chemosensors Review Advances in Antimicrobial Resistance Monitoring Using Sensors and Biosensors: A Review Eduardo C. Reynoso 1 , Serena Laschi 2, Ilaria Palchetti 3,* and Eduardo Torres 1,4 1 Ciencias Ambientales, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; [email protected] (E.C.R.); [email protected] (E.T.) 2 Nanobiosens Join Lab, Università degli Studi di Firenze, Viale Pieraccini 6, 50139 Firenze, Italy; [email protected] 3 Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy 4 Centro de Quìmica, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico * Correspondence: ilaria.palchetti@unifi.it Abstract: The indiscriminate use and mismanagement of antibiotics over the last eight decades have led to one of the main challenges humanity will have to face in the next twenty years in terms of public health and economy, i.e., antimicrobial resistance. One of the key approaches to tackling an- timicrobial resistance is clinical, livestock, and environmental surveillance applying methods capable of effectively identifying antimicrobial non-susceptibility as well as genes that promote resistance. Current clinical laboratory practices involve conventional culture-based antibiotic susceptibility testing (AST) methods, taking over 24 h to find out which medication should be prescribed to treat the infection. Although there are techniques that provide rapid resistance detection, it is necessary to have new tools that are easy to operate, are robust, sensitive, specific, and inexpensive. Chemical sensors and biosensors are devices that could have the necessary characteristics for the rapid diag- Citation: Reynoso, E.C.; Laschi, S.; nosis of resistant microorganisms and could provide crucial information on the choice of antibiotic Palchetti, I.; Torres, E. Advances in (or other antimicrobial medicines) to be administered. This review provides an overview on novel Antimicrobial Resistance Monitoring biosensing strategies for the phenotypic and genotypic determination of antimicrobial resistance and Using Sensors and Biosensors: A a perspective on the use of these tools in modern health-care and environmental surveillance. Review. Chemosensors 2021, 9, 232. https://doi.org/10.3390/ chemosensors9080232 Keywords: antimicrobial resistance; sensor; biosensor; antibiotic susceptibility test; phenotypic technique; genotypic technique Academic Editor: Philip Gardiner Received: 5 July 2021 Accepted: 16 August 2021 1. Antimicrobial Resistance Published: 19 August 2021 In recent years, antimicrobial resistance (AMR) has received a great deal of attention because of the impact resistant microorganisms have on public health. Consequently, Publisher’s Note: MDPI stays neutral it has been declared as a global public health concern [1–7]. According to the World with regard to jurisdictional claims in Health Organization (WHO), antimicrobial resistance occurs when bacteria adapt and published maps and institutional affil- grow in the presence of an antimicrobial (AM) agent [8]. It can also be described as a iations. phenomenon when microorganisms (bacteria, viruses, fungi, and parasites) are no longer affected by an AM to which it was previously sensitive, as a result of mutation of the microorganism to evade the effect of the antimicrobial or of the acquisition of the resistance gene [9,10]. It is estimated that by 2050, human deaths related to AMR will amount to Copyright: © 2021 by the authors. 10 million, resulting in an economic cost of about 100 billion dollars [11]. Although, there Licensee MDPI, Basel, Switzerland. is compelling economic justification for the development of new generations of antibiotics This article is an open access article by 2030 [12], the acquisition rate of biological resistance to new drugs is now a major distributed under the terms and consideration in preventing their introduction [7,13,14]. conditions of the Creative Commons The WHO has established a list of antimicrobials (limited to antibiotics) that are Attribution (CC BY) license (https:// important in human medicine and in veterinary practice. The top priority antimicrobials creativecommons.org/licenses/by/ are cephalosporins (3rd, 4th, and 5th generation), glycopeptides, macrolides and ketolides, 4.0/). Chemosensors 2021, 9, 232. https://doi.org/10.3390/chemosensors9080232 https://www.mdpi.com/journal/chemosensors Chemosensors 2021, 9, x FOR PEER REVIEW 2 of 28 Chemosensors 2021, 9,The 232 WHO has established a list of antimicrobials (limited to antibiotics) that are 2 of 27 important in human medicine and in veterinary practice. The top priority antimicrobials are cephalosporins (3rd, 4th, and 5th generation), glycopeptides, macrolides and ketolides, polymyxinspolymyxins and quinolones and quinolones [4,15 [4]., 15In]. 2017, In 2017, the the WHO WHO published published a a list list of of priority pathogens pathogens resistantresistant to antibiotics; to antibiotics; on this on this list, list, 12 12 families families of of ba bacteriacteria are are selected selected for for the the research and research and developmentdevelopment of of new new antibioticsantibiotics due due to theto the growing growing need forneed innovative for innovative treatments against treatments againstmulti-resistant multi-resistant bacteria bacteria in hospital in hospital environments environments (Figure 1(Figure)[16,17 ].1) [16,17]. Priority 3: MEDIUM Streptococcus pneumoniae (penicillin-non-susceptible) Haemophilus influenzae (amplicillin-resistant) Priority 1: CRITYCAL Shigella spp. Acinetobacter baumannii (carbapenem- (fluoroquinolone-resistant) resistant) Pseudomonas auruginosa (carbapenem- resistant) Priority 2: HIGH Enterococcus faecium (vancomycin- Enterobacteriaceae (carbapenem-resistant, resistant) ESBL-producing) Staphylococcus aureus (methicillin- resistant, vancomycin-intermediate and resistant) Helicobacter pylori (clarithromycin- resistant) Campylobacter spp. (fluoroquinolone- resistant) Salmonellae (fluoroquinolone-resistant) Neisseria gonorrhoeae (cephalosporin- resistant, fluoroquinolone-resistant) Figure 1. ListFigure of priority 1. List of pathogens priority pathogens for research for research and development and development of new of newantibiotics. antibiotics. One of the leadingOne causes of the contributing leading causes to contributing the global increase to the global in AMR increase is the in AMR empirical is the empirical use of broad-spectrumuse of broad-spectrum AMs in clinica AMsl inand clinical veterinary and veterinary practices practices [18]. [ 18For]. For the the early early detection detection of microorganisms,of microorganisms, for the for prevention the prevention of diseases of diseases and and spread spread of of AMR, AMR, it it is is essential to have well-equipped laboratories specialized in the diagnosis of infections [19]. It is essential to have well-equipped laboratories specialized in the diagnosis of infections [19]. difficult to meet this requirement in developing countries because of the lack of funds, It is difficult to meetshortage this requirement of trained personnel, in developing and lack countries of the required because infrastructures. of the lack of Accordingfunds, to the shortage of trainedEuropean personnel, Committee and lack on Antimicrobial of the required Susceptibility infrastructures. Testing (EUCAST)According guidelines, to the reliable European Committeeantimicrobial on Antimicrobial resistance tests Susceptibility require phenotypic Testing evaluation, (EUCAST) i.e., experimental guidelines, procedures reliable antimicrobialto monitor resistance the microbial tests require growth phenotypic in presence of evaluation, AM. The routine i.e., experimental procedure to determine procedures to monitorif a pathogen the microbial is resistant growth is through in presence isolation, of AM. including The routine enrichment procedure culture to (i.e., urine determine if a pathogenculture) is and resistant plate cultivation, is through identification isolation, including and finally enrichment antimicrobial culture susceptibility (i.e., testing urine culture) and(AST) plate using cultivation, different identification AM loads. The and results finally can beantimicrobial expressed as thesusceptibility lowest concentration of the antibiotic that prevents visible growth, i.e., the minimal inhibitory concentration testing (AST) using different AM loads. The results can be expressed as the lowest (MIC) [20]. ASTs based on culturing methods require from 24 to 72 h. This time lapse can be concentration of crucialthe antibiotic for the patient that prevents [21,22]. Another visible disadvantagegrowth, i.e., ofthe culturing-based minimal inhibitory techniques is that concentration (MIC)trained [20] personnel. ASTs based is required on culturing [23]. The methods disk diffusion require test, from introduced, 24 to in72 theh. 1960sThis by Bauer time lapse can beand crucial Kirby for to the determine patient [ the21,22 susceptibility]. Another todisadvantage antibiotics in ofStaphylococcus culturing-based strains , is still techniques is thatone trained of the personnel most frequently is required used phenotypic [23]. The methoddisk diffusion for AST [test,24,25 introduced,]. Broth microdilution in the 1960s byassays Bauer is anotherand Kirby commonly to determine used technique the [susceptibility26,27], based on to visually antibiotics identifiable in growth. Staphylococcus strainsAutomated,