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Werneburg GT, Hsieh MH. Clinical Microbiome Testing for Urology. Urol Clin North Am 2024; 51:493-504. [PMID: 39349017 DOI: 10.1016/j.ucl.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/02/2024]
Abstract
The urine culture is imperfect, and a series of alternative approaches are in development to assist in diagnosis, treatment, and prevention of urinary tract infection (UTI). Culture-independent approaches typically do not distinguish between viable and nonviable bacteria, and are generally not included in current clinical guidance. Next-generation sequencing may play an important future role in precise targeting of antibiotic treatment of asymptomatic bacteriuria prior to endourologic surgery or in pregnancy. Future studies are needed to determine whether microbiota modulation could prevent UTI. Possible modulation mechanisms may include fecal microbiota transplant, application of topical vaginal estrogen or probiotics, and bacteriophage therapy.
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Affiliation(s)
- Glenn T Werneburg
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Michael H Hsieh
- Division of Urology, Children's National Hospital, 111 Michigan Avenue Northwest, Washington, DC 20010, USA.
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Negi M, Kaushik N, Lamichhane P, Jaiswal A, Borkar SB, Patel P, Singh P, Choi EH, Kaushik NK. Biocompatible plasma-treated liquids: A sustainable approach for decontaminating gastrointestinal-infection causing pathogens. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134562. [PMID: 38743977 DOI: 10.1016/j.jhazmat.2024.134562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Nosocomial infections are a serious threat and difficult to cure due to rising antibiotic resistance in pathogens and biofilms. Direct exposure to cold atmospheric plasma (CAP) has been widely employed in numerous biological research endeavors. Nonetheless, plasma-treated liquids (PTLs) formulated with physiological solutions may offer additional benefits such as enhanced portability, and biocompatibility. Additionally, CAP-infused long-lived reactive oxygen and nitrogen species (RONS) such as nitrite (NO2-), nitrate (NO3-), and hydrogen peroxide (H2O2) can synergistically induce their antibacterial activity. Herein, we investigated those argon-plasma jet-treated liquids, including Ringer's lactate (RL), phosphate-buffered saline (PBS), and physiological saline, have significant antibacterial activity against nosocomial/gastrointestinal-causing pathogens, which might be due to ROS-mediated lipid peroxidation. Combining the conventional culture-based method with propidium iodide monoazide quantitative PCR (PMAxx™-qPCR) indicated that PTLs induce a minimal viable but non-culturable (VBNC) state and moderately affect culturable counts. Specifically, the PTL exposure resulted in pathogenicity dysfunction via controlling T3SS-related effector genes of S. enterica. Overall, this study provides insights into the effectiveness of PTLs for inducing ROS-mediated damage, controlling the virulence of diarrheagenic bacteria, and modulating homeostatic genes.
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Affiliation(s)
- Manorma Negi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong 18323, South Korea.
| | - Prajwal Lamichhane
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea
| | - Apurva Jaiswal
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea
| | - Shweta B Borkar
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea
| | - Paritosh Patel
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea.
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea.
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Lousada MB, Edelkamp J, Lachnit T, Fehrholz M, Pastar I, Jimenez F, Erdmann H, Bosch TCG, Paus R. Spatial Distribution and Functional Impact of Human Scalp Hair Follicle Microbiota. J Invest Dermatol 2024; 144:1353-1367.e15. [PMID: 38070726 DOI: 10.1016/j.jid.2023.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/17/2023] [Accepted: 11/01/2023] [Indexed: 02/26/2024]
Abstract
Human hair follicles (HFs) constitute a unique microbiota habitat that differs substantially from the skin surface. Traditional HF sampling methods fail to eliminate skin microbiota contaminants or assess the HF microbiota incompletely, and microbiota functions in human HF physiology remain ill explored. Therefore, we used laser-capture microdissection, metagenomic shotgun sequencing, and FISH to characterize the human scalp HF microbiota in defined anatomical compartments. This revealed significant compartment-, tissue lineage-, and donor age-dependent variations in microbiota composition. Greatest abundance variations between HF compartments were observed for viruses, archaea, Staphylococcus epidermidis, Cutibacterium acnes, and Malassezia restricta, with the latter 2 being the most abundant viable HF colonizers (as tested by propidium monoazide assay) and, surprisingly, most abundant in the HF mesenchyme. Transfection of organ-cultured human scalp HFs with S. epidermidis-specific lytic bacteriophages ex vivo downregulated transcription of genes known to regulate HF growth and development, metabolism, and melanogenesis, suggesting that selected microbial products may modulate HF functions. Indeed, HF treatment with butyrate, a metabolite of S. epidermidis and other HF microbiota, delayed catagen and promoted autophagy, mitochondrial activity, and gp100 and dermcidin expression ex vivo. Thus, human HF microbiota show spatial variations in abundance and modulate the physiology of their host, which invites therapeutic targeting.
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Affiliation(s)
- Marta B Lousada
- Monasterium Laboratory, Münster, Germany; Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | | | - Tim Lachnit
- Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | | | - Irena Pastar
- Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Francisco Jimenez
- Mediteknia Skin & Hair Lab, Las Palmas de Gran Canaria, Spain; Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | | | - Thomas C G Bosch
- Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | - Ralf Paus
- Monasterium Laboratory, Münster, Germany; Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA; CUTANEON, Hamburg, Germany.
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Dinu LD, Al-Zaidi QJ, Matache AG, Matei F. Improving the Efficiency of Viability-qPCR with Lactic Acid Enhancer for the Selective Detection of Live Pathogens in Foods. Foods 2024; 13:1021. [PMID: 38611327 PMCID: PMC11012224 DOI: 10.3390/foods13071021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Pathogenic Escherichia coli are the most prevalent foodborne bacteria, and their accurate detection in food samples is critical for ensuring food safety. Therefore, a quick technique named viability-qPCR (v-qPCR), which is based on the ability of a selective dye, such as propidium monoazide (PMA), to differentiate between alive and dead cells, has been developed. Despite diverse, successful applications, v-qPCR is impaired by some practical limitations, including the ability of PMA to penetrate the outer membrane of dead Gram-negative bacteria. The objective of this study is to evaluate the ability of lactic acid (LA) to improve PMA penetration and, thus, the efficiency of v-qPCR in detecting the live fraction of pathogens. The pre-treatment of E. coli ATCC 8739 cells with 10 mM LA greatly increased PMA penetration into dead cells compared to conventional PMA-qPCR assay, avoiding false positive results. The limit of detection when using LA-PMA qPCR is 1% viable cells in a mixture of dead and alive cells. The optimized LA-PMA qPCR method was reliably able to detect log 2 CFU/mL culturable E. coli in milk spiked with viable and non-viable bacteria. Lactic acid is cheap, has low toxicity, and can be used to improve the efficiency of the v-qPCR assay, which is economically interesting for larger-scale pathogen detection applications intended for food matrices.
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Affiliation(s)
- Laura-Dorina Dinu
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania; (Q.J.A.-Z.); (A.G.M.); (F.M.)
| | - Quthama Jasim Al-Zaidi
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania; (Q.J.A.-Z.); (A.G.M.); (F.M.)
| | - Adelina Georgiana Matache
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania; (Q.J.A.-Z.); (A.G.M.); (F.M.)
| | - Florentina Matei
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania; (Q.J.A.-Z.); (A.G.M.); (F.M.)
- Faculty of Food Industry and Tourism, Transilvania University of Brasov, 500015 Brasov, Romania
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Thilakarathna SH, Chui L. A Pilot Study to Detect Viable Salmonella spp. in Diarrheal Stool Using Viability Real-Time PCR as a Culture-Independent Diagnostic Tool in a Clinical Setting. Int J Mol Sci 2023; 24:9979. [PMID: 37373127 DOI: 10.3390/ijms24129979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Frontline laboratories are adopting culture-independent diagnostic testing (CIDT) such as nucleic acid amplification tests (NAATs) due to numerous advantages over culture-based testing methods. Paradoxically, the viability of pathogens, a crucial factor determining active infections, cannot be confirmed with current NAATs alone. A recent development of viability PCR (vPCR) was introduced to mitigate this limitation associated with real-time PCR (qPCR) by using a DNA-intercalating dye to remove residual and dead cell DNA. This study assessed the applicability of the vPCR assay on diarrheal stools. Eighty-five diarrheal stools confirmed for Salmonellosis were tested via qPCR and vPCR using in-house primers and probe targeting the invA gene. vPCR-negative stools (Ct cut off > 31) were enriched in mannitol selenite broth (MSB) to verify low bacterial loads. vPCR assay showed ~89% sensitivity (qPCR- and vPCR-positive stools: 76/85). vPCR-negative stools (9/85; qPCR-positive: 5; qPCR-negative: 4) were qPCR- and culture-positive post-MSB-enrichment and confirmed the presence of low viable bacterial loads. Random sampling error, low bacterial loads, and receiving stools in batches could contribute to false negatives. This is a pilot study and further investigations are warranted to explore vPCR to assess pathogen viability in a clinical setting, especially when culture-based testing is unavailable.
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Affiliation(s)
- Surangi H Thilakarathna
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Alberta Precision Laboratories, Public Health Laboratory (ProvLab), Edmonton, AB T6G 2J2, Canada
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Tjandra KC, Ram-Mohan N, Abe R, Wang TH, Yang S. Rapid Molecular Phenotypic Antimicrobial Susceptibility Test for Neisseria gonorrhoeae Based on Propidium Monoazide Viability PCR. ACS Infect Dis 2023; 9:1160-1167. [PMID: 37115656 DOI: 10.1021/acsinfecdis.3c00096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Neisseria gonorrhoeae (NG) is an urgent threat to antimicrobial resistance (AMR) worldwide. NG has acquired rapid resistance to all previously recommended treatments, leaving ceftriaxone monotherapy as the first and last line of therapy for uncomplicated NG. The ability to rapidly determine susceptibility, which is currently nonexistent for NG, has been proposed as a strategy to preserve ceftriaxone by using alternative treatments. Herein, we used a DNA-intercalating dye in combination with NG-specific primers/probes to generate qPCR cycle threshold (Ct) values at different concentrations of 2 NG-relevant antimicrobials. Our proof-of-concept dual-antimicrobial logistic regression model based on the differential Ct measurements achieved an AUC of 0.93 with a categorical agreement for the susceptibility of 84.6%. When surveying the performance against each antimicrobial separately, the model predicted 90 and 75% susceptible and resistant strains, respectively, to ceftriaxone and 66.7 and 83.3% susceptible and resistant strains, respectively, to ciprofloxacin. We further validated the model against the individual replicates and determined the accuracy of the model in classifying susceptibility agnostic of the inoculum size. We demonstrated a novel PCR-based approach to determine phenotypic ciprofloxacin and ceftriaxone susceptibility information for NG with reasonable accuracy within 30 min, a significant improvement compared to the conventional method which could take multiple days.
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Affiliation(s)
- Kristel C Tjandra
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California 94305, United States
| | - Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California 94305, United States
| | - Ryuichiro Abe
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California 94305, United States
| | - Tza-Huei Wang
- Departments of Mechanical Engineering and Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California 94305, United States
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Trinh KTL, Lee NY. Recent Methods for the Viability Assessment of Bacterial Pathogens: Advances, Challenges, and Future Perspectives. Pathogens 2022; 11:1057. [PMID: 36145489 PMCID: PMC9500772 DOI: 10.3390/pathogens11091057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022] Open
Abstract
Viability assessment is a critical step in evaluating bacterial pathogens to determine infectious risks to public health. Based on three accepted viable criteria (culturability, metabolic activity, and membrane integrity), current viability assessments are categorized into three main strategies. The first strategy relies on the culturability of bacteria. The major limitation of this strategy is that it cannot detect viable but nonculturable (VBNC) bacteria. As the second strategy, based on the metabolic activity of bacteria, VBNC bacteria can be detected. However, VBNC bacteria sometimes can enter a dormant state that allows them to silence reproduction and metabolism; therefore, they cannot be detected based on culturability and metabolic activity. In order to overcome this drawback, viability assessments based on membrane integrity (third strategy) have been developed. However, these techniques generally require multiple steps, bulky machines, and laboratory technicians to conduct the tests, making them less attractive and popular applications. With significant advances in microfluidic technology, these limitations of current technologies for viability assessment can be improved. This review summarized and discussed the advances, challenges, and future perspectives of current methods for the viability assessment of bacterial pathogens.
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Affiliation(s)
- Kieu The Loan Trinh
- Department of Industrial Environmental Engineering, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Korea
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