Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method

ABSTRACT 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...

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Autores principales:	Pascal M. Frey, Julian Baer, Judith Bergada-Pijuan, Conor Lawless, Philipp K. Bühler, Roger D. Kouyos, Katherine P. Lemon, Annelies S. Zinkernagel, Silvio D. Brugger
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2021
Materias:	quantitative fitness analysis antimicrobial resistance bacterial fitness image analysis Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/b8c8cb1627ec4306a5920f5ad1bcacab
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spelling	oai:doaj.org-article:b8c8cb1627ec4306a5920f5ad1bcacab2021-12-02T17:07:26ZQuantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method10.1128/mSystems.01323-202379-5077https://doaj.org/article/b8c8cb1627ec4306a5920f5ad1bcacab2021-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.01323-20https://doaj.org/toc/2379-5077ABSTRACT 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.Pascal M. FreyJulian BaerJudith Bergada-PijuanConor LawlessPhilipp K. BühlerRoger D. KouyosKatherine P. LemonAnnelies S. ZinkernagelSilvio D. BruggerAmerican Society for Microbiologyarticlequantitative fitness analysisantimicrobial resistancebacterial fitnessimage analysisMicrobiologyQR1-502ENmSystems, Vol 6, Iss 1 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	quantitative fitness analysis antimicrobial resistance bacterial fitness image analysis Microbiology QR1-502
spellingShingle	quantitative fitness analysis antimicrobial resistance bacterial fitness image analysis Microbiology QR1-502 Pascal M. Frey Julian Baer Judith Bergada-Pijuan Conor Lawless Philipp K. Bühler Roger D. Kouyos Katherine P. Lemon Annelies S. Zinkernagel Silvio D. Brugger Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method
description	ABSTRACT 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.
format	article
author	Pascal M. Frey Julian Baer Judith Bergada-Pijuan Conor Lawless Philipp K. Bühler Roger D. Kouyos Katherine P. Lemon Annelies S. Zinkernagel Silvio D. Brugger
author_facet	Pascal M. Frey Julian Baer Judith Bergada-Pijuan Conor Lawless Philipp K. Bühler Roger D. Kouyos Katherine P. Lemon Annelies S. Zinkernagel Silvio D. Brugger
author_sort	Pascal M. Frey
title	Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method
title_short	Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method
title_full	Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method
title_fullStr	Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method
title_full_unstemmed	Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method
title_sort	quantifying variation in bacterial reproductive fitness: a high-throughput method
publisher	American Society for Microbiology
publishDate	2021
url	https://doaj.org/article/b8c8cb1627ec4306a5920f5ad1bcacab
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Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method

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