diagnostics Article Evaluation of MicroScan Bacterial Identification Panels for Low-Resource Settings Sien Ombelet 1,2,* , Alessandra Natale 3, Jean-Baptiste Ronat 3,4,5, Olivier Vandenberg 6,7,8 , Liselotte Hardy 1 and Jan Jacobs 1,2 1 Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; [email protected] (L.H.); [email protected] (J.J.) 2 Immunology & Microbiology Department, KU Leuven, 3000 Leuven, Belgium 3 Médecins Sans Frontières, Operational Center Paris, 75019 Paris, France; [email protected] (A.N.); [email protected] (J.-B.R.) 4 Team ReSIST, INSERM U1184, School of Medicine, University Paris-Saclay, 94807 Villejuif, France 5 Bacteriology-Hygiene Unit, Assistance Publique—Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France 6 Center for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium; [email protected] 7 Innovation and Business Development Unit, Laboratoire Hospitalier Universitaire de Bruxelles—Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium 8 Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London WC1E 6BT, UK * Correspondence: [email protected] Abstract: Bacterial identification is challenging in low-resource settings (LRS). We evaluated the Mi- croScan identification panels (Beckman Coulter, Brea, CA, USA) as part of Médecins Sans Frontières’ Mini-lab Project. The MicroScan Dried Overnight Positive ID Type 3 (PID3) panels for Gram-positive Citation: Ombelet, S.; Natale, A.; organisms and Dried Overnight Negative ID Type 2 (NID2) panels for Gram-negative organisms were Ronat, J.-B.; Vandenberg, O.; Hardy, assessed with 367 clinical isolates from LRS. Robustness was studied by inoculating Gram-negative L.; Jacobs, J. Evaluation of MicroScan species on the Gram-positive panel and vice versa. The ease of use of the panels and readability of the Bacterial Identification Panels for instructions for use (IFU) were evaluated. Of species represented in the MicroScan database, 94.6% Low-Resource Settings. Diagnostics (185/195) of Gram-negative and 85.9% (110/128) of Gram-positive isolates were correctly identified 2021, 11, 349. https://doi.org/ 10.3390/diagnostics11020349 up to species level. Of species not represented in the database (e.g., Streptococcus suis and Bacillus spp.), 53.1% out of 49 isolates were incorrectly identified as non-related bacterial species. Testing Academic Editor: Raul Colodner of Gram-positive isolates on Gram-negative panels and vice versa (n = 144) resulted in incorrect identifications for 38.2% of tested isolates. The readability level of the IFU was considered too high Received: 17 January 2021 for LRS. Inoculation of the panels was favorably evaluated, whereas the visual reading of the panels Accepted: 17 February 2021 was considered error-prone. In conclusion, the accuracy of the MicroScan identification panels was Published: 19 February 2021 excellent for Gram-negative species and good for Gram-positive species. Improvements in stability, robustness, and ease of use have been identified to assure adaptation to LRS constraints. Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in Keywords: clinical bacteriology; low-resource settings; bacterial identification; blood cultures; Mi- published maps and institutional affil- croScan identification system iations. 1. Introduction Copyright: © 2021 by the authors. Bacterial Identification in Low-Resource Settings Licensee MDPI, Basel, Switzerland. Clinical bacteriology laboratories equipped to diagnose bacterial infections and per- This article is an open access article form antibiotic susceptibility testing (AST) are scarce in low-resource settings (LRS) [1,2]. distributed under the terms and conditions of the Creative Commons Correct identification of bacteria in clinical samples is a cornerstone for proper management Attribution (CC BY) license (https:// of bacterial infections because both empirical and directed antibiotic treatments depend on creativecommons.org/licenses/by/ the identified organism [3,4]. 4.0/). Diagnostics 2021, 11, 349. https://doi.org/10.3390/diagnostics11020349 https://www.mdpi.com/journal/diagnostics Diagnostics 2021, 11, x 2 of 20 Diagnostics 2021, 11, 349 Correct identification of bacteria in clinical samples is a cornerstone for proper manage-2 of 19 ment of bacterial infections because both empirical and directed antibiotic treatments de- pend on the identified organism [3,4]. CurrentCurrent “gold“gold standard”standard” identificationidentification methodsmethods inin high-resourcehigh-resource settings,settings, suchsuch asas matrix-assistedmatrix-assisted laser laser desorption/ionization desorption/ionization time-of-flight time-of-flight mass mass spectrometry spectrometry (MALDI-TOF (MALDI- MS)TOF and MS) molecular and molecular techniques techniques are not are adapted not adapted to diagnostic to diagnostic laboratories laboratories in LRS in [1 LRS,5]. Most [1,5]. laboratoriesMost laboratories in LRS in still LRS rely still onrely “conventional” on “conventional” phenotypic phenotypic identification identification techniques, techniques, in whichin which isolates isolates are inoculatedare inoculated on different on different culture culture media media containing containing different different carbohydrates carbohy- anddrates enzyme and enzyme substrates, substrates, and interpretation and interpretati of teston results of test is carriedresults outis carried using dichotomousout using di- decisionchotomous trees decision [6–8]. Commercializedtrees [6–8]. Commercialized panels consisting panels of consisting phenotypic of tests,phenotypic such as tests, the Analyticalsuch as the Profile Analytical Index (APIProfile®) panels Index (bioM(API®é)rieux, panels Marcy (bioMérieux, l’Etoile, France) Marcy offer l’Etoile, probability- France) basedoffer probability-based identification; combined identification; test results combined are compared test results to databases are compared containing to the databases profiles ofcontaining thousands the of profiles bacterial of isolates thousands [9]. of bacterial isolates [9]. InIn responseresponse toto thethe globalglobal riserise inin antimicrobialantimicrobial resistanceresistance andand thethe needneed toto implement implement context-tailoredcontext-tailored antibiotic antibiotic stewardship stewardship programs, programs, the non-governmentalthe non-governmental humanitarian humanitarian orga- nizationorganization Médecins Médecins Sans FrontiSans èFrontièresres (MSF) (MSF committed) committed to developing to developing an all-in-one, an all-in-one, affordable, af- andfordable, transportable and transportable clinical bacteriology clinical bacteriolo laboratory,gy laboratory, the Mini-lab the [ 10Mini-lab]. Because [10]. the Because Mini-lab the isMini-lab intended is forintended use in for LRS use by in non-expert LRS by non-ex laboratorypert laboratory technicians, technicians, a system fora system bacterial for identificationbacterial identification is required is that required is easy that to inoculate,is easy to easyinoculate, to read, easy inexpensive, to read, inexpensive, and with long and shelfwith life.long After shelf defining life. After technical defining specifications technical specifications (target product (target profile) product and performing profile) and a marketperforming analysis, a market the Dried analysis Overnight, the Dried MicroScan Overnight ID panels MicroScan by Beckman ID panels Coulter by (Brea, Beckman CA, USA)Coulter were (Brea, chosen CA, becauseUSA) were they chosen have abecause long shelf they life have and a can long be shelf read life without and can the be use read of automatedwithout the instruments. use of automated instruments. ToTo meetmeet Mini-lab Mini-lab specifications, specifications, Beckman Beckman Coulter Coulter developed developed a customized a customized “Research “Re- Usesearch Only” Use ID Only” panel ID containing panel containing all test wells all test for wells the identification for the identification of both Gram-negative of both Gram- andnegative Gram-positive and Gram-positive organisms organisms on one single on one panel, single coded panel, MSFNPID1. coded MSFNPID1. The Gram-negative The Gram- andnegative Gram-positive and Gram-positive test wells were test assembledwells were in assembled separate groups in separate on the groups panel, andon the therefore, panel, knowledgeand therefore, of the knowledge Gram stain of result the Gram is still stain essential result to readis still the essential panel correctly to read (Figure the panel1). The cor- primaryrectly (Figure objective 1). The of this primary study objective was to assess of this the study diagnostic was to accuracy assess the of diagnostic these identification accuracy panelsof these with identification clinical isolates panels originating with clinical from isolates LRS. A originating secondary from objective LRS. was A secondary to assess theob- easejective of usewas of to the assess system. the ease of use of the system. Figure 1. Example of an inoculated customized Médecins Sans Frontières (MSF) ID panel (MSFN- PID1): Gram-negative test wells on the top side and Gram-positive test wells on the opposite side. Gram-positive and Gram-negative test panels can thus be inoculated simultaneously; for reading, one of the two sides must be picked. Diagnostics