Andrews S (2010) FastQC: a quality control tool for high throughput sequence data.
Ayhan DH, Tamer YT, Akbar M, Bailey SM, Wong M, Daly SM, Greenberg DE, Toprak E (2016) Sequence-Specific Targeting of Bacterial Resistance Genes Increases Antibiotic Efficacy. PLoS Biol 14(9):e1002552. doi:10.1371/journal.pbio.1002552
Ayukekbong JA, Ntemgwa M, Atabe AN (2017) The threat of antimicrobial resistance in developing countries: causes and control strategies. Antimicrob Resist Infect Control 6:47. doi:10.1186/s13756-017-0208-x
Bahadur R, Chodisetti PK, Reddy M (2021) Cleavage of Braun's lipoprotein Lpp from the bacterial peptidoglycan by a paralog of l,d-transpeptidases, LdtF. Proc Natl Acad Sci U S A 118(19). doi:10.1073/pnas.2101989118
Bai Z, Ma W, Ma L, Velthof G, Wei Z, HavlÌk P, Oenema O, Lee MR, Zhang F (2018) China s livestock transition: Driving forces, impacts, and consequences. Sci Adv 4(7):eaar8534. doi: 10.1126/sciadv.aar8534
Baym M, Stone LK, Kishony R (2016) Multidrug evolutionary strategies to reverse antibiotic resistance. Science 351(6268):aad3292. doi:10.1126/science.aad3292
Bennion D, Charlson ES, Coon E, Misra R (2010) Dissection of β-barrel outer membrane protein assembly pathways through characterizing BamA POTRA 1 mutants of Escherichia coli. Mol Microbiol 77(5):1153-71. doi:10.1111/j.1365-2958.2010.07280.x
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114-20. doi:10.1093/bioinformatics/btu170
Broad Institute (2019) Picard toolkit. Broad Institute, GitHub repository
Browning DF, Matthews SA, Rossiter AE, Sevastsyanovich YR, Jeeves M, Mason JL, Wells TJ, Wardius CA, Knowles TJ, Cunningham AF, Bavro VN, Overduin M, Henderson IR (2013) Mutational and topological analysis of the Escherichia coli BamA protein. PLoS One 8(12):e84512. doi:10.1371/journal.pone.0084512
Cascales E, Lloubès R (2004) Deletion analyses of the peptidoglycan-associated lipoprotein Pal reveals three independent binding sequences including a TolA box. Mol Microbiol 51(3):873-85. doi:10.1046/j.1365-2958.2003.03881.x
Choi J, Yoo J, Lee M, Kim EG, Lee JS, Lee S, Joo S, Song SH, Kim EC, Lee JC, Kim HC, Jung YG, Kwon S (2014) A rapid antimicrobial susceptibility test based on single-cell morphological analysis. Sci Transl Med 6(267):267ra174. doi:10.1126/scitranslmed.3009650
Clarke DJ, Jacq A, Holland IB (1996) A novel DnaJ-like protein in Escherichia coli inserts into the cytoplasmic membrane with a type III topology. Mol Microbiol 20(6):1273-86. doi:10.1111/j.1365-2958.1996.tb02646.x
Clementz T, Zhou Z, Raetz CR (1997) Function of the Escherichia coli msbB gene, a multicopy suppressor of htrB knockouts, in the acylation of lipid A. Acylation by MsbB follows laurate incorporation by HtrB. J Biol Chem 272(16):10353-60. doi:10.1074/jbc.272.16.10353
Du D, Wang Z, James NR, Voss JE, Klimont E, Ohene-Agyei T, Venter H, Chiu W, Luisi BF (2014) Structure of the AcrAB-TolC multidrug efflux pump. Nature 509(7501):512-5. doi:10.1038/nature13205
Ebbensgaard A, Mordhorst H, Aarestrup FM, Hansen EB (2018) The Role of Outer Membrane Proteins and Lipopolysaccharides for the Sensitivity of Escherichia coli to Antimicrobial Peptides. Front Microbiol 9:2153. doi:10.3389/fmicb.2018.02153
European Union Regulations Commission (2010) Commission Regulation (EU) No 37/2010 of 22 December 2009 on pharmacologically active substances and their classification regarding maximum residue limits in foodstuffs of animal origin. Off J Eur Union 53(15):1-72
FAO-WHO (2018) Maximum Residue Limits (MRLs) and Risk Management Recommendations (RMRs) for Residues of Veterinary Drugs in Foods CX/MRL (2-2018). Codex Alimentarius, International Food Standards, Rome, Italy
Finlayson GD, Schiele B, Crowley JL Comprehensive colour image normalization. In, Berlin, Heidelberg, 1998. Computer Vision — ECCV'98. Springer Berlin Heidelberg, p 475-490
Founou LL, Founou RC, Essack SY (2016) Antibiotic Resistance in the Food Chain: A Developing Country-Perspective. Front Microbiol 7:1881. doi:10.3389/fmicb.2016.01881
Galili T (2015) dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics 31(22):3718-20. doi:10.1093/bioinformatics/btv428
Grennfelt P, Engleryd A, Forsius M, Hov Ø, Rodhe H, Cowling E (2020) Acid rain and air pollution: 50 years of progress in environmental science and policy. Ambio 49(4):849-864. doi:10.1007/s13280-019-01244-4
Guobiao standards (2019) National food safety standard—Maximum residue limits for veterinary drugs in foods (translated from Mandarin). In: Ministry of Agriculture and Rural Affairs of the People’s Republic of China, National Health Commission of the People’s Republic of China, State Administration for Market Regulation, (ed) GB 31650—2019.
Hassan MM, El Zowalaty ME, Lundkvist Å, Järhult JD, Khan Nayem MR, Tanzin AZ, Badsha MR, Khan SA, Ashour HM (2021) Residual antimicrobial agents in food originating from animals. Trends Food Sci Technol 111:141-150. doi:10.1016/j.tifs.2021.01.075
Hobbs EC, Yin X, Paul BJ, Astarita JL, Storz G (2012) Conserved small protein associates with the multidrug efflux pump AcrB and differentially affects antibiotic resistance. Proc Natl Acad Sci U S A 109(41):16696-701. doi:10.1073/pnas.1210093109
Hua Yan Water (2021) Ex-factory water report (translated from Mandarin). https://www.heisino.com/monitoring.aspx?nid=12. Accessed 30 June 2020
Inkscape Project (2020) Inkscape. 0.92.5 edn
Jerome M (2016) A generic webcam image acquisition plugin for ImageJ
Jindal S, Yang L, Day PJ, Kell DB (2019) Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli. BMC Microbiol 19(1):195. doi:10.1186/s12866-019-1561-0
Kay S, Zhao B, Sui D (2015) Can Social Media Clear the Air? A Case Study of the Air Pollution Problem in Chinese Cities. Prof Geogr 67:351-363
Kern B, Leiser OP, Misra R (2019) Suppressor Mutations in degS Overcome the Acute Temperature-Sensitive Phenotype of ΔdegP and ΔdegP Δtol-pal Mutants of Escherichia coli. J Bacteriol 201(11). doi:10.1128/jb.00742-18
Kim HJ, Jang S (2018) Optimization of a resazurin-based microplate assay for large-scale compound screenings against Klebsiella pneumoniae. 3 Biotech 8(1):3. doi:10.1007/s13205-017-1034-9
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-60. doi:10.1093/bioinformatics/btp324
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16):2078-9. doi:10.1093/bioinformatics/btp352
Li N, Ho KWK, Ying GG, Deng WJ (2017) Veterinary antibiotics in food, drinking water, and the urine of preschool children in Hong Kong. Environ Int 108:246-252. doi:10.1016/j.envint.2017.08.014
Linsen SEV (2020) Uses for a microbial culture reaction well, multiwell plate, culture bed, and method for detecting biological
activity (translated from Mandarin). China Patent
Linsen SEV (2021) Antibiotic residues in the environment: a table, an index and some reflections. Figshare
Liu A, Tran L, Becket E, Lee K, Chinn L, Park E, Tran K, Miller JH (2010) Antibiotic sensitivity profiles determined with an Escherichia coli gene knockout collection: generating an antibiotic bar code. Antimicrob Agents Chemother 54(4):1393-403. doi:10.1128/aac.00906-09
Liu G, Olsen JE, Thomsen LE (2019) Identification of Genes Essential for Antibiotic-Induced Up-Regulation of Plasmid-Transfer-Genes in Cephalosporin Resistant Escherichia coli. Front Microbiol 10:2203. doi:10.3389/fmicb.2019.02203
Llor C, Bjerrum L (2014) Antimicrobial resistance: risk associated with antibiotic overuse and initiatives to reduce the problem. Ther Adv Drug Saf 5(6):229-41. doi:10.1177/2042098614554919
Martinez JL (2009) Environmental pollution by antibiotics and by antibiotic resistance determinants. Environ Pollut 157(11):2893-902. doi:10.1016/j.envpol.2009.05.051
Mason KM, Munson RS, Jr., Bakaletz LO (2005) A mutation in the sap operon attenuates survival of nontypeable Haemophilus influenzae in a chinchilla model of otitis media. Infect Immun 73(1):599-608. doi:10.1128/iai.73.1.599-608.2005
Mitosch K, Rieckh G, Bollenbach T (2017) Noisy Response to Antibiotic Stress Predicts Subsequent Single-Cell Survival in an Acidic Environment. Cell Syst 4(4):393-403.e5. doi:10.1016/j.cels.2017.03.001
Morè N, Martorana AM, Biboy J, Otten C, Winkle M, Serrano CKG, Montón Silva A, Atkinson L, Yau H, Breukink E, den Blaauwen T, Vollmer W, Polissi A (2019) Peptidoglycan Remodeling Enables Escherichia coli To Survive Severe Outer Membrane Assembly Defect. mBio 10(1). doi:10.1128/mBio.02729-18
Mulani MS, Kamble EE, Kumkar SN, Tawre MS, Pardesi KR (2019) Emerging Strategies to Combat ESKAPE Pathogens in the Era of Antimicrobial Resistance: A Review. Front Microbiol 10:539. doi:10.3389/fmicb.2019.00539
Munteanu FD, Titoiu AM, Marty JL, Vasilescu A (2018) Detection of Antibiotics and Evaluation of Antibacterial Activity with Screen-Printed Electrodes. Sensors 18(3). doi:10.3390/s18030901
Nahrstedt H, Meinhardt F (2004) Structural and functional characterization of the Bacillus megaterium uvrBA locus and generation of UV-sensitive mutants. Appl Microbiol Biotechnol 65(2):193-9. doi:10.1007/s00253-004-1572-z
Navrátilová P (2008) Screening methods used for the detection of veterinary drug residues in raw cow milk a review. Czech J Food Sci 26(6):393-401
Nolivos S, Cayron J, Dedieu A, Page A, Delolme F, Lesterlin C (2019) Role of AcrAB-TolC multidrug efflux pump in drug-resistance acquisition by plasmid transfer. Science 364(6442):778-782. doi:10.1126/science.aav6390
Nüesch-Inderbinen M, Treier A, Zurfluh K, Stephan R (2019) Raw meat-based diets for companion animals: a potential source of transmission of pathogenic and antimicrobial-resistant Enterobacteriaceae. R Soc Open Sci 6(10):191170. doi:10.1098/rsos.191170
O'Neill J (2014) Antimicrobial resistance : tackling a crisis for the health and wealth of nations
R. Team (2014) R: A language and environment for statistical computing. MSOR connect
Raetz CR, Whitfield C (2002) Lipopolysaccharide endotoxins. Annu Rev Biochem 71:635-700. doi:10.1146/annurev.biochem.71.110601.135414
Reygaert WC (2018) An overview of the antimicrobial resistance mechanisms of bacteria. AIMS Microbiol 4(3):482-501. doi:10.3934/microbiol.2018.3.482
Rodriguez-Mozaz S, Vaz-Moreira I, Varela Della Giustina S, Llorca M, Barceló D, Schubert S, Berendonk TU, Michael-Kordatou I, Fatta-Kassinos D, Martinez JL, Elpers C, Henriques I, Jaeger T, Schwartz T, Paulshus E, O'Sullivan K, Pärnänen KMM, Virta M, Do TT, Walsh F, Manaia CM (2020) Antibiotic residues in final effluents of European wastewater treatment plants and their impact on the aquatic environment. Environ Int 140:105733. doi:10.1016/j.envint.2020.105733
Rueden CT, Schindelin J, Hiner MC, DeZonia BE, Walter AE, Arena ET, Eliceiri KW (2017) ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinform 18(1):529. doi:10.1186/s12859-017-1934-z
Schoenmakers K (2020) How China is getting its farmers to kick their antibiotics habit. Nature 586:S60-S62
Shepherd CJ, Jackson AJ (2013) Global fishmeal and fish-oil supply: inputs, outputs and markets. J Fish Biol 83(4):1046-66. doi:10.1111/jfb.12224
Stubbings W, Bostock J, Ingham E, Chopra I (2005) Deletion of the multiple-drug efflux pump AcrAB in Escherichia coli prolongs the postantibiotic effect. Antimicrob Agents Chemother 49(3):1206-8. doi:10.1128/aac.49.3.1206-1208.2005
Sugiyama Y, Nakamura A, Matsumoto M, Kanbe A, Sakanaka M, Higashi K, Igarashi K, Katayama T, Suzuki H, Kurihara S (2016) A Novel Putrescine Exporter SapBCDF of Escherichia coli. J Biol Chem 291(51):26343-26351. doi:10.1074/jbc.M116.762450
Szczepaniak J, Press C, Kleanthous C (2020) The multifarious roles of Tol-Pal in Gram-negative bacteria. FEMS Microbiol Rev 44(4):490-506. doi:10.1093/femsre/fuaa018
Taylor PL, Blakely KM, de Leon GP, Walker JR, McArthur F, Evdokimova E, Zhang K, Valvano MA, Wright GD, Junop MS (2008) Structure and function of sedoheptulose-7-phosphate isomerase, a critical enzyme for lipopolysaccharide biosynthesis and a target for antibiotic adjuvants. J Biol Chem 283(5):2835-45. doi:10.1074/jbc.M706163200
The Document Foundation (2020) LibreOffice Calc. 2020 (6.3.6) edn
Van Boeckel TP, Brower C, Gilbert M, Grenfell BT, Levin SA, Robinson TP, Teillant A, Laxminarayan R (2015) Global trends in antimicrobial use in food animals. Proc Natl Acad Sci U S A 112(18):5649-54. doi:10.1073/pnas.1503141112
Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA (2013) From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinform 43(1110):11.10.1-11.10.33. doi:10.1002/0471250953.bi1110s43
Van TTH, Yidana Z, Smooker PM, Coloe PJ (2020) Antibiotic use in food animals worldwide, with a focus on Africa: Pluses and minuses. J Glob Antimicrob Resist 20:170-177. doi:10.1016/j.jgar.2019.07.031
Wang H, Ren L, Yu X, Hu J, Chen Y, He G, Jiang Q (2017) Antibiotic residues in meat, milk and aquatic products in Shanghai and human exposure assessment. Food Control 80:217-225
Wang H, Tang C, Yang J, Wang N, Jiang F, Xia Q, He G, Chen Y, Jiang Q (2018) Predictors of urinary antibiotics in children of Shanghai and health risk assessment. Environ Int 121(Pt 1):507-514. doi:10.1016/j.envint.2018.09.032
Warnes MGR, Bolker B, Bonebakker L, Gentleman R, Huber W (2016) Package ‘gplots’. Various R programming tools for plotting data
Waternet (2021) Waterkwaliteit drinkwater Amsterdam. https://www.waternet.nl/service-en-contact/drinkwater/waterkwaliteit/. Accessed 30 June 2020
Werner J, Misra R (2005) YaeT (Omp85) affects the assembly of lipid-dependent and lipid-independent outer membrane proteins of Escherichia coli. Mol Microbiol 57(5):1450-9. doi:10.1111/j.1365-2958.2005.04775.x
Yajko DM, Madej JJ, Lancaster MV, Sanders CA, Cawthon VL, Gee B, Babst A, Hadley WK (1995) Colorimetric method for determining MICs of antimicrobial agents for Mycobacterium tuberculosis. J Clin Microbiol 33(9):2324-7. doi:10.1128/jcm.33.9.2324-2327.1995
Yethon JA, Vinogradov E, Perry MB, Whitfield C (2000) Mutation of the lipopolysaccharide core glycosyltransferase encoded by waaG destabilizes the outer membrane of Escherichia coli by interfering with core phosphorylation. J Bacteriol 182(19):5620-3. doi:10.1128/jb.182.19.5620-5623.2000