References
[1] Cormier, A., Zhang, P. L., Chalmers, G., Weese, J. S., Deckert, A., Mulvey, M., McAllister T., Boerlin, P. (2019). Diversity of CTX-M-positive Escherichia coli recovered from animals in Canada.Vet Microbiol , 231, 71-75. https://doi.org/10.1016/j.vetmic.2019.02.031
[2] Carvalho, I., Carvalho, J. A., Martínez-Álvarez, S., Sadi, M., Capita, R., Alonso-Calleja, C., Rabbi F, Dapkevicius MdLNE, Igrejas G, Torres C, Poeta, P. (2021). Characterization of ESBL-producingEscherichia coli and Klebsiella pneumoniae isolated from clinical samples in a northern Portuguese hospital: predominance of CTX-M-15 and high genetic diversity. Microorganisms , 9(9), 1914. https://doi.org/10.3390/microorganisms9091914
[3] Tian, M., He, X., Feng, Y., Wang, W., Chen, H., Gong, M., Liu, D., Clarke, J.L., van Eerde, A. (2021). Pollution by antibiotics and antimicrobial resistance in livestock and poultry manure in China, and Countermeasures. Antibiotics, 10, 539. https://doi.org/10.3390/antibiotics10050539
[4] Zhang, P.L., Shen, X., Chalmers, G., Reid-Smith, R.J., Slavic, D., Dick, H., Boerlin, P. (2018). Prevalence and mechanisms of extended spectrum cephalosporin resistance in clinical and fecal Enterobacteriaceae isolates from dogs in Ontario, Canada. Vet Microbiol, 213, 82–88. https://doi.org/10.1016/j.vetmic.2017.11.020
[5] Hernando-Amado, S., Coque, T. M., Baquero, F., Martínez, J. L. (2019). Defining and combating antibiotic resistance from One Health and Global Health perspectives. Nat. Microbiol, 4(9), 1432-1442. https://doi.org/10.1038/s41564-019-0503-9
[6] Taban, B. M., Numanoglu Cevik, Y. (2021). The efficiency of MALDI-TOF MS method in detecting Staphylococcus aureus isolated from raw milk and artisanal dairy foods. CyTA-J Food , 19(1), 739-750. https://doi.org/10.1080/19476337.2021.1977392
[7] Cheng, K., Chui, H., Domish, L., Hernandez, D., Wang, G. (2016). Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria. Proteomics–Clin Appl.10(4), 346-357. https://doi.org/10.1002/prca.201500086
[8] Stępień-Pyśniak, D., Hauschild, T., Dec, M., Marek, A., Urban-Chmiel, R., & Kosikowska, U., (2021). Phenotypic and genotypic characterization of Enterococcus spp. from yolk sac infections in broiler chicks with a focus on virulence factors. Poult Sci, 100(4), 100985. https://doi.org/10.1016/j.psj.2021.01.008
[9] Ha, S., M., Kim, C., K., Roh, J., Byun, J. H., Yang, S. J., Choi, S. B., Chun, J., Yong, D. (2019). Application of the whole genome-based bacterial identification system, TrueBac ID, using clinical isolates that were not identified with three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems. Ann Lab Med, 39(6), 530-536. https://doi.org/10.3343/alm.2019.39.6.530
[10] Cherkaoui, A., Hibbs, J., Emonet, S., Tangomo, M., Girard, M., Francois, P., & Schrenzel, J. (2010). Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry methods with conventional phenotypic identification for routine identification of bacteria to the species level. J. Clin. Microbiol, 48(4), 1169-1175. https://doi.org/10.1128/JCM.01881-09
[11] Faron, M.L., Buchan, B.W., Hyke, J., Madisen, N., Lillie, J.L., Granato, P.A, et al. (2015). Multicenter evaluation of the Bruker MALDI biotyper CA system for the identification of clinical aerobic gram-negative bacterial isolates. PLoS One 10, e0141350. https://doi.org/10.1371/journal.pone.0141350
[12] Clark, C. M., Costa, M. S., Sanchez, L. M., & Murphy, B. T. (2018). Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function.Proc. Natl. Acad. Sci, 115(19), 4981-4986. https://doi.org/10.1073/pnas.1801247115
[13] Suen, L., Siu, G., Guo, Y.P., Yeung, S., Lo, K., O’Donoghue, M. (2019). The public washroom - friend or foe? An observational study of washroom cleanliness combined with microbiological investigation of hand hygiene facilities. Antimicrob. Resist. Infect. Control 8, 47. https://doi.org/10.1186/s13756-019-0500-z
[14] Hou, T. Y., Chiang-Ni, C., Teng, S. H. (2019). Current status of MALDI-TOF mass spectrometry in clinical microbiology. J Food Drug Anal. 27(2), 404-414. https://doi.org/10.1016/j.jfda.2019.01.001
[15] Elbehiry, A., Marzouk, E., Abdeen, E., Al‐Dubaib, M., Alsayeqh, A., Ibrahem, M., Hamada, M., Alenzi, A., Moussa, I., Hemeg, H. A. (2019). Proteomic characterization and discrimination ofAeromonas species recovered from meat and water samples with a spotlight on the antimicrobial resistance of Aeromonas hydrophila.Microbiologyopen , 8(11), e782. https://doi.org/10.1002/mbo3.782
[16] Pantucek, R., Sedlacek, I., Indrakova, A., Vrbovska, V., Maslanova, I., Kovarovic, V., Svec, P., Kralova, S., Kristofova, L., Keklakova, J., Petras, P., Doskar, J. (2018). Staphylococcus edaphicus sp. nov., isolated in Antarctica, harbours mecC gene and genomic islands with suspected role in adaptation to extreme environment. Appl. Environ. Microbiol. 84 https://doi.org/10.1128/AEM.01746-17. AEM.01746-17
[17] Alharbi, A., Al-Dubaib, M., Elhassan, M. A., Elbehiry, A. (2021). Comparison of MALDI-TOF mass spectrometry with phenotypic methods for identification and characterization of Staphylococcus aureus causing mastitis. Trop. Biomed , 38(2), 9-24. https://doi.org/10.47665/tb.38.2.032
[18] Suzuki, Y., Niina, K., Matsuwaki, T., Nukazawa, K., & Iguchi, A. (2018). Bacterial flora analysis of coliforms in sewage, river water, and ground water using MALDI-TOF mass spectrometry. J. Environ. Sci. Health A. 53(2), 160-173. https://doi.org/10.1080/10934529.2017.1383128
[19] Jančová, P., Pachlová, V., Čechová, E., Cedidlová, K., Šerá, J., Pištěková, H., Buňka, F., Buňková, L. (2020). Occurrence of biogenic amines producers in the wastewater of the dairy industry.Molecules. 25, 5143. https://doi.org/10.3390/molecules25215143
[20] Ogutcu, H., Kantar, F., Alaylar, B., Numanoglu Cevik, Y., Gulluce, M. (2022). Isolation and characterization of hydrocarbon and petroleum degrading bacteria from polluted soil with petroleum and derivatives by MALDI-TOF MS method. Geomicrobiol J. 1-10. https://doi.org/10.1080/01490451.2022.2074575
[21] Araújo, T. M. C., Pereira, R. D. C. L., Freitag, I. G. R., Rusak, L. A., Botelho, L. A. B., Hofer, E., Hofer C. B., Vallim, D. C. (2020). Evaluation of MALDI–TOF MS as a tool for detection of Listeria spp. directly from selective enrichment broth from food and stool samples. J. Microbiol. Methods , 173, 105936. https://doi.org/10.1016/j.mimet.2020.105936
[22] Nees, M., Hess, M., Hess, C. (2022). Discrimination and characterization of Escherichia coli originating from clinical cases of femoral head necrosis in broilers by maldi-tof mass spectrometry confirms great heterogeneity of isolates.Microorganisms. 10, 1472. https://doi.org/10.3390/microorganisms10071472
[23] Dandachi, I., Sokhn, E. S., Dahdouh, E. A., Azar, E., El-Bazzal, B., Rolain, J. M., Daoud, Z. (2018). Prevalence and characterization of multi-drug-resistant gram-negative bacilli isolated from lebanese poultry: A nationwide study. Front. Microbiol. 9, 550. https://doi.org/10.3389/fmicb.2018.00550
[24] Krieg, N., Holt, J. (2005). Facultatively anaerobic gram-negative rods. Family I. Enterobacteriaceae. Bergey’s Manual of Systematic Bacteriology. Baltimore. Williams & Wilkins 1, 408–420.
[25] Wilson, G., McCabe, D. (2007). The use of antibiotic-containing agars for the isolation of extended-spectrum β-lactamase-producing organisms in intensive care units. Clin. Microbiol. Infect,13(4), 451-453. https://doi.org/10.1111/j.1469-0691.2006.01667.x
[26] Clinical and Laboratory Standards Institute (CLSI), 2018. M100S 28th Edition. Wayne, PA:Quinn PJ, Carter ME, Markey B, Carter GR. Clinical Veterinary Microbiology. London: Wolfe Publishing; 1994. p. 42-126.
[27] Saladin M., Cao V.T., Lambert T., Donay J.L., Herrmann J.L., Ould-Hocine Z. Verdet, C., Françoise Delisle, F., Philippon, A., Arlet G. (2002). Diversity of CTX-M β-lactamases and their promoter regions from Enterobacteriaceae isolated in three Parisian hospitals. FEMS Microbiol Lett, 209(2), 161-8. https://doi.org/10.1111/j.1574-6968.2002.tb11126.x
[28] Woodford, N., Fagan, E.J., Ellington, M.J. (2006). Multiplex PCR for rapid detection of genes encoding CTX-M extended-spectrum β-lactamases. J Antimicrob Chemother, 57(1), 154- 5. https://doi.org/10.1093/jac/dki412
[29] Dhanji, H., Doumith, M., Clermont, O., Denamur, E., Hope, R., Livermore, D. M., Woodford, N. (2010). Real-time PCR for detection of the O25b-ST131 clone of Escherichia coli and its CTX-M-15-like extended-spectrum β-lactamases. Int. J. Antimicrob. Agents, 6(4), 355-358. https://doi.org/10.1016/j.ijantimicag.2010.06.007
[30] Chanawong A., M’Zali F.H., Heritage J., Lulitanond A., Hawkey P.M. (2000). Characterisation of extended-spectrum β-lactamases of the SHV family using a combination of PCR-single strand conformational polymorphism (PCR-SSCP) and PCR-restriction fragment length polymorphism (PCR-RFLP). FEMS Microbiol Lett, 184(1), 85-9. https://doi.org/10.1111/j.1574-6968.2000.tb08995.x
[31] Vahaboglu H., Ozturk R., Akbal H., Saribas S., Tansel O., Coskunkan F. (1998). Practical approach for detection and identification of OXA-10-derived ceftazidime-hydrolyzing extended-spectrum β-lactamases. J Clin Microbiol, 36(3), 827-9. https://doi.org/10.1128/JCM.36.3.827-829.1998
[32] Arlet G., Rouvea M., Casin I., Bouvet P.J., Lagrange P.H., Philippon A. (1994). Molecular epidemiology of Klebsiella pneumoniae strains that produce SHV-4 β-lactamase and which were isolated in 14 French hospitals. J Clin Microbiol, 32, 2553-8. https://doi.org/10.1128/jcm.32.10.2553-2558.1994
[33] Pérez-Pérez F.J., Hanson N.D. (2002). Detection of plasmid-mediated AmpC β-lactamase genes in clinical isolates by using multiplex PCR. J Clin Microbiol. 40(6), 2153-62. https://doi.org/10.1128/JCM.40.6.2153-2162.2002
[34] Szabados, F., Tix, H., Anders, A., Kaase, M., Gatermann, S. G., Geis, G. (2012). Evaluation of species-specific score cutoff values of routinely isolated clinically relevant bacteria using a direct smear preparation for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based bacterial identification. Eur. J. Clin. Microbiol. Infect. Dis. 31, 1109-1119. https://doi.org/10.1007/s10096-011-1415-7
[35] Oviaño, M., Sparbier, K., Barba, M. J., Kostrzewa, M., Bou, G. (2016). Universal protocol for the rapid automated detection of carbapenem-resistant Gram-negative bacilli directly from blood cultures by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Int. J. Antimicrob. Agents, 48(6), 655-660. https://doi.org/10.1016/j.ijantimicag.2016.08.024
[36] Samad, R. A., Al Disi, Z., Ashfaq, M. Y. M., Wahib, S. M., & Zouari, N. (2020). The use of principle component analysis and MALDI-TOF MS for the differentiation of mineral forming Virgibacillus andBacillus species isolated from sabkhas. RSC Advances,  10(25), 14606- https://doi.org/14616.10.1039/D0RA01229G
[37] Zhang, H., Yamamoto, E., Murphy, J., & Locas, A. (2020). Microbiological safety of ready-to-eat fresh-cut fruits and vegetables sold on the Canadian retail market.  Int. J. Food Microbiol,  335, 108855. https://doi.org/10.1016/j.ijfoodmicro.2020.108855
[38] Yang, F., Zhang, Sd., Shang, X., Wang, X., Wang, L., Yan, Z., Li, H. (2018). Prevalence and characteristics of extended spectrum β-lactamase-producing Escherichia coli  from bovine mastitis cases in China. J. Integr. Agric, 17(6), 1246-1251. https://doi.org/10.1016/S2095-3119(17)61830-6
[39] Badr, H., Reda, R. M., Hagag, N. M., Kamel, E., Elnomrosy, S. M., Mansour, A. I., Shahein, M.A., Ali S. F., Ali, H. R. (2022). Multidrug-resistant and genetic characterization of extended-spectrum beta-lactamase-producing E. coli recovered from chickens and humans in Egypt. Animals , 12(3), 346. https://doi.org/10.3390/ani12030346
[40] Gazal, L. E. D. S., Medeiros, L. P., Dibo, M., Nishio, E. K., Koga, V. L., Gonçalves, B. C., Grassotti T.T., Camargo T.C.L., Pinherio J. J., Vespero, Brito K. C. T., Brito B. G., Nakazato, G., Kobayashi, R. K. T. (2021). Detection of ESBL/AmpC-producing and fosfomycin-resistantEscherichia coli from different sources in poultry production in Southern Brazil. Front in Microbiol, 11, 604544. https://doi.org/10.3389/fmicb.2020.604544
[41] Fournier, C., Aires-de-Sousa, M., Nordmann, P., Poirel, L., 2020. Occurrence of CTX-M-15-and MCR-1-producing Enterobacterales in pigs in Portugal: Evidence of direct links with antibiotic selective pressure. Int. J. Antimicrob. Agents, 55(2), 105802. https://doi.org/10.1016/j.ijantimicag.2019.09.006
[42] Higgins, O., Chueiri, A., O’Connor, L., Lahiff, S., Burke, L., Morris, D., Pfeifer N.M., Smith, T. J. (2022). Portable differential detection of CTX-M ESBL gene variants, bla ctx-m-1and bla ctx-m-15, from Escherichia coliisolates and animal fecal samples using loop-primer endonuclease cleavage loop-mediated isothermal amplification. Microbiol Spectr, e03316-22. https://doi.org/10.1128/spectrum.03316-22
[43] Gajdács, M., Ábrók, M., Lázár, A., Burián, K. (2020). Differential epidemiology and antibiotic resistance of lactose-fermenting and non-fermenting Escherichia coli: Is it just a matter of taste?. Biol Futura.  71, 175-182. https://doi.org/10.1007/s42977-020-00016-6
[44] Sun, H. (2022). Equilibrium properties of E. colilactose permease symport—A random-walk model approach. PloS One , 17(2), e0263286. https://doi.org/10.1371/journal.pone.0263286
[45] Ank, N., Sydenham, T.V., Iversen, L.H., Justesen, U.S., Wang, M. (2015). International journal of antimicrobial agents characterisation of a multidrug-resistant Bacteroides fragilis isolate recovered from blood of a patient in Denmark using whole-genome sequencing. Int. J. Antimicrob. Agents, 46, 117–120. https://doi.org/10.1016/j. ijantimicag.2015.02.024.
[46] Vrioni, G., Tsiamis, C., Oikonomidis, G., Theodoridou, K., Kapsimali, V., Tsakris, A., 2018. MALDI-TOF mass spectrometry technology for detecting biomarkers of antimicrobial resistance: current achievements and future perspectives. Ann. Transl. Med, 6, 240. https://doi.org/10.21037/atm.2018.06.28
[47] Flores-Trevino, S., Garza-Gonzalez, E., Mendoza-Olazar´ an, S., Morfín-Otero, R., Camacho-Ortiz, A., Rodríguez-Noriega, E., Bocanegra-Ibarias, P. (2019). Screening of biomarkers of drug resistance or virulence in ESCAPE pathogens by MALDI-TOF mass spectrometry.Sci. Rep, 9, 1–10. https://doi.org/10.1038/s41598-019-55430-1
[48] Doukyu, N., Taguchi, K. (2021). Involvement of catalase and superoxide dismutase in hydrophobic organic solvent tolerance ofEscherichia coli.  AMB Express , 11(1), 1-11. https://doi.org/10.1186/s13568-021-01258-w
[49] Schwidder, M., Heinisch, L., Schmidt, H. (2019). Genetics, toxicity, and distribution of enterohemorrhagic Escherichia colihemolysin. Toxins, 11(9), 502. https://doi.org/10.3390/toxins11090502
[50] Ndegwa, E., Alahmde, A., Kim, C., Kaseloo, P., O’Brien, D. (2020). Age related differences in phylogenetic diversity, prevalence of Shiga toxins, Intimin, Hemolysin genes and select serogroups ofEscherichia coli from pastured meat goats detected in a longitudinal cohort study. BMC Vet Res,  16(1), 1-15. https://doi.org/10.1186/s12917-020-02479-0
[51] Rezwan, F., Lan, R., & Reeves, P. R. (2004). Molecular basis of the indole-negative reaction in Shigella strains: extensive damages to the tna operon by insertion sequences. J. Bacteriol.  186(21), 7460-7465. https://doi.org/10.1128/JB.186.21.7460-7465.2004
[52] Torres-Corral, Y., Santos, Y. (2022). Predicting antimicrobial resistance of Lactococcus garvieae: PCR detection of resistance genes versus MALDI-TOF protein profiling. Aquaculture, 553, 738098. https://doi.org/10.1016/j.aquaculture.2022.738098
[53] Ashfaq, M. Y., Da’na, D. A., & Al-Ghouti, M. A. (2022). Application of MALDI-TOF MS for identification of environmental bacteria: A review. J. Environ. Manage , 305, 114359. https://doi.org/10.1016/j.jenvman.2021.114359
[54] Ribeiro, D.G., Carmo, L., Santos, I.R., Almeida, R.F., Silva, L.P., Oliveira-Neto, O.B., Scherwinski-Pereira, J.E., Mehta, A. (2020). MALDI TOF MS-profiling: applications for bacterial and plant sample differentiation and biological variability assessment. J. Proteonomics, 213, 103619. https://doi.org/10.1016/j.jprot.2019.103619.
[55] Macek, B., Forchhammer, K., Hardouin, J., Weber-Ban, E., Grangeasse, C., Mijakovic, I. (2019). Protein post-translational modifications in bacteria. Nat Rev Microbiol, 17(11), 651-664. https://doi.org/10.1038/s41579-019-0243-0
[56] Ranjbar, R., Farahani, A. (2019). Study of genetic diversity, biofilm formation, and detection of Carbapenemase, MBL, ESBL, and tetracycline resistance genes in multidrug-resistant Acinetobacter baumannii isolated from burn wound infections in Iran. Antimicrobial Resistance & Infection Control8 , 1-11. https://doi.org/10.1186/s13756-019-0612-5
[57] Silago, V., Kovacs, D., Samson, H., Seni, J., Matthews, L., Oravcová, K., Lupindu, A.M., Hoza, A.S., Mshana, S.E. (2021). Existence of multiple ESBL genes among phenotypically confirmed ESBL producingKlebsiella pneumoniae and Escherichia coli concurrently isolated from clinical, colonization and contamination samples from Neonatal Units at Bugando Medical Center, Mwanza, Tanzania.Antibiotics, 10, 476. https://doi.org/10.3390/antibiotics10050476
[58] Wibisono, F. J., Sumiarto, B., Untari, T., Effendi, M. H., Permatasari, D. A., Witaningrum, A. M. (2020). CTX Gene of extended spectrum beta-lactamase (ESBL) producing Escherichia coli on broilers in Blitar, Indonesia. Sys Rev Pharm, 11(7).
[59] Laudy, A. E., Róg, P., Smolińska-Król, K., Ćmiel, M., Słoczyńska, A., Patzer, J., Dzierżanowska, D., Wolinowska, R., Starościak, B., Tyski, S. (2017). Prevalence of ESBL-producingPseudomonas aeruginosa isolates in Warsaw, Poland, detected by various phenotypic and genotypic methods. PloS one, 12(6), e0180121. https://doi.org/10.1371/journal.pone.0180121
[60] Tang, W., Ranganathan, N., Shahrezaei, V., & Larrouy-Maumus, G. (2019). MALDI-TOF mass spectrometry on intact bacteria combined with a refined analysis framework allows accurate classification of MSSA and MRSA. PloS one,  14(6), e0218951. https://doi.org/10.1371/journal.pone.0218951