Browsing by Author "Zhang, Liyang"

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    Characterizing the Host-Pathogen Interactions and Inter-Strain Competition in Pathogenic Bacteria
    (2023-06-01) Zhang, Liyang; Kirienko, Natasha V; Warmflash, Aryeh; Gao, Yang; van der Hoeven, Ransome V; Igoshin, Oleg A
    Pathogens are of significant importance in medicine and public health, as they are responsible for a wide range of infectious diseases that can have serious consequences for human and animal populations. Whether infection gets established, depends on multiple factors, including environment, the host, and interactions with other bacteria. Understanding these factors and their impact is a prerequisite for developing therapies for resisting or disarming pathogenic bacteria. Adhesins are proteins present on the microbial cell surface that mediate the interactions with or attachment to the host or substance. As one type of virulence factors, adhesin proteins play a crucial role in the ability of the fungal pathogen Candida albicans to undergo cellular morphogenesis, develop robust biofilms, colonize, and cause infection in a host. By performing a comprehensive, high-throughput screen of a library of adhesin mutants in the model nematode Caenorhabditis elegans as a simplified host system, I identified mutants critical for virulence of C. albicans. Colonization is generally considered a prerequisite for infection, but this event is context-dependent, as evidenced by the differing ability of the human pathogen Pseudomonas aeruginosa to efficiently colonize C. elegans on agar but not in liquid pathogenesis. I showed that the transition to a liquid environment reduces food uptake, decreases specific adhesins, slightly upregulates host immunity, and induces a pathogen-driven dormancy of C. elegans, which restricts pathogenic colonization. My study also found that pathogenic colonization was still required for the virulence of Enterococcus faecalis even in the liquid. I conclude that poor colonization in liquid is likely due to a combination of environmental factors and host-pathogen interactions. These results provide new insights into mechanisms for colonization in different models, enabling pathogenesis models to be fine-tuned to more accurately represent the conditions seen in human infections so that new tools for curbing bacterial and fungal infections can be developed. Competition shapes the life spectrum in nature, resulting in organisms with better fitness taking a position of dominance and prevalence. The high-risk clone of P. aeruginosa ST111 predominates in hematopoietic cell transplant and hematologic malignancy (HCT/HM) bloodstream infection (BSI) patients via a fitness benefit due to the loss of functional OprD, a porin responsible for the import of carbapenems. Further study revealed that not only ST111 but also several international high-risk sequence types produce the bactericidal R5 pyocin that targets P. aeruginosa with mutations on WaaL, an O-antigen ligase of lipopolysaccharide. These findings suggest a novel approach for evaluating risks associated with emerging prevalent P. aeruginosa strains and may inform the development of strategies to mitigate the impact of ST111 and other high-risk clones on public health. In conclusion, my dissertation research provides valuable insights into the virulence of pathogens and their interactions with the host. Having a thorough understanding of the features of each infection model can power researchers to do pathogenesis research and hereby develop effective treatments or interventions for infectious diseases. The identification of R5 pyocin producers and their fitness benefits in causing infection highlights the need for ongoing monitoring and surveillance to inform public health strategies to mitigate the impact of emerging pathogens on human health.
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    Comprehensive genetic analysis of adhesin proteins and their role in virulence of Candida albicans
    (Oxford University Press, 2021) Rosiana, Sierra; Zhang, Liyang; Kim, Grace H.; Revtovich, Alexey V.; Uthayakumar, Deeva; Sukumaran, Arjun; Geddes-McAlister, Jennifer; Kirienko, Natalia V.; Shapiro, Rebecca S.
    Candida albicans is a microbial fungus that exists as a commensal member of the human microbiome and an opportunistic pathogen. Cell surface-associated adhesin proteins play a crucial role in C. albicans’ ability to undergo cellular morphogenesis, develop robust biofilms, colonize, and cause infection in a host. However, a comprehensive analysis of the role and relationships between these adhesins has not been explored. We previously established a CRISPR-based platform for efficient generation of single- and double-gene deletions in C. albicans, which was used to construct a library of 144 mutants, comprising 12 unique adhesin genes deleted singly, and every possible combination of double deletions. Here, we exploit this adhesin mutant library to explore the role of adhesin proteins in C. albicans virulence. We perform a comprehensive, high-throughput screen of this library, using Caenorhabditis elegans as a simplified model host system, which identified mutants critical for virulence and significant genetic interactions. We perform follow-up analysis to assess the ability of high- and low-virulence strains to undergo cellular morphogenesis and form biofilms in vitro, as well as to colonize the C. elegans host. We further perform genetic interaction analysis to identify novel significant negative genetic interactions between adhesin mutants, whereby combinatorial perturbation of these genes significantly impairs virulence, more than expected based on virulence of the single mutant constituent strains. Together, this study yields important new insight into the role of adhesins, singly and in combinations, in mediating diverse facets of virulence of this critical fungal pathogen.
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    High-Throughput Approaches for the Identification of Pseudomonas aeruginosa Antivirulents
    (American Society for Microbiology, 2021) Kang, Donghoon; Zhang, Liyang; Kirienko, Natalia V.
    Antimicrobial resistance is a serious medical threat, particularly given the decreasing rate of discovery of new treatments. Although attempts to find new treatments continue, it has become clear that merely discovering new antimicrobials, even if they are new classes, will be insufficient. It is essential that new strategies be aggressively pursued. Toward that end, the search for treatments that can mitigate bacterial virulence and tilt the balance of host-pathogen interactions in favor of the host has become increasingly popular. In this review, we will discuss recent progress in this field, with a special focus on synthetic small molecule antivirulents that have been identified from high-throughput screens and on treatments that are effective against the opportunistic human pathogen Pseudomonas aeruginosa.
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    Long-Term Dominance of Carbapenem-Non-Susceptible Pseudomonas aeruginosa ST111 in Hematologic Malignancy Patients and Hematopoietic Cell Transplant Recipients
    (Frontiers Media S.A., 2022) Zhang, Liyang; Tan, Filemon C.; Strasfeld, Lynne; Hakki, Morgan; Kirienko, Natalia V.
    An epidemiological study uncovered that fluoroquinolone (FQ) neutropenic prophylaxis in hematopoietic cell transplant and hematologic malignancy (HCT/HM) patients was associated with breakthrough Pseudomonas aeruginosa bloodstream infections (BSIs) with isolates non-susceptible to both FQs and meropenem. The molecular epidemiology of the FQ/meropenem-non-susceptible P. aeruginosa isolates causing FQ-breakthrough BSIs in the HCT/HM patients remains unclear. Through whole genome sequencing on 57 P. aeruginosa isolates from 54 patients diagnosed with HM or receiving an HCT, we found that ST111 strains predominated, accounting for 22 (38.6%) of the isolates. 17 of 33 (51.5%) FQ-breakthrough BSIs were caused by ST111 strains, of which 15 (88.2%) were meropenem non-susceptible. ST111 strains, but not other oprD-deficient, meropenem-non-susceptible clinical strains, were found to have a colonization advantage over P. aeruginosa strain PA14 in C. elegans and to outcompete PA14 in in vitro co-culture assays. Together, we found that breakthrough P. aeruginosa BSIs during FQ prophylaxis in HCT/HM patients are dominated by clonally-related FQ/meropenem non-susceptible strains, predominantly ST111 type, and that the dominance of ST111 strains may be explained by a relative fitness advantage over other clinical strains. Additional work is necessary to better understand the factors driving the dominance and persistence of these ST111 strains.
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    Pathogen-induced dormancy in liquid limits gastrointestinal colonization of Caenorhabditis elegans
    (Taylor & Francis, 2023) Zhang, Liyang; Gade, Vyshnavi; Kirienko, Natalia V.
    Colonization is generally considered a prerequisite for infection, but this event is context-dependent, as evidenced by the differing ability of the human pathogen Pseudomonas aeruginosa to efficiently colonize Caenorhabditis elegans on agar but not in liquid . In this study, we examined the impact of the environment, pathogen, host, and their interactions on host colonization. We found that the transition to a liquid environment reduces food uptake by about two-fold. Also expression of specific adhesins was significantly altered in liquid-based assays for P. aeruginosa, suggesting that it may be one factor driving diminished colonization. Unexpectedly, host immune pathways did not appear to play a significant role in decreased colonization in liquid. Although knocking down key immune pathways (e.g. daf-16 or zip-2), either alone or in combination, significantly reduced survival, the changes in colonization were very small. In spite of the limited bacterial accumulation in the liquid setting, pathogenic colonization was still required for the virulence of Enterococcus faecalis. In addition, we found that a pathogen-induced dormancy was displayed by C. elegans in liquid medium after pathogen exposure, resulting in cessation of pharyngeal pumping and a decrease in bacterial intake. We conclude that poor colonization in liquid is likely due to a combination of environmental factors and host-pathogen interactions. These results provide new insights into mechanisms for colonization in different models, enabling pathogenesis models to be fine-tuned to more accurately represent the conditions seen in human infections so that new tools for curbing bacterial and fungal infections can be developed.