Clinically relevant antibiotic resistance genes are linked to a limited … – Nature.com

Murray, C. J. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629655 (2022).

Article CAS Google Scholar

Brito, I. L. et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature 535, 435439 (2016).

Article ADS CAS PubMed PubMed Central Google Scholar

Pehrsson, E. C. et al. Interconnected microbiomes and resistomes in low-income human habitats. Nature 533, 212216 (2016).

Article ADS CAS PubMed PubMed Central Google Scholar

Zhang, Z. et al. Assessment of global health risk of antibiotic resistance genes. Nat. Commun. 13, 1553 (2022).

Article ADS CAS PubMed PubMed Central Google Scholar

Zhou, H., Beltrn, J. F. & Brito, I. L. Functions predict horizontal gene transfer and the emergence of antibiotic resistance. Sci. Adv. 7, eabj5056 (2021).

Article ADS CAS PubMed PubMed Central Google Scholar

Smillie, C. S. et al. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480, 241244 (2011).

Article ADS CAS PubMed Google Scholar

Maier, L. et al. Unravelling the collateral damage of antibiotics on gut bacteria. Nature 599, 120124 (2021).

Article ADS CAS PubMed PubMed Central Google Scholar

Lamberte, L. E. & van Schaik, W. Antibiotic resistance in the commensal human gut microbiota. Curr. Opin. Microbiol. 68, 102150 (2022).

Article CAS PubMed Google Scholar

Ghosh, T. S., Gupta, S. S., Nair, G. B. & Mande, S. S. In silico analysis of antibiotic resistance genes in the gut microflora of individuals from diverse geographies and age-groups. PLoS ONE 8, e83823 (2013).

Article ADS PubMed PubMed Central Google Scholar

Rahman, S. F., Olm, M. R., Morowitz, M. J. & Banfield, J. F. Machine learning leveraging genomes from metagenomes identifies influential antibiotic resistance genes in the infant gut microbiome. mSystems 3, e0012317 (2018).

Article CAS PubMed PubMed Central Google Scholar

Gibson, M. K. et al. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nat. Microbiol. 1, 110 (2016).

Article Google Scholar

Hu, Y. et al. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat. Commun. 4, 2151 (2013).

Article ADS PubMed Google Scholar

Yassour, M. et al. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci. Transl. Med. 8, 343ra81343ra81 (2016).

Article PubMed PubMed Central Google Scholar

Forster, S. C. et al. Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome. Nat. Commun. 13, 1445 (2022).

Article ADS CAS PubMed PubMed Central Google Scholar

Jiang, X. et al. Dissemination of antibiotic resistance genes from antibiotic producers to pathogens. Nat. Commun. 8, 15784 (2017).

Article ADS CAS PubMed PubMed Central Google Scholar

Ronda, C., Chen, S. P., Cabral, V., Yaung, S. J. & Wang, H. H. Metagenomic engineering of the mammalian gut microbiome in situ. Nat. Methods 16, 167170 (2019).

Article CAS PubMed PubMed Central Google Scholar

Munck, C., Sheth, R. U., Freedberg, D. E. & Wang, H. H. Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform. Nat. Commun. 11, 95 (2020).

Article ADS CAS PubMed PubMed Central Google Scholar

Sawa, T., Kooguchi, K. & Moriyama, K. Molecular diversity of extended-spectrum -lactamases and carbapenemases, and antimicrobial resistance. J. Intensive Care 8, 13 (2020).

Article PubMed PubMed Central Google Scholar

Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong DT, Beghini F, Malik F, Ramos M, Dowd JB, Huttenhower C, Morgan M, Segata N, Waldron L. Accessible, curated metagenomic data through ExperimentHub. Nat Methods. 14, 10231024 (2017).

Alcock, B. P. et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 51, D690D699 (2023).

Article CAS PubMed Google Scholar

WHO model list of essential medicines 22nd list. https://www.who.int/publications-detail-redirect/WHO-MHP-HPS-EML-2021.02 (2021)

Du, D. et al. Multidrug efflux pumps: structure, function and regulation. Nat. Rev. Microbiol. 16, 523539 (2018).

Article CAS PubMed Google Scholar

Nielsen, T. K., Browne, P. D. & Hansen, L. H. Antibiotic resistance genes are differentially mobilized according to resistance mechanism. GigaScience 11, giac072 (2022).

Article PubMed PubMed Central Google Scholar

Lopatkin, A. J. et al. Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science 371, eaba0862 (2021).

Article CAS PubMed PubMed Central Google Scholar

Pasolli, E. et al. Accessible, curated metagenomic data through ExperimentHub. Nat. Methods 14, 10231024 (2017).

Article CAS PubMed PubMed Central Google Scholar

Hendriksen, R. S. et al. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat. Commun. 10, 1124 (2019).

Article ADS PubMed PubMed Central Google Scholar

Munk, P. et al. Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nat. Commun. 13, 7251 (2022).

Article ADS CAS PubMed PubMed Central Google Scholar

Maugeri, A., Barchitta, M., Puglisi, F. & Agodi, A. Socio-economic, governance and health indicators shaping antimicrobial resistance: an ecological analysis of 30 european countries. Glob. Health 19, 12 (2023).

Article Google Scholar

Collignon, P., Beggs, J. J., Walsh, T. R., Gandra, S. & Laxminarayan, R. Anthropological and socioeconomic factors contributing to global antimicrobial resistance: a univariate and multivariable analysis. Lancet Planet. Health 2, e398e405 (2018).

Article PubMed Google Scholar

Zhang, Z. et al. Genetic diversity and characteristics of blaNDM-positive plasmids in Escherichia coli. Front. Microbiol. 12, 729952 (2021).

Article PubMed PubMed Central Google Scholar

Philippon, A., Arlet, G. & Jacoby, G. A. Plasmid-determined AmpC-type -lactamases. Antimicrob. Agents Chemother. 46, 111 (2002).

Article CAS PubMed PubMed Central Google Scholar

Wexler, A. G. & Goodman, A. L. An insiders perspective: bacteroides as a window into the microbiome. Nat. Microbiol. 2, 111 (2017).

Article Google Scholar

Montassier, E. et al. Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner. Nat. Microbiol. 6, 10431054 (2021).

Article CAS PubMed PubMed Central Google Scholar

Anthony, W. E. et al. Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults. Cell Rep. 39, 110649 (2022).

Article CAS PubMed PubMed Central Google Scholar

WHO report on surveillance of antibiotic consumption. https://www.who.int/publications-detail-redirect/who-report-on-surveillance-of-antibiotic-consumption.

Feng, Y. et al. Rapid detection of new delhi metallo--lactamase gene using recombinase-aided amplification directly on clinical samples from children. Front. Microbiol. 12, 691289 (2021).

Article PubMed PubMed Central Google Scholar

Day, K. M. et al. Prevalence and molecular characterization of Enterobacteriaceae producing NDM-1 carbapenemase at a military hospital in Pakistan and evaluation of two chromogenic media. Diagn. Microbiol. Infect. Dis. 75, 187191 (2013).

Article CAS PubMed Google Scholar

Yong, D. et al. Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob. Agents Chemother. 53, 50465054 (2009).

Article CAS PubMed PubMed Central Google Scholar

Moquet, O. et al. Class D OXA-48 Carbapenemase in Multidrug-Resistant Enterobacteria, Senegal. Emerg. Infect. Dis. 17, 143144 (2011).

Article PubMed PubMed Central Google Scholar

Evans, B. A. & Amyes, S. G. B. OXA -Lactamases. Clin. Microbiol. Rev. 27, 241263 (2014).

Article PubMed PubMed Central Google Scholar

Zaheer, R. et al. Comparative diversity of microbiomes and resistomes in beef feedlots, downstream environments and urban sewage influent. BMC Microbiol. 19, 197 (2019).

Article PubMed PubMed Central Google Scholar

Zaheer, R. et al. Impact of sequencing depth on the characterization of the microbiome and resistome. Sci. Rep. 8, 5890 (2018).

Article ADS PubMed PubMed Central Google Scholar

Yokoyama, M. et al. Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing. PLoS ONE 18, e0282584 (2023).

Article CAS PubMed PubMed Central Google Scholar

Yan, J. et al. A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients. Sci. Data 9, 219 (2022).

Article PubMed PubMed Central Google Scholar

Xiao, L. et al. A reference gene catalogue of the pig gut microbiome. Nat. Microbiol. 1, 16 (2016).

Article Google Scholar

Wu, D. et al. Inhalable antibiotic resistomes emitted from hospitals: metagenomic insights into bacterial hosts, clinical relevance, and environmental risks. Microbiome 10, 19 (2022).

Article CAS PubMed PubMed Central Google Scholar

Talat, A., Blake, K. S., Dantas, G. & Khan, A. U. Metagenomic insight into microbiome and antibiotic resistance genes of high clinical concern in urban and rural hospital wastewater of northern India origin: a major reservoir of antimicrobial resistance. Microbiol. Spectr. 11, e04102e04122 (2023).

Article PubMed PubMed Central Google Scholar

Takahashi, E. et al. Metagenomic analysis of diarrheal stools in Kolkata, India, indicates the possibility of subclinical infection of Vibrio cholerae O1. Sci. Rep. 12, 19473 (2022).

Article ADS CAS PubMed PubMed Central Google Scholar

Schneider, D., Amann, N., Wicke, D., Poehlein, A. & Daniel, R. Metagenomes of wastewater at different treatment stages in central Germany. Microbiol. Resour. Announc. 9, e00201e00220 (2020).

Article PubMed PubMed Central Google Scholar

Majeed, H. J. et al. Evaluation of metagenomic-enabled antibiotic resistance surveillance at a conventional wastewater treatment plant. Front. Microbiol. 12, 657954 (2021).

Article PubMed PubMed Central Google Scholar

Lira, F., Vaz-Moreira, I., Tamames, J., Manaia, C. M. & Martnez, J. L. Metagenomic analysis of an urban resistome before and after wastewater treatment. Sci. Rep. 10, 8174 (2020).

Article ADS CAS PubMed PubMed Central Google Scholar

King, P. et al. Longitudinal metagenomic analysis of hospital air identifies clinically relevant microbes. PLoS ONE 11, e0160124 (2016).

Read more here:
Clinically relevant antibiotic resistance genes are linked to a limited ... - Nature.com