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Senghore M, Read H, Oza P, Johnson S, Passarelli-Araujo H, Taylor BP, Ashley S, Grey A, Callendrello A, Lee R, Goddard MR, Lumley T, Hanage WP, Wiles S. Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data. Nat Commun 2023; 14:6397. [PMID: 37907520 PMCID: PMC10618251 DOI: 10.1038/s41467-023-42211-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
Identifying and interrupting transmission chains is important for controlling infectious diseases. One way to identify transmission pairs - two hosts in which infection was transmitted from one to the other - is using the variation of the pathogen within each single host (within-host variation). However, the role of such variation in transmission is understudied due to a lack of experimental and clinical datasets that capture pathogen diversity in both donor and recipient hosts. In this work, we assess the utility of deep-sequenced genomic surveillance (where genomic regions are sequenced hundreds to thousands of times) using a mouse transmission model involving controlled spread of the pathogenic bacterium Citrobacter rodentium from infected to naïve female animals. We observe that within-host single nucleotide variants (iSNVs) are maintained over multiple transmission steps and present a model for inferring the likelihood that a given pair of sequenced samples are linked by transmission. In this work we show that, beyond the presence and absence of within-host variants, differences arising in the relative abundance of iSNVs (allelic frequency) can infer transmission pairs more precisely. Our approach further highlights the critical role bottlenecks play in reserving the within-host diversity during transmission.
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Affiliation(s)
- Madikay Senghore
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA.
| | - Hannah Read
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Priyali Oza
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Sarah Johnson
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Hemanoel Passarelli-Araujo
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Minas Gerais, Brazil
| | - Bradford P Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Stephen Ashley
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Alex Grey
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Alanna Callendrello
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Robyn Lee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
- University of Toronto Dalla Lana School of Public Health, Toronto, ON, Canada
| | - Matthew R Goddard
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- School of Life and Environmental Sciences, University of Lincoln, Lincoln, UK
| | - Thomas Lumley
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand.
- Te Pūnaha Matatini, Centre of Research Excellence in Complex Systems, Auckland, New Zealand.
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Břinda K, Callendrello A, Ma KC, MacFadden DR, Charalampous T, Lee RS, Cowley L, Wadsworth CB, Grad YH, Kucherov G, O'Grady J, Baym M, Hanage WP. Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing. Nat Microbiol 2020; 5:455-464. [PMID: 32042129 PMCID: PMC7044115 DOI: 10.1038/s41564-019-0656-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/06/2019] [Indexed: 11/09/2022]
Abstract
Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empirical antibiotic therapy. However, traditional molecular epidemiology does not typically occur on a timescale that could affect patient treatment and outcomes. Here, we present a method called 'genomic neighbour typing' for inferring the phenotype of a bacterial sample by identifying its closest relatives in a database of genomes with metadata. We show that this technique can infer antibiotic susceptibility and resistance for both Streptococcus pneumoniae and Neisseria gonorrhoeae. We implemented this with rapid k-mer matching, which, when used on Oxford Nanopore MinION data, can run in real time. This resulted in the determination of resistance within 10 min (91% sensitivity and 100% specificity for S. pneumoniae and 81% sensitivity and 100% specificity for N. gonorrhoeae from isolates with a representative database) of starting sequencing, and within 4 h of sample collection (75% sensitivity and 100% specificity for S. pneumoniae) for clinical metagenomic sputum samples. This flexible approach has wide application for pathogen surveillance and may be used to greatly accelerate appropriate empirical antibiotic treatment.
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Affiliation(s)
- Karel Břinda
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Alanna Callendrello
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Kevin C Ma
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Derek R MacFadden
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Themoula Charalampous
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robyn S Lee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Lauren Cowley
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Crista B Wadsworth
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Gregory Kucherov
- CNRS/LIGM Université Paris-Est, Marne-la-Vallée, France
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Justin O'Grady
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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Lee RS, Millar EV, Callendrello A, English CE, Krasniewski AE, Bennett JW, Hanage WP. 561. Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in Two Cohorts of High-Risk Military Trainees. Open Forum Infect Dis 2019. [PMCID: PMC6811119 DOI: 10.1093/ofid/ofz360.630] [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] [Indexed: 11/25/2022] Open
Abstract
Background Methicillin-resistant Staphylococcus aureus (MRSA) skin and soft-tissue infections (SSTIs) are common among military recruits. Identifying which strains are responsible for SSTI and understanding the underlying transmission dynamics is critical to developing appropriate interventions for this high-risk population. Methods A cohort study of US Army Infantry trainees at Fort Benning, GA (June and September 2015). Participants from two training Companies were screened for colonization on multiple anatomic sites throughout the 14-week cycle as well as the time of clinical infection. MRSA+ samples were sequenced with Illumina HiSeq. Multi-locus sequence type (MLST) and virulence genes were identified in silico. Single nucleotide polymorphism (SNP) distances between soldiers’ bacteria were compared with assessing for potential transmission. Results Of 383 soldiers enrolled, 84 (22%) were colonized with MRSA during the study. Forty-two of 84 had a single positive colonization sample, of which 76% were from anatomical sites other than the nares (36% oropharyngeal, 26% perianal, 14% inguinal). Twelve trainees had MRSA SSTI during training (50% had colonization detected prior to or at infection). All were PFGE-type US300 (ST8) and were lukS/lukF-positive. SNP-based phylogenetic analyses and epidemiologic data indicate that most MRSA positives at baseline were due to unique importations from various community origins, suggesting that the ongoing MRSA epidemic is not due to a single endemic strain circulating on base. Following importation, extensive transmission then occurred, with multiple STs implicated. Transmission appeared restricted to within Companies, and predominantly within platoons. Conclusion Frequent colonization at baseline suggests a need for extensive MRSA screening and decolonization upon arrival to base, followed by ongoing infection control measures throughout training to prevent recolonization/infection. As multiple anatomical sites appear to play a role in transmission of MRSA, this may have important implications for screening protocols and control both in community and hospital-based settings. ![]()
Disclosures All authors: No reported disclosures.
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Affiliation(s)
- Robyn S Lee
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Eugene V Millar
- Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | | | - Caroline E English
- Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | | | - Jason W Bennett
- Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - William P Hanage
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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Chang Q, Abuelaish I, Biber A, Jaber H, Callendrello A, Andam CP, Regev-Yochay G, Hanage WP, On Behalf Of The Picr Study Group. Genomic epidemiology of meticillin-resistant Staphylococcus aureus ST22 widespread in communities of the Gaza Strip, 2009. ACTA ACUST UNITED AC 2019; 23. [PMID: 30153881 PMCID: PMC6113745 DOI: 10.2807/1560-7917.es.2018.23.34.1700592] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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] [Indexed: 12/13/2022]
Abstract
Remarkably high carriage prevalence of a community-associated meticillin-resistant Staphylococcus aureus (MRSA) strain of sequence type (ST) 22 in the Gaza strip was reported in 2012. This strain is linked to the pandemic hospital-associated EMRSA-15. The origin and evolutionary history of ST22 in Gaza communities and the genomic elements contributing to its widespread predominance are unknown. Methods: We generated high-quality draft genomes of 61 ST22 isolates from Gaza communities and, along with 175 ST22 genomes from global sources, reconstructed the ST22 phylogeny and examined genotypes unique to the Gaza isolates. Results: The Gaza isolates do not exhibit a close relationship with hospital-associated ST22 isolates, but rather with a basal population from which EMRSA-15 emerged. There were two separate resistance acquisitions by the same MSSA lineage, followed by diversification of other genetic determinants. Nearly all isolates in the two distinct clades, one characterised by staphylococcal cassette chromosome mec (SCCmec) IVa and the other by SCCmec V and MSSA isolates, contain the toxic shock syndrome toxin-1 gene. Discussion: The genomic diversity of Gaza ST22 isolates is not consistent with recent emergence in the region. The results indicate that two divergent Gaza clones evolved separately from susceptible isolates. Researchers should not assume that isolates identified as ST22 in the community are examples of EMRSA-15 that have escaped their healthcare roots. Future surveillance of MRSA is essential to the understanding of ST22 evolutionary dynamics and to aid efforts to slow the further spread of this lineage.
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Affiliation(s)
- Qiuzhi Chang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Izzeldin Abuelaish
- Global Health Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Asaf Biber
- Infectious Disease Unit, Sheba Medical Center, affiliated to the Sackler School of Medicine, Tel Aviv University, Ramat Gan, Israel
| | - Hanaa Jaber
- Infectious Disease Unit, Sheba Medical Center, affiliated to the Sackler School of Medicine, Tel Aviv University, Ramat Gan, Israel
| | - Alanna Callendrello
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Cheryl P Andam
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Gili Regev-Yochay
- These authors contributed equally.,Infectious Disease Epidemiology Section, the Gertner Institute for Epidemiology and Health Policy Research, Ramat Gan, Israel.,Infectious Disease Unit, Sheba Medical Center, affiliated to the Sackler School of Medicine, Tel Aviv University, Ramat Gan, Israel
| | - William P Hanage
- These authors contributed equally.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, United States
| | - On Behalf Of The Picr Study Group
- These authors contributed equally.,Infectious Disease Epidemiology Section, the Gertner Institute for Epidemiology and Health Policy Research, Ramat Gan, Israel.,Infectious Disease Unit, Sheba Medical Center, affiliated to the Sackler School of Medicine, Tel Aviv University, Ramat Gan, Israel.,Global Health Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, United States
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Mitchell PK, Azarian T, Croucher NJ, Callendrello A, Thompson CM, Pelton SI, Lipsitch M, Hanage WP. Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13. Microb Genom 2019; 5. [PMID: 30777813 PMCID: PMC6421351 DOI: 10.1099/mgen.0.000252] [Citation(s) in RCA: 10] [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] [Indexed: 11/19/2022] Open
Abstract
The 13-valent pneumococcal conjugate vaccine (PCV-13) was introduced in the United States in 2010. Using a large paediatric carriage sample collected from shortly after the introduction of PCV-7 to several years after the introduction of PCV-13, we investigate alterations in the composition of the pneumococcal population following the introduction of PCV-13, evaluating the extent to which the post-vaccination non-vaccine type (NVT) population mirrors that from prior to vaccine introduction and the effect of PCV-13 on vaccine type lineages. Draft genome assemblies from 736 newly sequenced and 616 previously published pneumococcal carriage isolates from children in Massachusetts between 2001 and 2014 were analysed. Isolates were classified into one of 22 sequence clusters (SCs) on the basis of their core genome sequence. We calculated the SC diversity for each sampling period as the probability that any two randomly drawn isolates from that period belong to different SCs. The sampling period immediately after the introduction of PCV-13 (2011) was found to have higher diversity than preceding (2007) or subsequent (2014) sampling periods {Simpson’s D 2007: 0.915 [95 % confidence interval (CI) 0.901, 0.929]; 2011: 0.935 [0.927, 0.942]; 2014 : 0.912 [0.901, 0.923]}. Amongst NVT isolates, we found the distribution of SCs in 2011 to be significantly different from that in 2007 or 2014 (Fisher’s exact test P=0.018, 0.0078), but did not find a difference comparing 2007 to 2014 (Fisher’s exact test P=0.24), indicating greater similarity between samples separated by a longer time period than between samples from closer time periods. We also found changes in the accessory gene content of the NVT population between 2007 and 2011 to have been reduced by 2014. Amongst the new serotypes targeted by PCV-13, four were present in our sample. The proportion of our sample composed of PCV-13-only vaccine serotypes 19A, 6C and 7F decreased between 2007 and 2014, but no such reduction was seen for serotype 3. We did, however, observe differences in the genetic composition of the pre- and post-PCV-13 serotype 3 population. Our isolates were collected during discrete sampling periods from a small geographical area, which may limit the generalizability of our findings. Pneumococcal diversity increased immediately following the introduction of PCV-13, but subsequently returned to pre-vaccination levels. This is reflected in the distribution of NVT lineages, and, to a lesser extent, their accessory gene frequencies. As such, there may be a period during which the population is particularly disrupted by vaccination before returning to a more stable distribution. The persistence and shifting genetic composition of serotype 3 is a concern and warrants further investigation.
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Affiliation(s)
- Patrick K Mitchell
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Taj Azarian
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Nicholas J Croucher
- 2MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Alanna Callendrello
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Claudette M Thompson
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Stephen I Pelton
- 3Division of Pediatric Infectious Diseases, Maxwell Finland Laboratory for Infectious Diseases, Boston Medical Center, Boston, MA, USA
| | - Marc Lipsitch
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - William P Hanage
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
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Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WP. Diversification of bacterial genome content through distinct mechanisms over different timescales. Nat Commun 2014; 5:5471. [PMID: 25407023 PMCID: PMC4263131 DOI: 10.1038/ncomms6471] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [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: 07/31/2014] [Accepted: 10/03/2014] [Indexed: 12/16/2022] Open
Abstract
Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled genomes, we show that Streptococcus pneumoniae lineages are typically characterized by combinations of infrequently transferred stable genomic islands: those moving primarily through transformation, along with integrative and conjugative elements and phage-related chromosomal islands. The only lineage containing extensive unique sequence corresponds to a set of atypical unencapsulated isolates that may represent a distinct species. However, prophage content is highly variable even within lineages, suggesting frequent horizontal transmission that would necessitate rapidly diversifying anti-phage mechanisms to prevent these viruses sweeping through populations. Correspondingly, two loci encoding Type I restriction-modification systems able to change their specificity over short timescales through intragenomic recombination are ubiquitous across the collection. Hence short-term pneumococcal variation is characterized by movement of phage and intragenomic rearrangements, with the slower transfer of stable loci distinguishing lineages. Populations of the pathogenic bacterium Streptococcus pneumoniae consist of distinct co-circulating lineages. Here, the authors show lineages are characterized by particular combinations of stable genomic islands, whereas prophage and restriction-modification systems vary over short timescales.
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Affiliation(s)
- Nicholas J Croucher
- 1] Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA [2] Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College, London W2 1PG, UK
| | - Paul G Coupland
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Abbie E Stevenson
- Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA
| | - Alanna Callendrello
- Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA
| | - Stephen D Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - William P Hanage
- Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA
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Stresser DM, Ho T, Callendrello A, Clark RJ, Santone E, Fox LG, Zhang G. HUMAN HEPATOCYTE INDUCTION STUDIES TO EVALUATE POTENTIAL OF CYP3A4 INDUCTION IN VIVO: TWENTY COMPOUNDS WITH THREE DONORS. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.892.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Thuy Ho
- Corning Life SciencesWoburnMA
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