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 Control , 8 ,
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