaceae DNA was sequenced from multiple calcium oxalate kidney stones. E. coli selectively aggregated on and around calcium oxalate monohydrate crystals. Mice inoculated with glyoxalate and uropathogenic E. coli had higher bacterial burdens, increased kidney calcium oxalate deposits and an increased kidney innate immune response compared to mice with only calcium oxalate deposits or only pyelonephritis. Conclusions In a murine model, the presence of calcium oxalate deposits increases pyelonephritis risk, likely due to preferential aggregation of bacteria on and around calcium oxalate crystals. When both calcium oxalate deposits and uropathogenic bacteria were present, calcium oxalate deposit number increased along with renal gene transcription of inner stone core matrix proteins increased. Therefore renal calcium oxalate deposits may be a modifiable risk factor for infections of the kidney and urinary tract. Furthermore, bacteria may be present in calcium oxalate deposits and potentially contribute to calcium oxalate renal disease.
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Affiliation(s)
- Evan Barr-Beare
- The Research Institute at Nationwide Children’s Hospital, Center for Clinical and Translational Research, Columbus, Ohio, United States of America
| | - Vijay Saxena
- The Research Institute at Nationwide Children’s Hospital, Center for Clinical and Translational Research, Columbus, Ohio, United States of America
| | - Evann E. Hilt
- Loyola University Chicago, Stritch School of Medicine, Department of Microbiology and Immunology, Chicago, Illinois, United States of America
| | - Krystal Thomas-White
- Loyola University Chicago, Stritch School of Medicine, Department of Microbiology and Immunology, Chicago, Illinois, United States of America
| | - Megan Schober
- Nationwide Children’s Hospital, Division of Urology, Columbus, Ohio, United States of America
| | - Birong Li
- The Research Institute at Nationwide Children’s Hospital, Center for Clinical and Translational Research, Columbus, Ohio, United States of America
| | - Brian Becknell
- The Research Institute at Nationwide Children’s Hospital, Center for Clinical and Translational Research, Columbus, Ohio, United States of America
- Nationwide Children’s Hospital, Division of Nephrology, Columbus, Ohio, United States of America
| | - David S. Hains
- Lebonheur Children’s Hospital, Division of Nephrology, Memphis, Tennessee, United States of America
| | - Alan J. Wolfe
- Loyola University Chicago, Stritch School of Medicine, Department of Microbiology and Immunology, Chicago, Illinois, United States of America
| | - Andrew L. Schwaderer
- Loyola University Chicago, Stritch School of Medicine, Department of Microbiology and Immunology, Chicago, Illinois, United States of America
- Nationwide Children’s Hospital, Division of Nephrology, Columbus, Ohio, United States of America
- * E-mail:
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Thomas-White KJ, Hilt EE, Fok C, Pearce MM, Mueller ER, Kliethermes S, Jacobs K, Zilliox MJ, Brincat C, Price TK, Kuffel G, Schreckenberger P, Gai X, Brubaker L, Wolfe AJ. Incontinence medication response relates to the female urinary microbiota. Int Urogynecol J 2015; 27:723-33. [PMID: 26423260 DOI: 10.1007/s00192-015-2847-x] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/09/2015] [Indexed: 01/26/2023]
Abstract
INTRODUCTION AND HYPOTHESIS Many adult women have resident urinary bacteria (urinary microbiome/microbiota). In adult women affected by urinary urgency incontinence (UUI), the etiologic and/or therapeutic role of the urinary microbiome/microbiota remains unknown. We hypothesized that microbiome/microbiota characteristics would relate to clinically relevant treatment response to UUI medication per os. METHODS Adult women initiating medication treatment orally for UUI and a comparator group of unaffected women were recruited in a tertiary care health-care system. All participants provided baseline clinical data and urine samples. Women with UUI were given 5 mg solifenacin, with potential dose escalation to 10 mg for inadequate UUI symptom control at 4 weeks. Additional data and urine samples were collected from women with UUI at 4 and 12 weeks. The samples were assessed using 16S ribosomal RNA (rRNA) gene sequencing and enhanced quantitative urine culturing. The primary outcome was treatment response as measured by the validated Patient Global Symptom Control (PGSC) questionnaire. Clinically relevant UUI symptom control was defined as a 4 or 5 score on the PGSC. RESULTS Diversity and composition of the urinary microbiome/microbiota of women with and without UUI differed at baseline. Women with UUI had more bacteria and a more diverse microbiome/microbiota. The clinical response to solifenacin in UUI participants was related to baseline microbiome/microbiota, with responders more likely to have fewer bacteria and a less diverse community at baseline. Nonresponders had a more diverse community that often included bacteria not typically found in responders. CONCLUSIONS Knowledge of an individual's urinary microbiome/microbiota may help refine UUI treatment. Complementary tools, DNA sequencing, and expanded urine culture provide information about bacteria that appear to be related to UUI incontinence status and treatment response in this population of adult women.
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Affiliation(s)
- Krystal J Thomas-White
- Departments of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Evann E Hilt
- Departments of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Cynthia Fok
- Department of Urology, University of Minnesota, Minneapolis, MN, USA
| | - Meghan M Pearce
- Departments of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Elizabeth R Mueller
- Departments of Obstetrics & Gynecology and Urology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.,Departments of Obstetrics and Gynecology and Urology, Division of Female Pelvic Medicine and Reconstructive Surgery, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Stephanie Kliethermes
- Departments of Medicine and Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Kristin Jacobs
- Department of Obstetrics & Gynecology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Michael J Zilliox
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Cynthia Brincat
- Departments of Obstetrics & Gynecology and Urology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.,Departments of Obstetrics and Gynecology and Urology, Division of Female Pelvic Medicine and Reconstructive Surgery, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Travis K Price
- Departments of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Gina Kuffel
- Center for Biomedical Informatics, Loyola Genomics Facility, Loyola University Chicago, Maywood, IL, USA
| | - Paul Schreckenberger
- Department of Pathology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Xiaowu Gai
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Linda Brubaker
- Departments of Obstetrics & Gynecology and Urology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA. .,Departments of Obstetrics and Gynecology and Urology, Division of Female Pelvic Medicine and Reconstructive Surgery, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | - Alan J Wolfe
- Departments of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
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