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EP-4739997-A1 - METHOD AND SYSTEM FOR IDENTIFYING MICRO-ORGANISMS TAKING COLONY FORM

EP4739997A1EP 4739997 A1EP4739997 A1EP 4739997A1EP-4739997-A1

Abstract

The invention relates to a method for identifying a microbial strain taking the form of a colony, comprising acquiring a set of at least three spectral channels of the colony contained in the visible and infrared spectrum; and making, by means of a computer, a prediction of the species depending on the acquired spectral channels. The three channels of said set that contribute the most to the performance of the prediction are selected from a first spectral band [730-780] nm and from a second spectral band [550-650] nm.

Inventors

  • LEROUX, DENIS
  • LE MAUFF, Frédéric

Assignees

  • bioMérieux

Dates

Publication Date
20260513
Application Date
20240702

Claims (13)

  1. 1. Method for identifying a microbial strain in the form of a colony, comprising: A. acquisition of a set of at least three spectral channels of the colony included in the visible and infrared spectrum; B. the computer implementation of a prediction of the species based on the acquired spectral channels, characterized in that the three channels of said set which contribute most to the performance of the prediction are chosen from: - a first spectral band [730-780]nm; - a second spectral band [550-660]nm.
  2. 2. Method for identifying a microorganism likely to be contained in a biological sample of a predefined type, comprising: A. the acquisition of at least one multispectral digital image of at most ten channels of at least one microbial colony having grown on a culture medium following the spreading of the sample on said medium; B. the prediction, implemented by computer, of the microbial species forming said colony among a predetermined panel of microbial species as a function of the digital multispectral image(s) acquired; characterized in that: - the panel of microbial species, the optical filters and the identification algorithm are chosen so that the specificity of the identification is greater than or equal to 90%, and preferably greater than or equal to 94%; - if the prediction model delivers the identity of a species o then said identity is confirmed without implementing another method of identifying the microorganism; o otherwise another method of identifying the microorganism is implemented.
  3. 3. Method according to claim 1 or 2, characterized in that each spectral channel has a width between 8nm and 50nm.
  4. 4. Method according to claim 1, 2 or 3, in which said set of channels comprises a fourth channel contributing most to the performance of the prediction included in the second spectral band.
  5. 5. Method according to one of the preceding claims, in which said set of channels comprises a fourth channel contributing most to the performance of the prediction included in the spectral band [490-540]nm.
  6. 6. Method according to one of the preceding claims, characterized in that - the acquisition is carried out by means of a monochromatic image sensor in front of which are removably positioned band-pass filters corresponding to the spectral channels; and - the spectral width at mid-height of said filters is between 8nm and 50nm.
  7. 7. Method according to any one of the preceding claims, characterized in that the set of spectral channels comprises at most 10 channels, and preferably at most 8 spectral channels.
  8. 8. Method according to any one of the claims, characterized in that the prediction of the species of the bacterial strain implements a decision tree in which each node comprises a prediction made according to a single spectral channel of the set of spectral channels.
  9. 9. Method according to any one of the preceding claims, characterized in that the bacterial species is a uropathogen among the species Escherichia coli, Enterococcus faecalis. Staphylococcus aureus, Proteus mirabilis, Proteus vulgaris, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Streptococcus agalactiae.
  10. 10. Device for identifying a microbial colony from a predetermined panel of microbial species responsible for pathogenic infections of a predetermined type, in particular urinary infections, comprising: A. a digital camera configured to acquire a digital image of said colony; B. and a computer processing unit connected to said camera for receiving the digital image of the colony; characterized in that the digital camera comprises: A.1. a monochromatic image sensor capable of capturing incident light in the wavelength range [390-900] nm; A.2. a lens capable of forming an image on said sensor in said range; A.3.a set of not more than ten optical bandpass filters centred respectively on different wavelengths in the wavelength range [390-900] nm, each having a bandwidth in the range [8-50] nm, each said filters being configured to be removably placed in front of the objective so as to acquire a multispectral digital image of the microbial colony; and in that the three channels of said set which contribute most to the performance of the prediction are chosen from: - a first spectral band [730-780]nm; - a second spectral band [550-660]nm
  11. 11. Device for identifying a microbial colony from a predetermined panel of microbial species responsible for pathogenic infections of a predetermined type, in particular urinary infections, comprising: A. a digital camera configured to acquire a digital image of said colony; B. and a computer processing unit connected to said camera for receiving the digital image of the colony; characterized in that the digital camera comprises: A.1. a monochromatic image sensor capable of capturing incident light in the wavelength range [390-900] nm; A.2. a lens capable of forming an image on said sensor in said range; A.3.a set of at most ten optical bandpass filters respectively centered on different wavelengths of the wavelength range [390-900] nm, each having a bandwidth in the range [8-50] nm, each of said filters being configured to be removably placed in front of the objective so as to acquire a multispectral digital image of the microbial colony; in that the computer processing unit is configured to implement an algorithm for identifying the species forming the colony based on the digital images, in that the panel of microbial species corresponds to a prevalence of at least 70% of pathological infections, and preferably greater than or equal to 80%, and in that the panel of microbial species, the optical filters and the identification algorithm are chosen such that the specificity of the identification is greater than or equal to 90%, and preferably greater than or equal to 94%.
  12. 12. Device for characterizing a microbial colony, comprising: A. a digital camera configured to acquire a digital image of said colony; B. and a computer processing unit connected to said camera for receiving the digital image of the colony; characterized in that the digital camera comprises: A.1. a monochromatic image sensor capable of capturing incident light in the wavelength range [390-900] nm; A.2. a lens capable of forming an image on said sensor in said range; A.3.a set of up to ten optical bandpass filters, each having a bandwidth in the range [8-50]nm, each of said filters being configured to be removably placed in front of the objective so as to acquire a multispectral digital image of the microbial colony; in that the set of up to 10 filters comprises: A.3.1.a first filter centered on a wavelength in the range [415-440]nm; A.3.2.second filters centered respectively on different wavelengths of the wavelength range [390-900] nm and in that the computer processing unit is configured to identify: B.1.1e gram of the species forming the colony based on the digital image of said colony acquired using the first filter; B.2. the identity of the species forming the colony based on the digital images acquired using the second filters.
  13. 13. Device according to one of claims 10 to 12, characterized in that it is configured to implement a method according to one of claims 1 to 10.

Description

METHOD AND SYSTEM FOR IDENTIFYING MICROORGANISMS IN COLONY FORM FIELD OF THE INVENTION The invention relates to the field of microbiological analysis, and in particular to the identification of bacteria, yeasts and molds having grown in the form of a colony on a nutrient medium, for example poured into a Petri dish, and preferably a non-chromogenic, non-fluorogenic and dye-free nutrient medium. Advantageously, the invention can be implemented using a portable device such as a smartphone or tablet. STATE OF THE ART It is known that the visible and near infrared spectrum contains the information necessary for identifying the species of a bacterial colony grown on a culture medium, for example contained in a Petri dish, the medium and the dish being hereinafter referred to together as "Petri dish". For example, the Applicant achieves an accuracy of identification of the species forming a colony by analysis by means of automated learning of the image of this colony of about ten pixels taken by a hyperspectral camera with 240 spectral channels in the range [390-900] nm greater than 95%, very often greater than 98%. Reference may be made to the documents Feng, Y. Z & al., "Invasive weed optimization for optimizing one -agar -for -all classification of bacterial colonies based on hyperspectral imaging. "? Sensors and Actuators B-Chemical (2018) 269: 264-270 and the document "Hyperspectral image analysis for rapid and accurate discrimination of bacterial infections: A benchmark study" by Arrigoni et al., Computers in Biology and Medicine 88 (2017) Although hyperspectral technology is now mature and inexpensive, with a camera of this type costing around ten thousand euros, it remains inaccessible in many situations, particularly in developing countries. In addition to the cost, which remains too high, hyperspectral technology is also too immobile. The cameras, which are bulky, remain permanently in laboratories, while microbiologists travel to reach patients located in remote areas of the country. In this context, there is a need for identification that can be carried out by means of even less expensive, mobile, space-saving devices that perform all of the identification work on their own. identification, from image capture to analysis rendering, and this with performances equal to or very close to those obtained by the use of hyperspectral imaging having hundreds of spectral channels. PRESENTATION OF THE INVENTION The aim of the present invention is to propose an efficient method for identifying microorganisms in the form of colonies by analyzing a limited number of channels in the visible and near infrared. For this purpose, the invention relates to a method for identifying a microbial strain in the form of a colony, comprising: A. the acquisition of a set of at least three spectral channels of the colony included in the visible and infrared spectrum; and B. computer implementation of a species prediction based on the acquired spectral channels. According to the invention, the three channels of said set which contribute most to the performance of the prediction are chosen from: - a first spectral band [730-780]nm; - a second spectral band [550-650]nm. The invention also relates to a method for identifying a microorganism likely to be contained in a biological sample of a predefined type, comprising: A. the acquisition of at least one multispectral digital image of at most ten channels of at least one microbial colony having grown on a culture medium following the spreading of the sample on said medium; B. the prediction, implemented by computer, of the microbial species forming said colony among a predetermined panel of microbial species based on the digital multispectral image(s) acquired; According to the invention, the panel of microbial species, the optical filters and the identification algorithm are chosen so that the specificity of the identification is greater than or equal to 90%, and preferably greater than or equal to 94%; - if the prediction model delivers the identity of a species o then said identity is confirmed without implementing another method of identifying the microorganism; o otherwise another method of identifying the microorganism is implemented. The invention also relates to a device for identifying a microbial colony from a predetermined panel of microbial species responsible for pathogenic infections of a predetermined type, in particular urinary infections, comprising: A. a digital camera configured to acquire a digital image of said colony; B. and a computer processing unit connected to said camera for receiving the digital image of the colony; According to the invention, the digital camera comprises: A.1. a monochromatic image sensor capable of capturing incident light in the wavelength range [390-900] nm; A.2. a lens capable of forming an image on said sensor in said range; A.3.a set of up to ten optical bandpass filters respectively centered on different wavelengths of the wavelen