Chala, B. & Hamde, F. Emerging and re-emerging vector-borne infectious diseases and the challenges for control: A review. Front. Public Health 9, 715759 (2021).
Nolte, O. Antimicrobial resistance in the 21st century: A multifaceted challenge. Protein Peptide Lett. 21, 330–335 (2014).
Tóth, A. G. et al. Antimicrobial resistance genes in raw milk for human consumption. Sci. Rep. 10, 7464 (2020).
Tóth, A. G. et al. A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt. Sci. Rep. 10, 1–12 (2020).
Tóth, A. G. et al. Mobile antimicrobial resistance genes in probiotics. Antibiotics 10, 1287 (2021).
Nagy, S. Á., Tóth, A. G., Papp, M., Kaplan, S. & Solymosi, N. Antimicrobial resistance determinants in silage. Sci. Rep. 12, 1–10 (2022).
Tóth, A. G. et al. Canine saliva as a possible source of antimicrobial resistance genes. Antibiotics 11, 1490 (2022).
Tóth, A. G., Judge, M. F., Nagy, S. Á., Papp, M. & Solymosi, N. A survey on antimicrobial resistance genes of frequently used probiotic bacteria, 1901 to 2022. EuroSurveillance 28, 2200272 (2023).
Organization, W. H., UNICEF et al. Global vector control response 2017–2030. (2017).
Brites-Neto, J., Duarte, K. M. R. & Martins, T. F. Tick-borne infections in human and animal population worldwide. Vet. World 8, 301 (2015).
Schneider, J. G. Human ehrlichiosis: A case study. Clin. Lab. Sci. 22, 3 (2009).
Billeter, S. A., Cáceres, A. G., Gonzales-Hidalgo, J., Luna-Caypo, D. & Kosoy, M. Y. Molecular detection of Bartonella species in ticks from Peru. J. Med. Entomol. 48, 1257–1260 (2011).
Duan, C. et al. Complete genome sequence of rickettsia heilongjiangensis, an emerging tick-transmitted human pathogen (2011).
Bakken, J. S. & Dumler, J. S. Human granulocytic anaplasmosis. Infect. Dis. Clin. 29, 341–355 (2015).
Bush, L. M. & Vazquez-Pertejo, M. T. Tick borne illness-lyme disease. Dis. Month 64, 195–212 (2018).
Koka, H., Sang, R., Kutima, H. L. & Musila, L. Coxiella burnetii detected in tick samples from pastoral communities in kenya. BioMed Res. Int. 2018 (2018).
Yeni, D. K., Büyük, F., Ashraf, A. & Shah, M. Tularemia: A re-emerging tick-borne infectious disease. Folia Microbiologica 66, 1–14 (2021).
De Coster, W., D’hert, S., Schultz, D. T., Cruts, M. & Van Broeckhoven, C. Nanopack: Visualizing and processing long-read sequencing data. Bioinformatics 34, 2666–2669 (2018).
Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).
Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).
Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).
Zimin, A. V. et al. Hybrid assembly of the large and highly repetitive genome of aegilops tauschii, a progenitor of bread wheat, with the masurca mega-reads algorithm. Genome Res. 27, 787–792 (2017).
Hyatt, D. et al. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).
McArthur, A. G. et al. The comprehensive antibiotic resistance database. Antimicrob. Agents Chemother. 57, 3348–3357 (2013).
Jia, B. et al. CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 45, D566–D573 (2017).
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
Krawczyk, P. S., Lipinski, L. & Dziembowski, A. PlasFlow: Predicting plasmid sequences in metagenomic data using genome signatures. Nucleic Acids Res. 46, e35 (2018).
Johansson, M. H. et al. Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J. Antimicrob. Chemother. 76, 101–109 (2021).
Guo, J. et al. VirSorter2: A multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9, 37 (2021).
Feldgarden, M. et al. Amrfinderplus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci. Rep. 11, 1–9 (2021).
Clausen, P. T., Zankari, E., Aarestrup, F. M. & Lund, O. Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data. J. Antimicrob. Chemother. 71, 2484–2488 (2016).
Clausen, P. T., Aarestrup, F. M. & Lund, O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinform. 19, 1–8 (2018).
R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria (2021).
Antunes, N. T., Frase, H., Toth, M. & Vakulenko, S. B. The class A \(\beta\)-lactamase FTU-1 is native to Francisella tularensis. Antimicrob. Agents Chemother. 56, 666–671 (2012).
Friendly, M. A fourfold display for 2 by 2 by k tables. Tech. Rep., Technical Report 217, Psychology Department, York University (1994).
Cycoń, M., Mrozik, A. & Piotrowska-Seget, Z. Antibiotics in the soil environment-degradation and their impact on microbial activity and diversity. Front. Microbiol. 10, 338 (2019).
Zainab, S. M., Junaid, M., Xu, N. & Malik, R. N. Antibiotics and antibiotic resistant genes (args) in groundwater: A global review on dissemination, sources, interactions, environmental and human health risks. Water Res. 187, 116455 (2020).
Kim, D.-W. & Cha, C.-J. Antibiotic resistome from the one-health perspective: Understanding and controlling antimicrobial resistance transmission. Expe. Mol. Med. 53, 301–309 (2021).
Rogers, S. W., Shaffer, C. E., Langen, T. A., Jahne, M. & Welsh, R. Antibiotic-resistant genes and pathogens shed by wild deer correlate with land application of residuals. EcoHealth 15, 409–425 (2018).
Dias, D., Fonseca, C., Mendo, S. & Caetano, T. A closer look on the variety and abundance of the faecal resistome of wild boar. Environ. Pollut. 292, 118406 (2022).
Allen, H. K. et al. Call of the wild: Antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8, 251–259 (2010).
Sacristán, I. et al. Antibiotic resistance genes as landscape anthropization indicators: Using a wild felid as sentinel in Chile. Sci. Total Environ. 703, 134900 (2020).
Finley, R. L. et al. The scourge of antibiotic resistance: The important role of the environment. Clin. Infect. Dis. 57, 704–710 (2013).
D’Costa, V. M., Griffiths, E. & Wright, G. D. Expanding the soil antibiotic resistome: Exploring environmental diversity. Curr. Opin. Microbiol. 10, 481–489 (2007).
D’Costa, V. M. et al. Antibiotic resistance is ancient. Nature 477, 457–461 (2011).
Sims, D., Sudbery, I., Ilott, N. E., Heger, A. & Ponting, C. P. Sequencing depth and coverage: Key considerations in genomic analyses. Nat. Rev. Genet. 15, 121–132 (2014).
Papp, M. & Solymosi, N. Review and comparison of antimicrobial resistance gene databases. Antibiotics 11, 339 (2022).
Matei, I. A. et al. A review on the eco-epidemiology and clinical management of human granulocytic anaplasmosis and its agent in Europe. Parasites & Vectors 12, 1–19 (2019).
Atif, F. A. Anaplasma marginale and anaplasma phagocytophilum: Rickettsiales pathogens of veterinary and public health significance. Parasitol. Res. 114, 3941–3957 (2015).
Ismail, N., Bloch, K. C. & McBride, J. W. Human ehrlichiosis and anaplasmosis. Clin. Lab. Med. 30, 261–292 (2010).
Botelho-Nevers, E., Socolovschi, C., Raoult, D. & Parola, P. Treatment of Rickettsia spp. infections: A review. Expert Rev. Anti-infective Ther. 10, 1425–1437 (2012).
Brennan, R. E. & Samuel, J. E. Evaluation of Coxiella burnetii antibiotic susceptibilities by real-time PCR assay. J. Clin. Microbiol. 41, 1869–1874 (2003).
Kersh, G. J. Antimicrobial therapies for Q fever. Expert Rev. Anti-infective Ther. 11, 1207–1214 (2013).
Koetsveld, J. et al. In vitro antimicrobial susceptibility of clinical isolates of Borrelia miyamotoi. Antimicrob. Agents Chemother 62, e00419-18 (2018).
Stanek, G., Wormser, G. P., Gray, J. & Strle, F. Lyme borreliosis. The Lancet 379, 461–473 (2012).
Biswas, S. & Rolain, J.-M. Bartonella infection: Treatment and drug resistance. Futur. Microbiol. 5, 1719–1731 (2010).
Caspar, Y. & Maurin, M. Francisella tularensis susceptibility to antibiotics: A comprehensive review of the data obtained in vitro and in animal models. Front. Cell. Infect. Microbiol. 7, 122 (2017).
Maurin, M., Abergel, C. & Raoult, D. DNA gyrase-mediated natural resistance to fluoroquinolones in Ehrlichia spp. Antimicrob. Agents Chemother. 45, 2098–2105 (2001).
Branger, S., Rolain, J. & Raoult, D. Evaluation of antibiotic susceptibilities of Ehrlichia canis, Ehrlichia chaffeensis, and Anaplasma phagocytophilum by real-time PCR. Antimicrob. Agents Chemother. 48, 4822–4828 (2004).
Raoult, D., Torres, H. & Drancourt, M. Shell-vial assay: Evaluation of a new technique for determining antibiotic susceptibility, tested in 13 isolates of Coxiella burnetii. Antimicrob. Agents Chemother. 35, 2070–2077 (1991).
Caspar, Y., Hennebique, A. & Maurin, M. Antibiotic susceptibility of Francisella tularensis subsp. holarctica strains isolated from tularaemia patients in France between 2006 and 2016. J. Antimicrob. Chemother. 73, 687–691 (2018).
Heine, H. S., Miller, L., Halasohoris, S. & Purcell, B. K. In vitro antibiotic susceptibilities of Francisella tularensis determined by broth microdilution following CLSI methods. Antimicrob. Agents Chemother. 61, e00612-17 (2017).
Kreizinger, Z. et al. Antimicrobial susceptibility of Francisella tularensis subsp. holarctica strains from Hungary, Central Europe. J. Antimicrob. Chemother. 68, 370–373 (2013).
Dantas, G. & Sommer, M. O. Context matters-the complex interplay between resistome genotypes and resistance phenotypes. Curr. Opin. Microbiol. 15, 577–582 (2012).
McArthur, A. G. & Tsang, K. K. Antimicrobial resistance surveillance in the genomic age. Ann. N. Y. Acad. Sci 1388, 78–91 (2017).
Boolchandani, M., D’Souza, A. W. & Dantas, G. Sequencing-based methods and resources to study antimicrobial resistance. Nat. Rev. Genet. 20, 356–370 (2019).
Pawlowski, A. C. et al. A diverse intrinsic antibiotic resistome from a cave bacterium. Nat. Commun. 7, 1–10 (2016).
Stratton, C. W. In vitro susceptibility testing versus in vivo effectiveness. Med. Clin. 90, 1077–1088 (2006).
Mehta, H. H., Ibarra, D., Marx, C. J., Miller, C. R. & Shamoo, Y. Mutational switch-backs can accelerate evolution of Francisella to a combination of ciprofloxacin and doxycycline. Front. Microbiol. 13 (2022).
Aminov, R. I. & Mackie, R. I. Evolution and ecology of antibiotic resistance genes. FEMS Microbiol. Lett. 271, 147–161 (2007).
Oz, T. et al. Strength of selection pressure is an important parameter contributing to the complexity of antibiotic resistance evolution. Mol. Biol. Evol. 31, 2387–2401 (2014).
Martínez, J. L., Coque, T. M. & Baquero, F. What is a resistance gene? Ranking risk in resistomes. Nat. Rev. Microbiol. 13, 116–123 (2015).
Battilani, M., De Arcangeli, S., Balboni, A. & Dondi, F. Genetic diversity and molecular epidemiology of Anaplasma. Infect. Genet. Evol. 49, 195–211 (2017).
Rikihisa, Y. Anaplasma phagocytophilum and Ehrlichia chaffeensis: Subversive manipulators of host cells. Nat. Rev. Microbiol. 8, 328–339 (2010).
Paddock, C. D. & Childs, J. E. Ehrlichia chaffeensis: A prototypical emerging pathogen. Clin. Microbiol. Rev. 16, 37–64 (2003).
Cutler, S. et al. A new Borrelia on the block: Borrelia miyamotoi-a human health risk?. Eurosurveillance 24, 1800170 (2019).
Wagemakers, A., Staarink, P. J., Sprong, H. & Hovius, J. W. Borrelia miyamotoi: A widespread tick-borne relapsing fever spirochete. Trends Parasitol. 31, 260–269 (2015).
Satjanadumrong, J., Robinson, M. T., Hughes, T. & Blacksell, S. D. Distribution and ecological drivers of spotted fever group Rickettsia in asia. Ecohealth 16, 611–626 (2019).
Tomassone, L., Portillo, A., Nováková, M., De Sousa, R. & Oteo, J. A. Neglected aspects of tick-borne rickettsioses. Parasites & Vectors 11, 1–11 (2018).
Schotthoefer, A. M. & Frost, H. M. Ecology and epidemiology of Lyme borreliosis. Clin. Lab. Med. 35, 723–743 (2015).
González-Barrio, D. & Ruiz-Fons, F. Coxiella burnetii in wild mammals: A systematic review. Transbound. Emerg. Dis. 66, 662–671 (2019).
Telford, S. R. III. & Goethert, H. K. Ecology of Francisella tularensis. Annu. Rev. Entomol. 65, 351 (2020).
Hayes, B. M. et al. Ticks resist skin commensals with immune factor of bacterial origin. Cell 183, 1562–1571 (2020).
Forestal, C. A. et al. Francisella tularensis has a significant extracellular phase in infected mice. J. Infect. Dis. 196, 134–137 (2007).
Yu, J.-J. et al. The presence of infectious extracellular Francisella tularensis subsp. novicida in murine plasma after pulmonary challenge. Eur. J. Clin. Microbiol. Infect. Dis. 27, 323–325 (2008).
Durão, P., Balbontín, R. & Gordo, I. Evolutionary mechanisms shaping the maintenance of antibiotic resistance. Trends Microbiol. 26, 677–691 (2018).
Martinez, J. L. General principles of antibiotic resistance in bacteria. Drug Discov. Today Technol. 11, 33–39 (2014).