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Hira J, Singh B, Halder T, Mahmutovic A, Ajayi C, Sekh AA, Hegstad K, Johannessen M, Lentz CS. Single-cell phenotypic profiling and backtracing exposes and predicts clinically relevant subpopulations in isogenic Staphylococcus aureus communities. Commun Biol 2024; 7:1228. [PMID: 39354092 PMCID: PMC11445386 DOI: 10.1038/s42003-024-06894-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 09/13/2024] [Indexed: 10/03/2024] Open
Abstract
Isogenic bacterial cell populations are phenotypically heterogenous and may include subpopulations of antibiotic tolerant or heteroresistant cells. The reversibility of these phenotypes and lack of biomarkers to differentiate functionally different, but morphologically identical cells is a challenge for research and clinical detection. To overcome this, we present ´Cellular Phenotypic Profiling and backTracing (CPPT)´, a fluorescence-activated cell sorting platform that uses fluorescent probes to visualize and quantify cellular traits and connects this phenotypic profile with a cell´s experimentally determined fate in single cell-derived growth and antibiotic susceptibility analysis. By applying CPPT on Staphylococcus aureus we phenotypically characterized dormant cells, exposed bimodal growth patterns in colony-derived cells and revealed different culturability of single cells on solid compared to liquid media. We demonstrate that a fluorescent vancomycin conjugate marks cellular subpopulations of vancomycin-intermediate S. aureus with increased likelihood to survive antibiotic exposure, showcasing the value of CPPT for discovery of clinically relevant biomarkers.
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Affiliation(s)
- Jonathan Hira
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Bhupender Singh
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Tirthankar Halder
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Anel Mahmutovic
- Early Biometrics & Statistical Innovation Data Science & AI AstraZeneca, Biopharmaceuticals RD AstraZeneca, Mölndal, Sweden
| | - Clement Ajayi
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | | | - Kristin Hegstad
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Mona Johannessen
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Christian S Lentz
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway.
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2
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Keller N, Boumasmoud M, Andreoni F, Tarnutzer A, von Matt M, Scheier TC, Epprecht J, Weller D, Gómez-Mejia A, Huemer M, von Reibnitz D, Fontein DBY, Marques-Maggio E, Schuepbach RA, Mairpady-Shambat S, Brugger SD, Zinkernagel AS. Investigating group A Streptococcus antibiotic tolerance in necrotizing fasciitis. mSphere 2024; 9:e0063424. [PMID: 39189777 PMCID: PMC11423592 DOI: 10.1128/msphere.00634-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 07/31/2024] [Indexed: 08/28/2024] Open
Abstract
Group A Streptococcus (GAS) necrotizing fasciitis (NF) is a difficult-to-treat bacterial infection associated with high morbidity and mortality despite extensive surgery and targeted antibiotic treatment. Difficult-to-treat infections are often characterized by the presence of bacteria surviving prolonged antibiotic exposure without displaying genetic resistance, referred to as persisters. In the present study, we investigated the presence of GAS persisters in tissue freshly debrided from patients as well as in an in vivo mouse model of NF and examined the phenomenon of antibiotic tolerance. Time-lapse imaging of GAS plated directly upon isolation from NF debrided tissue and an antibiotic challenge-based persisters assay were used to assess the presence of persisters. We show for the first time that GAS recovered directly from freshly debrided NF tissue is characterized by heterogeneous and overall delayed colony appearance time, suggesting the presence of persisters. Acidic pH or nutrient stress exposure, mimicking the NF-like environment in vitro, led to a similar phenotypic heterogeneity and resulted in enhanced survival upon antibiotic challenge, confirming the presence of GAS persisters. GAS persisters might contribute to NF treatment failure, despite extensive surgery and adequate antibiotic treatment.IMPORTANCEDifficult-to-treat and recurrent infections are a global problem burdening society and the health care system alike. Unraveling the mechanisms by which bacteria can survive antibiotic treatment without developing genetic resistance is of utmost importance to lay the foundation for new, effective therapeutic approaches. For the first time, we describe the phenomenon of antibiotic tolerance in group A Streptococcus (GAS) isolated from necrotizing fasciitis (NF) patients. Dormant, non-replicating cells (persisters) are tolerant to antibiotics and their occurrence in vivo is reported in an increasing number of bacterial species. Tailored treatment options, including the use of persisters-targeting drugs, need to be developed to specifically target dormant bacteria causing difficult-to-treat and recurrent infections.
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Affiliation(s)
- Nadia Keller
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mathilde Boumasmoud
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Federica Andreoni
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Andrea Tarnutzer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Manuela von Matt
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas C. Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jana Epprecht
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - David Weller
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alejandro Gómez-Mejia
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Markus Huemer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Donata von Reibnitz
- Department of Plastic Surgery and Hand Surgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Duveken B. Y. Fontein
- Department of Plastic Surgery and Hand Surgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ewerton Marques-Maggio
- Division of Clinical Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Reto A. Schuepbach
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Srikanth Mairpady-Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Silvio D. Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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3
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Niu H, Gu J, Zhang Y. Bacterial persisters: molecular mechanisms and therapeutic development. Signal Transduct Target Ther 2024; 9:174. [PMID: 39013893 PMCID: PMC11252167 DOI: 10.1038/s41392-024-01866-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 07/18/2024] Open
Abstract
Persisters refer to genetically drug susceptible quiescent (non-growing or slow growing) bacteria that survive in stress environments such as antibiotic exposure, acidic and starvation conditions. These cells can regrow after stress removal and remain susceptible to the same stress. Persisters are underlying the problems of treating chronic and persistent infections and relapse infections after treatment, drug resistance development, and biofilm infections, and pose significant challenges for effective treatments. Understanding the characteristics and the exact mechanisms of persister formation, especially the key molecules that affect the formation and survival of the persisters is critical to more effective treatment of chronic and persistent infections. Currently, genes related to persister formation and survival are being discovered and confirmed, but the mechanisms by which bacteria form persisters are very complex, and there are still many unanswered questions. This article comprehensively summarizes the historical background of bacterial persisters, details their complex characteristics and their relationship with antibiotic tolerant and resistant bacteria, systematically elucidates the interplay between various bacterial biological processes and the formation of persister cells, as well as consolidates the diverse anti-persister compounds and treatments. We hope to provide theoretical background for in-depth research on mechanisms of persisters and suggest new ideas for choosing strategies for more effective treatment of persistent infections.
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Affiliation(s)
- Hongxia Niu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Jiaying Gu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Ying Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250022, Shandong, China.
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4
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Ndiaye A, Fliss I, Filteau M. High-throughput characterization of the effect of sodium chloride and potassium chloride on 31 lactic acid bacteria and their co-cultures. Front Microbiol 2024; 15:1328416. [PMID: 38435689 PMCID: PMC10904479 DOI: 10.3389/fmicb.2024.1328416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/26/2024] [Indexed: 03/05/2024] Open
Abstract
Salt (NaCl) is associated with a risk of hypertension and the development of coronary heart disease, so its consumption should be limited. However, salt plays a key role in the quality and safety of food by controlling undesirable microorganisms. Since studies have focused primarily on the effect of salts on the overall counts of the lactic acid bacteria (LAB) group, we have not yet understood how salt stress individually affects the strains and the interactions between them. In this study, we characterized the effect of sodium chloride (NaCl) and potassium chloride (KCl) on the growth and acidification of 31 LAB strains. In addition, we evaluated the effect of salts on a total of 93 random pairwise strain combinations. Strains and co-cultures were tested at 3% NaCl, 5% NaCl, and 3% KCl on solid medium using an automated approach and image analysis. The results showed that the growth of LAB was significantly reduced by up to 68% at 5% NaCl (p < 0.0001). For the co-cultures, a reduction of up to 57% was observed at 5% NaCl (p < 0.0001). However, acidification was less affected by salt stress, whether for monocultures or co-cultures. Furthermore, KCl had a lesser impact on both growth and acidification compared to NaCl. Indeed, some strains showed a significant increase in growth at 3% KCl, such as Lactococcus lactis subsp. lactis 74310 (23%, p = 0.01). More importantly, co-cultures appeared to be more resilient and had more varied responses to salt stress than the monocultures, as several cases of suppression of the significant effect of salts on acidification and growth were detected. Our results highlight that while salts can modulate microbial interactions, these latter can also attenuate the effect of salts on LAB.
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Affiliation(s)
- Amadou Ndiaye
- Département des Sciences des Aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Ismail Fliss
- Département des Sciences des Aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
| | - Marie Filteau
- Département des Sciences des Aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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5
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Dengler Haunreiter V, Tarnutzer A, Bär J, von Matt M, Hertegonne S, Andreoni F, Vulin C, Künzi L, Menzi C, Kiefer P, Christen P, Vorholt JA, Zinkernagel AS. C-di-AMP levels modulate Staphylococcus aureus cell wall thickness, response to oxidative stress, and antibiotic resistance and tolerance. Microbiol Spectr 2023; 11:e0278823. [PMID: 37948390 PMCID: PMC10715141 DOI: 10.1128/spectrum.02788-23] [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] [Received: 07/07/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Antibiotic resistance and tolerance are substantial healthcare-related problems, hampering effective treatment of bacterial infections. Mutations in the phosphodiesterase GdpP, which degrades cyclic di-3', 5'-adenosine monophosphate (c-di-AMP), have recently been associated with resistance to beta-lactam antibiotics in clinical Staphylococcus aureus isolates. In this study, we show that high c-di-AMP levels decreased the cell size and increased the cell wall thickness in S. aureus mutant strains. As a consequence, an increase in resistance to cell wall targeting antibiotics, such as oxacillin and fosfomycin as well as in tolerance to ceftaroline, a cephalosporine used to treat methicillin-resistant S. aureus infections, was observed. These findings underline the importance of investigating the role of c-di-AMP in the development of tolerance and resistance to antibiotics in order to optimize treatment in the clinical setting.
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Affiliation(s)
- Vanina Dengler Haunreiter
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Andrea Tarnutzer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Julian Bär
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Manuela von Matt
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Federica Andreoni
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Clément Vulin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lisa Künzi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Carmen Menzi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Patrick Kiefer
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Philipp Christen
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Julia A. Vorholt
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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6
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Jones EW, Derrick J, Nisbet RM, Ludington WB, Sivak DA. First-passage-time statistics of growing microbial populations carry an imprint of initial conditions. Sci Rep 2023; 13:21340. [PMID: 38049502 PMCID: PMC10696051 DOI: 10.1038/s41598-023-48726-w] [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] [Received: 08/25/2023] [Accepted: 11/29/2023] [Indexed: 12/06/2023] Open
Abstract
In exponential population growth, variability in the timing of individual division events and environmental factors (including stochastic inoculation) compound to produce variable growth trajectories. In several stochastic models of exponential growth we show power-law relationships that relate variability in the time required to reach a threshold population size to growth rate and inoculum size. Population-growth experiments in E. coli and S. aureus with inoculum sizes ranging between 1 and 100 are consistent with these relationships. We quantify how noise accumulates over time, finding that it encodes-and can be used to deduce-information about the early growth rate of a population.
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Affiliation(s)
- Eric W Jones
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
| | - Joshua Derrick
- Department of Biological Sciences and Engineering, Carnegie Institution for Science, Baltimore, MD, 21218, USA
| | - Roger M Nisbet
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - William B Ludington
- Department of Biological Sciences and Engineering, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - David A Sivak
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
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7
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Arora P, Tewary S, Krishnamurthi S, Kumari N. An experimental setup and segmentation method for CFU counting on agar plate for the assessment of drinking water. J Microbiol Methods 2023; 214:106829. [PMID: 37797659 DOI: 10.1016/j.mimet.2023.106829] [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] [Received: 07/05/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
Quantification of bacterial colonies on an agar plate is a daily routine for a microbiologist to determine the number of viable microorganisms in the sample. In general, microbiologists perform a visual assessment of bacterial colonies which is time-consuming (takes 2 min per plate), tedious, and subjective. Some automatic counting algorithms are developed that save labour and time, but their results are affected by the non-illumination on an agar plate. To improve this, the present manuscript aims to develop an inexpensive and efficient device to acquire S.aureus images via an automatic counting method using image processing techniques under real laboratory conditions. The proposed method (P_ColonyCount) includes the region of interest extraction and color space transformation followed by filtering, thresholding, morphological operation, distance transform, and watershed technique for the quantification of isolated and overlapping colonies. The present work also shows a comparative study on grayscale, K, and green channels by applying different filter and thresholding techniques on 42 images. The results of all channels were compared with the score provided by the expert (manual count). Out of all the proposed method (P_ColonyCount), the K channel gives the best outcome in comparison with the other two channels (grayscale and green) in terms of precision, recall, and F-measure which are 0.99, 0.99, and 0.99 (2 h), 0.98, 0.99, and 0.98 (4 h), and 0.98, 0.98, 0.98 (6 h) respectively. The execution time of the manual and the proposed method (P_ColonyCount) for 42 images ranges from 19 to 113 s and 15 to 31 s respectively. Apart from this, a user-friendly graphical user interface is also developed for the convenient enumeration of colonies without any expert knowledge/training. The developed imaging device will be useful for researchers and teaching lab settings.
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Affiliation(s)
- Prachi Arora
- Thin Film Coating Facility/Materials Science and Sensor Applications, CSIR-Central Scientific Instruments Organisation (CSIR-CSIO), Sector 30-C, Chandigarh 160030, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suman Tewary
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Advanced Materials and Processes, CSIR-National Metallurgical Laboratory (CSIR-NML), Jamshedpur 831007, India
| | - Srinivasan Krishnamurthi
- MTCC-Gene bank, CSIR-Institute of Microbial Technology (CSIR-IMTECH), Sector 39-A, Chandigarh 160039, India
| | - Neelam Kumari
- Thin Film Coating Facility/Materials Science and Sensor Applications, CSIR-Central Scientific Instruments Organisation (CSIR-CSIO), Sector 30-C, Chandigarh 160030, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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8
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Balmages I, Liepins J, Zolins S, Bliznuks D, Broks R, Lihacova I, Lihachev A. Tools for classification of growing/non-growing bacterial colonies using laser speckle imaging. Front Microbiol 2023; 14:1279667. [PMID: 37928664 PMCID: PMC10623326 DOI: 10.3389/fmicb.2023.1279667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Prior research has indicated the feasibility of assessing growth-associated activity in bacterial colonies through the application of laser speckle imaging techniques. A subpixel correlation method was employed to identify variations in sequential laser speckle images, thereby facilitating the visualization of specific zones indicative of microbial growth within the colony. Such differentiation between active (growing) and inactive (non-growing) bacterial colonies holds considerable implications for medical applications, like bacterial response to certain drugs or antibiotics. The present study substantiates the capability of laser speckle imaging to categorize bacterial colonies as growing or non-growing, a parameter which nonvisible in colonies when observed under white light illumination.
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Affiliation(s)
- Ilya Balmages
- Faculty of Computer Science and Information Technology, Riga Technical University, Riga, Latvia
- Institute of Atomic Physics and Spectroscopy, University of Latvia, Riga, Latvia
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | | | - Dmitrijs Bliznuks
- Faculty of Computer Science and Information Technology, Riga Technical University, Riga, Latvia
| | - Renars Broks
- Faculty of Computer Science and Information Technology, Riga Technical University, Riga, Latvia
- Department of Biology and Microbiology, Riga Stradins University, Riga, Latvia
| | - Ilze Lihacova
- Institute of Atomic Physics and Spectroscopy, University of Latvia, Riga, Latvia
| | - Alexey Lihachev
- Institute of Atomic Physics and Spectroscopy, University of Latvia, Riga, Latvia
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9
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Räz AK, Andreoni F, Boumasmoud M, Bergada-Pijuan J, Schweizer TA, Mairpady Shambat S, Hasse B, Zinkernagel AS, Brugger SD. Limited Adaptation of Staphylococcus aureus during Transition from Colonization to Invasive Infection. Microbiol Spectr 2023; 11:e0259021. [PMID: 37341598 PMCID: PMC10433843 DOI: 10.1128/spectrum.02590-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Staphylococcus aureus carriage is a risk factor for invasive infections. Unique genetic elements favoring the transition from colonizing to invasive phenotype have not yet been identified, and phenotypic adaptation traits are understudied. We therefore assessed phenotypic and genotypic profiles of 11 S. aureus isolate pairs sampled from colonized patients simultaneously suffering from invasive S. aureus infections. Ten out of 11 isolate pairs displayed the same spa and multilocus sequence type, suggesting colonization as an origin for the invasive infection. Systematic analysis of colonizing and invasive isolate pairs showed similar adherence, hemolysis, reproductive fitness properties, antibiotic tolerance, and virulence in a Galleria mellonella infection model, as well as minimal genetic differences. Our results provide insights into the similar phenotypes associated with limited adaptation between colonizing and invasive isolates. Disruption of the physical barriers of mucosa or skin was identified in the majority of patients, further emphasizing colonization as a major risk factor for invasive disease. IMPORTANCE S. aureus is a major pathogen of humans, causing a wide range of diseases. The difficulty to develop a vaccine and antibiotic treatment failure warrant the exploration of novel treatment strategies. Asymptomatic colonization of the human nasal passages is a major risk factor for invasive disease, and decolonization procedures have been effective in preventing invasive infections. However, the transition of S. aureus from a benign colonizer of the nasal passages to a major pathogen is not well understood, and both host and bacterial properties have been discussed as being relevant for this behavioral change. We conducted a thorough investigation of patient-derived strain pairs reflecting colonizing and invasive isolates in a given patient. Although we identified limited genetic adaptation in certain strains, as well as slight differences in adherence capacity among colonizing and invasive isolates, our work suggests that barrier breaches are a key event in the disease continuum of S. aureus.
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Affiliation(s)
- Anna K. Räz
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Federica Andreoni
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mathilde Boumasmoud
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Judith Bergada-Pijuan
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Tiziano A. Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Barbara Hasse
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Silvio D. Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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10
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Makrai L, Fodróczy B, Nagy SÁ, Czeiszing P, Csabai I, Szita G, Solymosi N. Annotated dataset for deep-learning-based bacterial colony detection. Sci Data 2023; 10:497. [PMID: 37507412 PMCID: PMC10382471 DOI: 10.1038/s41597-023-02404-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Quantifying bacteria per unit mass or volume is a common task in various fields of microbiology (e.g., infectiology and food hygiene). Most bacteria can be grown on culture media. The unicellular bacteria reproduce by dividing into two cells, which increases the number of bacteria in the population. Methodologically, this can be followed by culture procedures, which mostly involve determining the number of bacterial colonies on the solid culture media that are visible to the naked eye. However, it is a time-consuming and laborious professional activity. Addressing the automation of colony counting by convolutional neural networks in our work, we have cultured 24 bacteria species of veterinary importance with different concentrations on solid media. A total of 56,865 colonies were annotated manually by bounding boxes on the 369 digital images of bacterial cultures. The published dataset will help developments that use artificial intelligence to automate the counting of bacterial colonies.
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Affiliation(s)
- László Makrai
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, 1143, Budapest, Hungary
| | - Bettina Fodróczy
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, 1143, Budapest, Hungary
- Centre for Bioinformatics, University of Veterinary Medicine, 1078, Budapest, Hungary
| | - Sára Ágnes Nagy
- Centre for Bioinformatics, University of Veterinary Medicine, 1078, Budapest, Hungary
| | - Péter Czeiszing
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, 1143, Budapest, Hungary
- Centre for Bioinformatics, University of Veterinary Medicine, 1078, Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Géza Szita
- Centre for Bioinformatics, University of Veterinary Medicine, 1078, Budapest, Hungary
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine, 1078, Budapest, Hungary.
- Department of Physics of Complex Systems, Eötvös Loránd University, 1117, Budapest, Hungary.
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11
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Houchmandzadeh B, Ballet P. A novel procedure for CFU plating and counting. J Microbiol Methods 2023; 206:106693. [PMID: 36863534 DOI: 10.1016/j.mimet.2023.106693] [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: 12/13/2022] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023]
Abstract
We present a novel method to automate plating for the Colony Forming Unit (CFU) counting procedure. The apparatus we developed for the application of this method is based on motorized stages and a syringe in order to spread fine drops of a liquid containing a solution of interest on a plate without direct contact with the surface. The apparatus can be used in two different modes. In the the first method which follows the same principle as the classical CFU count, fine drops of liquid are deposited homogeneously on an agar plate and microorganisms are allowed to form colonies. In the second, novel method that we call P0, isolated drops of the order of 10 μL containing both the microbes and the nutrient medium are deposited directly on a regular grid on a hard surface (plastic or glass); after incubation, drops that show no sign of growth inside are used to determine the microbes concentration. This new method removes the need for preparing agar surfaces and allows for easy disposal of waste and reuse of consumables. The apparatus is simple to build and use, the plating is fast and the CFU count in both type of plating is extremely reproducible and robust.
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Affiliation(s)
- Bahram Houchmandzadeh
- Univ. Grenoble Alpes & Centre National de la Recherche Scientifique, LIPhy, F-38000 Grenoble, France.
| | - Patrice Ballet
- Univ. Grenoble Alpes & Centre National de la Recherche Scientifique, LIPhy, F-38000 Grenoble, France
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12
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Mobile Element Integration Reveals a Chromosome Dimer Resolution System in Legionellales. mBio 2022; 13:e0217122. [PMID: 36314797 PMCID: PMC9765430 DOI: 10.1128/mbio.02171-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In bacteria, the mechanisms used to repair DNA lesions during genome replication include homologous recombination between sister chromosomes. This can lead to the formation of chromosome dimers if an odd number of crossover events occurs. The dimers must be resolved before cell separation to ensure genomic stability and cell viability. Dimer resolution is achieved by the broadly conserved dif/Xer system, which catalyzes one additional crossover event immediately prior to cell separation. While dif/Xer systems have been characterized or predicted in the vast majority of proteobacteria, no homologs to dif or xer have been identified in the order Legionellales. Here, we report the discovery of a distinct single-recombinase dif/Xer system in the intracellular pathogen Legionella pneumophila. The dif site was uncovered by our analysis of Legionella mobile element-1 (LME-1), which harbors a dif site mimic and integrates into the L. pneumophila genome via site-specific recombination. We demonstrate that lpg1867 (here named xerL) encodes a tyrosine recombinase that is necessary and sufficient for catalyzing recombination at the dif site and that deletion of dif or xerL causes filamentation along with extracellular and intracellular growth defects. We show that the dif/XerL system is present throughout Legionellales and that Coxiella burnetii XerL and its cognate dif site can functionally substitute for the native system in L. pneumophila. Finally, we describe an unexpected link between C. burnetii dif/Xer and the maintenance of its virulence plasmids. IMPORTANCE The maintenance of circular chromosomes depends on the ability to resolve aberrant chromosome dimers after they form. In most proteobacteria, broadly conserved Xer recombinases catalyze single crossovers at short, species-specific dif sites located near the replication terminus. Chromosomal dimerization leads to the formation of two copies of dif within the same molecule, leading to rapid site-specific recombination and conversion back into chromosome monomers. The apparent absence of chromosome dimer resolution mechanisms in Legionellales has been a mystery to date. By studying a phage-like mobile genetic element, LME-1, we have identified a previously unknown single-recombinase dif/Xer system that is not only widespread across Legionellales but whose activity is linked to virulence in two important human pathogens.
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13
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Gómez-Mejia A, Arnold K, Bär J, Singh KD, Scheier TC, Brugger SD, Zinkernagel AS, Sinues P. Rapid detection of Staphylococcus aureus and Streptococcus pneumoniae by real-time analysis of volatile metabolites. iScience 2022; 25:105080. [PMID: 36157573 PMCID: PMC9490032 DOI: 10.1016/j.isci.2022.105080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/06/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Early detection of pathogenic bacteria is needed for rapid diagnostics allowing adequate and timely treatment of infections. In this study, we show that secondary electrospray ionization–high resolution mass spectrometry (SESI-HRMS) can be used as a diagnostic tool for rapid detection of bacterial infections as a supportive system for current state-of-the-art diagnostics. Volatile organic compounds (VOCs) produced by growing S. aureus or S. pneumoniae cultures on blood agar plates were detected within minutes and allowed for the distinction of these two bacteria on a species and even strain level within hours. Furthermore, we obtained a fingerprint of clinical patient samples within minutes of measurement and predominantly observed a separation of samples containing live bacteria compared to samples with no bacterial growth. Further development of this technique may reduce the time required for microbiological diagnosis and should help to improve patient’s tailored treatment. Real-time mass spectrometry shows potential as a tool for microbiological diagnosis Bacterial volatile metabolites from 1 × 103 CFUs are detected within minutes S. aureus and S. pneumoniae can be distinguished on species and even strain level Complex clinical samples cluster according to presence or absence of viable bacteria
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Affiliation(s)
- Alejandro Gómez-Mejia
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zürich, 8091 Zurich, Switzerland
| | - Kim Arnold
- University Children's Hospital Basel (UKBB), 4056 Basel, Switzerland.,Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Julian Bär
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zürich, 8091 Zurich, Switzerland
| | - Kapil Dev Singh
- University Children's Hospital Basel (UKBB), 4056 Basel, Switzerland.,Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Thomas C Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zürich, 8091 Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zürich, 8091 Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zürich, 8091 Zurich, Switzerland
| | - Pablo Sinues
- University Children's Hospital Basel (UKBB), 4056 Basel, Switzerland.,Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
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14
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Dönmez Sİ, Needs SH, Osborn HMI, Reis NM, Edwards AD. Label-free 1D microfluidic dipstick counting of microbial colonies and bacteriophage plaques. LAB ON A CHIP 2022; 22:2820-2831. [PMID: 35792607 DOI: 10.1039/d2lc00280a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Counting viable bacterial cells and functional bacteriophage is fundamental to microbiology underpinning research, surveillance, biopharmaceuticals and diagnostics. Colony forming unit (CFU) and plaque forming unit (PFU) counting still requires slow and laborious solid culture on agar in Petri dishes or plates. Here, we show that dip-stick microfluidic strips can be used without growth indicator dye for rapid and simple CFU ml-1 and PFU ml-1 measurement. We demonstrate for the first time that fluoropolymer microcapillaries combined with digital imaging allow bacteriophage plaques to be counted rapidly in a dip-and-test format. The microfluidic length scales offer a linear 1-dimensional alternative to a 2D solid agar medium surface, with colonies or plaques clearly visible as "dashes" or "gaps". An inexpensive open source darkfield biosensor system using Raspberry Pi imaging permits label-free detection and counting of colonies or plaques within 4-8 hours in a linear, liquid matrix within ∼200 μm inner diameter microcapillaries. We obtained full quantitative agreement between 1D microfluidic colony counting in dipsticks versus conventional 2D solid agar Petri dish plates for S. aureus and E. coli, and for T2 phage and phage K, but up to 6 times faster. Time-lapse darkfield imaging permitted detailed kinetic analysis of colony growth in the microcapillaries, providing new insight into microfluidic microbiology and colony growth, not possible with Petri dishes. Surprisingly, whilst E. coli colonies appeared earlier, subsequent colony expansion was faster along the microcapillaries for S. aureus. This may be explained by the microenvironment offered for 1D colony growth within microcapillaries, linked to a mass balance between nutrient (glucose) diffusion and bacterial growth kinetics. Counting individual colonies in liquid medium was not possible for motile strains that spread rapidly along the capillary, however inclusion of soft agar inhibited spreading, making this new simple dip-and-test counting method applicable to both motile and non-motile bacteria. Label-free dipstick colony and plaque counting has potential for many analytical microbial tasks, and the innovation of 1D colony counting has relevance to other microfluidic microbiology.
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Affiliation(s)
| | - Sarah H Needs
- Reading School of Pharmacy, University of Reading, Whiteknights, RG6 6AD, UK.
| | - Helen M I Osborn
- Reading School of Pharmacy, University of Reading, Whiteknights, RG6 6AD, UK.
| | - Nuno M Reis
- Department of Chemical Engineering and Centre for Biosensors, Biodevices and Bioelectronics (C3Bio), University of Bath, Claverton Down, Bath BA2 7AY, UK
- Capillary Film Technology Ltd, Daux Road, Billingshurst, West Sussex RH14 9SJ, UK
| | - Alexander D Edwards
- Reading School of Pharmacy, University of Reading, Whiteknights, RG6 6AD, UK.
- Capillary Film Technology Ltd, Daux Road, Billingshurst, West Sussex RH14 9SJ, UK
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15
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Nakar A, Pistiki A, Ryabchykov O, Bocklitz T, Rösch P, Popp J. Label-free differentiation of clinical E. coli and Klebsiella isolates with Raman spectroscopy. JOURNAL OF BIOPHOTONICS 2022; 15:e202200005. [PMID: 35388631 DOI: 10.1002/jbio.202200005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/18/2022] [Accepted: 04/04/2022] [Indexed: 05/14/2023]
Abstract
Raman spectroscopy is a promising spectroscopic technique for microbiological diagnostics. In routine diagnostic, the differentiation of pathogens of the Enterobacteriaceae family remain challenging. In this study, Raman spectroscopy was applied for the differentiation of 24 clinical E. coli, Klebsiella pneumoniae and Klebsiella oxytoca isolates. Spectra were collected with two spectroscopic approaches: UV-Resonance Raman spectroscopy (UVRR) and single-cell Raman microspectroscopy with 532 nm excitation. A description of the different biochemical profiles provided by the different excitation wavelengths was performed followed by machine-learning models for the classification at the genus and species levels. UVRR was shown to outperform 532 nm excitation, enabling correct classification at the genus level of 23/24 isolates. Furthermore, for the first time, Klebsiella species were correctly classified at the species level with 92% accuracy, classifying all three K. oxytoca isolates correctly. These findings should guide future applicative studies, increasing the scope of Raman spectroscopy's suitability for clinical applications.
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Affiliation(s)
- Amir Nakar
- Leibniz Institute of Photonic Technology Jena-Member of the Research Alliance "Leibniz Health Technologies", Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
- Research Campus Infectognostics, Jena, Germany
| | - Aikaterini Pistiki
- Leibniz Institute of Photonic Technology Jena-Member of the Research Alliance "Leibniz Health Technologies", Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
- Research Campus Infectognostics, Jena, Germany
| | - Oleg Ryabchykov
- Leibniz Institute of Photonic Technology Jena-Member of the Research Alliance "Leibniz Health Technologies", Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
| | - Thomas Bocklitz
- Leibniz Institute of Photonic Technology Jena-Member of the Research Alliance "Leibniz Health Technologies", Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
- Research Campus Infectognostics, Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
- Research Campus Infectognostics, Jena, Germany
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology Jena-Member of the Research Alliance "Leibniz Health Technologies", Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
- Research Campus Infectognostics, Jena, Germany
- Jena Biophotonics and Imaging Laboratory, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
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16
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Marro FC, Laurent F, Josse J, Blocker AJ. Methods to monitor bacterial growth and replicative rates at the single-cell level. FEMS Microbiol Rev 2022; 46:6623663. [PMID: 35772001 PMCID: PMC9629498 DOI: 10.1093/femsre/fuac030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 01/09/2023] Open
Abstract
The heterogeneity of bacterial growth and replicative rates within a population was proposed a century ago notably to explain the presence of bacterial persisters. The term "growth rate" at the single-cell level corresponds to the increase in size or mass of an individual bacterium while the "replicative rate" refers to its division capacity within a defined temporality. After a decades long hiatus, recent technical innovative approaches allow population growth and replicative rates heterogeneity monitoring at the single-cell level resuming in earnest. Among these techniques, the oldest and widely used is time-lapse microscopy, most recently combined with microfluidics. We also discuss recent fluorescence dilution methods informing only on replicative rates and best suited. Some new elegant single cell methods so far only sporadically used such as buoyant mass measurement and stable isotope probing have emerged. Overall, such tools are widely used to investigate and compare the growth and replicative rates of bacteria displaying drug-persistent behaviors to that of bacteria growing in specific ecological niches or collected from patients. In this review, we describe the current methods available, discussing both the type of queries these have been used to answer and the specific strengths and limitations of each method.
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Affiliation(s)
- Florian C Marro
- Evotec ID Lyon, In Vitro Biology, Infectious Diseases and Antibacterials Unit, Gerland, 69007 Lyon, France,CIRI – Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007 Lyon, France
| | - Frédéric Laurent
- CIRI – Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007 Lyon, France,Institut des Sciences Pharmaceutiques et Biologiques (ISPB), Université Claude Bernard Lyon 1, Lyon, France,Centre de Référence pour la prise en charge des Infections ostéo-articulaires complexes (CRIOAc Lyon; www.crioac-lyon.fr), Hospices Civils de Lyon, Lyon, France,Laboratoire de bactériologie, Institut des Agents Infectieux, French National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France
| | - Jérôme Josse
- CIRI – Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007 Lyon, France,Institut des Sciences Pharmaceutiques et Biologiques (ISPB), Université Claude Bernard Lyon 1, Lyon, France,Centre de Référence pour la prise en charge des Infections ostéo-articulaires complexes (CRIOAc Lyon; www.crioac-lyon.fr), Hospices Civils de Lyon, Lyon, France
| | - Ariel J Blocker
- Corresponding author. Evotec ID Lyon, In Vitro Biology, Infectious Diseases and Antibacterials Unit, France. E-mail:
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17
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Diep TT, Bizley S, Edwards AD. 3D-Printed Dip Slides Miniaturize Bacterial Identification and Antibiotic Susceptibility Tests Allowing Direct Mastitis Sample Analysis. MICROMACHINES 2022; 13:mi13060941. [PMID: 35744555 PMCID: PMC9231150 DOI: 10.3390/mi13060941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023]
Abstract
The early detection of antimicrobial resistance remains an essential step in the selection and optimization of antibiotic treatments. Phenotypic antibiotic susceptibility testing including the measurement of minimum inhibitory concentration (MIC) remains critical for surveillance and diagnostic testing. Limitations to current testing methods include bulky labware and laborious methods. Furthermore, the requirement of a single strain of bacteria to be isolated from samples prior to antibiotic susceptibility testing delays results. The mixture of bacteria present in a sample may also have an altered resistance profile to the individual strains, and so measuring the susceptibility of the mixtures of organisms found in some samples may be desirable. To enable simultaneous MIC and bacterial species detection in a simple and rapid miniaturized format, a 3D-printed frame was designed for a multi-sample millifluidic dip-slide device that combines panels of identification culture media with a range of antibiotics (Ampicillin, Amoxicillin, Amikacin, Ceftazidime, Cefotaxime, Ofloxacin, Oxytetracycline, Streptomycin, Gentamycin and Imipenem) diluted in Muëller-Hinton Agar. Our proof-of-concept evaluation confirmed that the direct detection of more than one bacterium parallel to measuring MIC in samples is possible, which is validated using reference strains E. coli ATCC 25922, Klebsiella pneumoniae ATCC 13883, Pseudomonas aeruginosa ATCC 10145, and Staphylococcus aureus ATCC 12600 and with mastitis milk samples collected from Reading University Farm. When mixtures were tested, a MIC value was obtained that reflected the most resistant organism present (i.e., highest MIC), suggesting it may be possible to estimate a minimum effective antibiotic concentration for mixtures directly from samples containing multiple pathogens. We conclude that this simple miniaturized approach to the rapid simultaneous identification and antibiotic susceptibility testing may be suitable for directly testing agricultural samples, which is achieved through shrinking conventional tests into a simple "dip-and-incubate" device that can be 3D printed anywhere.
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18
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Harmel C, Sid Ahmed S, Koch R, Tünnermann J, Distler T, Imle A, Giorgetti L, Bahn E, Fackler OT, Graw F. VisuStatR: visualizing motility and morphology statistics on images in R. Bioinformatics 2022; 38:2970-2972. [PMID: 35561161 DOI: 10.1093/bioinformatics/btac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/01/2022] [Accepted: 04/19/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Live-cell microscopy has become an essential tool for analyzing dynamic processes in various biological applications. Thereby, high-throughput and automated tracking analyses allow the simultaneous evaluation of large numbers of objects. However, to critically assess the influence of individual objects on calculated summary statistics, and to detect heterogeneous dynamics or possible artifacts, such as misclassified or -tracked objects, a direct mapping of gained statistical information onto the actual image data would be necessary. RESULTS We present VisuStatR as a platform independent software package that allows the direct visualization of time-resolved summary statistics of morphological characteristics or motility dynamics onto raw images. The software contains several display modes to compare user-defined summary statistics and the underlying image data in various levels of detail. AVAILABILITY AND IMPLEMENTATION VisuStatR is a free and open-source R-package, containing a user-friendly graphical-user interface and is available via GitHub at https://github.com/grrchrr/VisuStatR/ under the MIT+ license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Christoph Harmel
- BioQuant-Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Samy Sid Ahmed
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Robin Koch
- Department of Radiation Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jana Tünnermann
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Tania Distler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Andrea Imle
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Emanuel Bahn
- Department of Radiation Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Oliver T Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Frederik Graw
- BioQuant-Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, 69120 Heidelberg, Germany
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19
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Zheng EJ, Andrews IW, Grote AT, Manson AL, Alcantar MA, Earl AM, Collins JJ. Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies. Nat Commun 2022; 13:2525. [PMID: 35534481 PMCID: PMC9085803 DOI: 10.1038/s41467-022-30272-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/22/2022] [Indexed: 01/21/2023] Open
Abstract
Antibiotic tolerance, or the ability of bacteria to survive antibiotic treatment in the absence of genetic resistance, has been linked to chronic and recurrent infections. Tolerant cells are often characterized by a low metabolic state, against which most clinically used antibiotics are ineffective. Here, we show that tolerance readily evolves against antibiotics that are strongly dependent on bacterial metabolism, but does not arise against antibiotics whose efficacy is only minimally affected by metabolic state. We identify a mechanism of tolerance evolution in E. coli involving deletion of the sodium-proton antiporter gene nhaA, which results in downregulated metabolism and upregulated stress responses. Additionally, we find that cycling of antibiotics with different metabolic dependencies interrupts evolution of tolerance in vitro, increasing the lifetime of treatment efficacy. Our work highlights the potential for limiting the occurrence and extent of tolerance by accounting for antibiotic dependencies on bacterial metabolism.
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Affiliation(s)
- Erica J Zheng
- Program in Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Ian W Andrews
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alexandra T Grote
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Miguel A Alcantar
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - James J Collins
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, 02139, USA.
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20
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Pineda D, Pérez J, Gaviria D, Ospino-Villalba K, Camargo O. MEDUSA: An open-source and webcam based multispectral imaging system. HARDWAREX 2022; 11:e00282. [PMID: 35509904 PMCID: PMC9058717 DOI: 10.1016/j.ohx.2022.e00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/07/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Multispectral imaging is at the forefront of contactless surface analysis. Standard multispectral imaging systems use sophisticated software, cameras and light filtering optics. This paper discloses the building of a customizable and cost-effective multispectral imaging and analysis system. It integrates a web camera, light emitting diodes (LEDs) lighting, a semisphere for even lightening, an open-source Arduino™ development board and a free Python application to automatically obtain and visually analyze multispectral images. The device is hereafter called MEDUSA and its optical performance was tested for repeated Imaging consistency, visible and near infrared band sensitivity and lighting evenness. Four proof of concept tests were run in order to understand the advantageous use of this system, as compared to a simple visual score of diverse samples. Each of three qualitative tests used sets of 12 LED band spectral images to analyze ink changes in a counterfeit bill, surface bruises on Hass avocado fruits and transient changes in petri dish grown bacterial colonies. A fourth test used single band imaging in a set of standard laboratory analyzed plant samples, to quantitatively relate a red band light reflectance to its nitrogen content. These tests indicate that MEDUSA made images may yield qualitative and quantitative spectral information unseen to the naked eye, suggesting potential use in currency counterfeit tests, food quality analyses, microbial phenotyping and agricultural plant chemistry. MEDUSA can be freely reproduced and customized from this research, making it a powerful and affordable analytical tool to analyze a wide range of subtle chemical properties in samples at industrial and science fields.
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Affiliation(s)
- Daniel Pineda
- Facultad de Ciencias Universidad Nacional de Colombia Sede Medellín, Facultad de Ciencias Agrarias, Carrera 65 #59a-110, Medellín, Antioquia, Colombia
| | - Juan Pérez
- Facultad de Ciencias Universidad Nacional de Colombia Sede Medellín, Facultad de Ciencias Agrarias, Carrera 65 #59a-110, Medellín, Antioquia, Colombia
| | - Daniel Gaviria
- Facultad de Ciencias Agrarias. Carrera 65 #59a-110, Medellín, Antioquia, Colombia
| | | | - Omar Camargo
- Facultad de Ciencias Agrarias. Carrera 65 #59a-110, Medellín, Antioquia, Colombia
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21
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Generation of microbial colonies dataset with deep learning style transfer. Sci Rep 2022; 12:5212. [PMID: 35338253 PMCID: PMC8956727 DOI: 10.1038/s41598-022-09264-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/21/2022] [Indexed: 01/02/2023] Open
Abstract
We introduce an effective strategy to generate an annotated synthetic dataset of microbiological images of Petri dishes that can be used to train deep learning models in a fully supervised fashion. The developed generator employs traditional computer vision algorithms together with a neural style transfer method for data augmentation. We show that the method is able to synthesize a dataset of realistic looking images that can be used to train a neural network model capable of localising, segmenting, and classifying five different microbial species. Our method requires significantly fewer resources to obtain a useful dataset than collecting and labeling a whole large set of real images with annotations. We show that starting with only 100 real images, we can generate data to train a detector that achieves comparable results (detection mAP \documentclass[12pt]{minimal}
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\begin{document}$$=4.49$$\end{document}=4.49) to the same detector but trained on a real, several dozen times bigger dataset (mAP \documentclass[12pt]{minimal}
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\begin{document}$$=4.31$$\end{document}=4.31), containing over 7 k images. We prove the usefulness of the method in microbe detection and segmentation, but we expect that it is general and flexible and can also be applicable in other domains of science and industry to detect various objects.
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Bär J, Boumasmoud M, Mairpady Shambat S, Vulin C, Huemer M, Schweizer TA, Gómez-Mejia A, Eberhard N, Achermann Y, Zingg PO, Mestres C, Brugger SD, Schuepbach RA, Kouyos RD, Hasse B, Zinkernagel AS. Quantification of within-patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations. Clin Microbiol Infect 2022; 28:1022.e1-1022.e7. [DOI: 10.1016/j.cmi.2022.01.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 12/21/2022]
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23
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Harvey HJ, Chubynsky MV, Sprittles JE, Shor LM, Mooney SJ, Wildman RD, Avery SV. Application of microfluidic systems in modelling impacts of environmental structure on stress-sensing by individual microbial cells. Comput Struct Biotechnol J 2022; 20:128-138. [PMID: 34976317 PMCID: PMC8689086 DOI: 10.1016/j.csbj.2021.11.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/28/2021] [Accepted: 11/28/2021] [Indexed: 11/03/2022] Open
Abstract
Environmental structure describes physical structure that can determine heterogenous spatial distribution of biotic and abiotic (nutrients, stressors etc.) components of a microorganism's microenvironment. This study investigated the impact of micrometre-scale structure on microbial stress sensing, using yeast cells exposed to copper in microfluidic devices comprising either complex soil-like architectures or simplified environmental structures. In the soil micromodels, the responses of individual cells to inflowing medium supplemented with high copper (using cells expressing a copper-responsive pCUP1-reporter fusion) could be described neither by spatial metrics developed to quantify proximity to environmental structures and surrounding space, nor by computational modelling of fluid flow in the systems. In contrast, the proximities of cells to structures did correlate with their responses to elevated copper in microfluidic chambers that contained simplified environmental structure. Here, cells within more open spaces showed the stronger responses to the copper-supplemented inflow. These insights highlight not only the importance of structure for microbial responses to their chemical environment, but also how predictive modelling of these interactions can depend on complexity of the system, even when deploying controlled laboratory conditions and microfluidics.
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Affiliation(s)
- Harry J Harvey
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | | | - Leslie M Shor
- Department of Chemical and Biomolecular Engineering, University of Connecticut, USA
| | - Sacha J Mooney
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Ricky D Wildman
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - Simon V Avery
- School of Life Sciences, University of Nottingham, Nottingham, UK
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Pandey S, Park Y, Ankita A, Phillips GJ. Scan4CFU: Low-cost, open-source bacterial colony tracking over large areas and extended incubation times. HARDWAREX 2021; 10:e00249. [PMID: 35607694 PMCID: PMC9123444 DOI: 10.1016/j.ohx.2021.e00249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/01/2021] [Accepted: 11/21/2021] [Indexed: 02/08/2023]
Abstract
A hallmark of bacterial populations cultured in vitro is their homogeneity of growth, where the majority of cells display identical growth rate, cell size and content. Recent insights, however, have revealed that even cells growing in exponential growth phase can be heterogeneous with respect to variables typically used to measure cell growth. Bacterial heterogeneity has important implications for how bacteria respond to environmental stresses, such as antibiotics. The phenomenon of antimicrobial persistence, for example, has been linked to a small subpopulation of cells that have entered into a state of dormancy where antibiotics are no longer effective. While methods have been developed for identifying individual non-growing cells in bacterial cultures, there has been less attention paid to how these cells may influence growth in colonies on a solid surface. In response, we have developed a low-cost, open-source platform to perform automated image capture and image analysis of bacterial colony growth on multiple nutrient agar plates simultaneously. The descriptions of the hardware and software are included, along with details about the temperature-controlled growth chamber, high-resolution scanner, and graphical interface to extract and plot the colony lag time and growth kinetics. Experiments were conducted using a wild type strain of Escherichia coli K12 to demonstrate the feasibility and operation of our setup. By automated tracking of bacterial growth kinetics in colonies, the system holds the potential to reveal new insights into understanding the impact of microbial heterogeneity on antibiotic resistance and persistence.
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25
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Molecular reprogramming and phenotype switching in Staphylococcus aureus lead to high antibiotic persistence and affect therapy success. Proc Natl Acad Sci U S A 2021; 118:2014920118. [PMID: 33574060 DOI: 10.1073/pnas.2014920118] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Staphylococcus aureus causes invasive infections and easily acquires antibiotic resistance. Even antibiotic-susceptible S. aureus can survive antibiotic therapy and persist, requiring prolonged treatment and surgical interventions. These so-called persisters display an arrested-growth phenotype, tolerate high antibiotic concentrations, and are associated with chronic and recurrent infections. To characterize these persisters, we assessed S. aureus recovered directly from a patient suffering from a persistent infection. We show that host-mediated stress, including acidic pH, abscess environment, and antibiotic exposure promoted persister formation in vitro and in vivo. Multiomics analysis identified molecular changes in S. aureus in response to acid stress leading to an overall virulent population. However, further analysis of a persister-enriched population revealed major molecular reprogramming in persisters, including down-regulation of virulence and cell division and up-regulation of ribosomal proteins, nucleotide-, and amino acid-metabolic pathways, suggesting their requirement to fuel and maintain the persister phenotype and highlighting that persisters are not completely metabolically inactive. Additionally, decreased aconitase activity and ATP levels and accumulation of insoluble proteins involved in transcription, translation, and energy production correlated with persistence in S. aureus, underpinning the molecular mechanisms that drive the persister phenotype. Upon regrowth, these persisters regained their virulence potential and metabolically active phenotype, including reduction of insoluble proteins, exhibiting a reversible state, crucial for recurrent infections. We further show that a targeted antipersister combination therapy using retinoid derivatives and antibiotics significantly reduced lag-phase heterogeneity and persisters in a murine infection model. Our results provide molecular insights into persisters and help explain why persistent S. aureus infections are so difficult to treat.
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Sulaiman JE, Lam H. Evolution of Bacterial Tolerance Under Antibiotic Treatment and Its Implications on the Development of Resistance. Front Microbiol 2021; 12:617412. [PMID: 33717007 PMCID: PMC7952611 DOI: 10.3389/fmicb.2021.617412] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/12/2021] [Indexed: 01/08/2023] Open
Abstract
Recent laboratory evolution studies have shown that upon repetitive antibiotic treatments, bacterial populations will adapt and eventually became tolerant and resistant to the drug. Drug tolerance rapidly evolves upon frequent, intermittent antibiotic treatments, and such emerging drug tolerance seems to be specific to the treatment conditions, complicating clinical practice. Moreover, it has been shown that tolerance often promotes the development of resistance, which further reinforces the need of clinical diagnostics for antibiotic tolerance to reduce the occurrence of acquired resistance. Here, we discuss the laboratory evolution studies that were performed to track the development of tolerance in bacterial populations, and highlight the urgency of developing a comprehensive knowledge base of various tolerance phenotypes and their detection in clinics. Finally, we propose future directions for basic research in this growing field.
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Affiliation(s)
- Jordy Evan Sulaiman
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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27
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Abstract
Reproductive fitness of bacteria is a major factor in the evolution and persistence of antimicrobial resistance and may play an important role as a pathogen factor in severe infections. With a computational approach to quantify fitness in bacteria growing competitively on agar plates, our high-throughput method has been designed to obtain additional phenotypic data for antimicrobial resistance analysis at a low cost. To evaluate changes in reproductive fitness of bacteria, e.g., after acquisition of antimicrobial resistance, a low-cost high-throughput method to analyze bacterial growth on agar is desirable for broad usability. In our bacterial quantitative fitness analysis (BaQFA), arrayed cultures are spotted on agar and photographed sequentially while growing. These time-lapse images are analyzed using a purpose-built open-source software to derive normalized image intensity (NI) values for each culture spot. Subsequently, a Gompertz growth model is fitted to NI values, and fitness is calculated from model parameters. To represent a range of clinically important pathogenic bacteria, we used different strains of Enterococcus faecium, Escherichia coli, and Staphylococcus aureus, with and without antimicrobial resistance. Relative competitive fitness (RCF) was defined as the mean fitness ratio of two strains growing competitively on one plate.BaQFA permitted the accurate construction of growth curves from bacteria grown on semisolid agar plates and fitting of Gompertz models. Normalized image intensity values showed a strong association with the total CFU/ml count per spotted culture (P < 0.001) for all strains of the three species. BaQFA showed relevant reproductive fitness differences between individual strains, suggesting substantially higher fitness of methicillin-resistant S. aureus JE2 than Cowan (RCF, 1.58; P < 0.001). Similarly, the vancomycin-resistant E. faecium ST172b showed higher competitive fitness than susceptible E. faecium ST172 (RCF, 1.59; P < 0.001). Our BaQFA method allows detection of fitness differences between bacterial strains and may help to estimate epidemiological antimicrobial persistence or contribute to the prediction of clinical outcomes in severe infections. IMPORTANCE Reproductive fitness of bacteria is a major factor in the evolution and persistence of antimicrobial resistance and may play an important role in severe infections. With a computational approach to quantify fitness in bacteria growing competitively on agar plates, our high-throughput method has been designed to obtain additional phenotypic data for antimicrobial resistance analysis at a low cost. Furthermore, our bacterial quantitative fitness analysis (BaQFA) enables the investigation of a link between bacterial fitness and clinical outcomes in severe invasive bacterial infections. This may allow future use of our method for patient management and risk stratification of clinical outcomes. Our proposed method uses open-source software and a hardware setup that can utilize consumer electronics. This will enable a wider community of researchers, including those from low-resource countries, where the burden of antimicrobial resistance is highest, to obtain valuable information about emerging bacterial strains.
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Huemer M, Mairpady Shambat S, Brugger SD, Zinkernagel AS. Antibiotic resistance and persistence-Implications for human health and treatment perspectives. EMBO Rep 2020; 21:e51034. [PMID: 33400359 PMCID: PMC7726816 DOI: 10.15252/embr.202051034] [Citation(s) in RCA: 251] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/13/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial resistance (AMR) and persistence are associated with an elevated risk of treatment failure and relapsing infections. They are thus important drivers of increased morbidity and mortality rates resulting in growing healthcare costs. Antibiotic resistance is readily identifiable with standard microbiological assays, and the threat imposed by antibiotic resistance has been well recognized. Measures aiming to reduce resistance development and spreading of resistant bacteria are being enforced. However, the phenomenon of bacteria surviving antibiotic exposure despite being fully susceptible, so-called antibiotic persistence, is still largely underestimated. In contrast to antibiotic resistance, antibiotic persistence is difficult to measure and therefore often missed, potentially leading to treatment failures. In this review, we focus on bacterial mechanisms allowing evasion of antibiotic killing and discuss their implications on human health. We describe the relationship between antibiotic persistence and bacterial heterogeneity and discuss recent studies that link bacterial persistence and tolerance with the evolution of antibiotic resistance. Finally, we review persister detection methods, novel strategies aiming at eradicating bacterial persisters and the latest advances in the development of new antibiotics.
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Affiliation(s)
- Markus Huemer
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
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