122:. These resistance cassettes also contain sequences that reflect recent horizontal gene transfer and provide the mechanism for how that transfer occurred. These antibiotic resistant genes also retain their functionality even after they are entirely removed from the context of their original host, emphasizing their compatibility with a wide range of hosts, including pathogens. Interestingly, the high conservation of resistance gene identity also was observed in the human gut microbiome. Although the average amino acid similarity between human gut microbiota and resistant pathogens was only around 30.2 to 45.5%, their resistance genes perfectly matched those of the pathogenic bacteria, suggesting the resistomes of the human gastrointestinal tract, soil, and clinical pathogens are all connected. It should be noted, however, that the risk of transmission cannot simply be extrapolated from abundance of resistome genes in a population, and a multifaceted approach to risk analyses should be considered to fully understand the risks posed. For example, the mobility of antibiotic resistant genes has been observed to be dependent on if the population is pathogenic or not, with pathogen communities having far higher proportions of mobile genetic elements.
140:
useful tools for understanding how human impact influences the spread of resistance genes. An effect of the introduction of high levels of human-made antibiotics in the environment is the promotion of antibiotic resistance even in the absence of natural antibiotic production. Secondary stress conditions like heavy metal pollution cause higher HGT as a stress response, which also likely contributes to the dissemination of antibiotic resistant genes. Also, rapid increase in human populations without adequate wastewater treatment allows for more chance for human pathogens to be in contact with environmental resistance-carrying bacteria, so it's important to look to wastewater treatment as a source of HGT.
126:
and blood systems, and our saliva readily transfers bacteria to other people, so there are several ways for antibiotic resistant bacteria in the oral micriobiome to readily transfer their resistance genes to other, potentially pathogenic bacterial communities. Additionally, soil and pathogenic resistomes have been observed not to be distinct, so itâs essential that we understand environmental resistance in aquatic and other environments with high likelihood of human pathogen interaction. In the hyper-antibiotic resistant
57:
antibiotics regardless of where they'd originated. In this study, they observed nearly 200 different resistance profiles among the bacteria sequenced, indicating a diverse and robust response to the antibiotics tested regardless of their bacterial target or natural or synthetic origin. Antibiotic resistant bacteria have observed through
139:
for antibiotic resistance naturally in the environment. For this reason, studying natural antibiotics and the patterns of antibiotic resistance that naturally arise in the wild may help us to predict and respond to antibiotic resistance in clinical settings. Analyses of metagenomic sequence data are
125:
When antibiotic resistance is present in the environment, it is important to consider how human pathogens are interacting or integrated into those environments, and how antibiotic resistance is being exchanged there. For example, mouth bacteria can reach other parts of the body through the digestive
134:
Our understanding of how humans create additional positive selective pressure for antibiotic resistance in non-clinical environments is essential now more than ever. The rise in antibiotic resistance has severely reduced the efficacy of antibiotic drugs, posing severe cause for concern in the realm
47:
The resistome was first used to describe the resistance capabilities of bacteria preventing the effectiveness of antibiotics . Although antibiotics and their accompanying antibiotic resistant genes come from natural habitats, before next-generation sequencing, most studies of antibiotic resistance
113:
were present at all levels of filtration, and these mobile elements harbored genes for resistance. These soil and water-based resistant communities are known as reservoirs, from which resistance can transfer to pathogenic bacteria. Metagenomic sequencing and short-read based assembly have revealed
56:
next-generation sequencing techniques have revealed significant reservoirs of antibiotic resistant bacteria outside of clinical settings. Repeated testing of soil metagenomes revealed that in urban, agricultural, and forest environments, spore-forming soil bacteria showed resistance to most major
163:
can be used to help define the size and position of the resistome, this set of genes conferring an inherited immune response. Because of mutation, the âuniversal resistomeâ, a set of resistance genes shared among all mice, similar to the concept of the pan-microbiome, is likely extremely small.
61:
surveys in non-clinical environments such as water treatment facilities and human microbiomes like the mouth. We now know that the antibiotic resistome exists in every environmental niche on Earth, and sequences from ancient permafrost reveal that antibiotic resistance has been around millennia
69:
was created to compile a database of resistance genes from this rapidly increasingly available bacterial genomic data. The CARD is a compilation of sequence data and identification of resistance genes in unannotated genome sequences. The database "includes bioinformatic tools that enable the
130:
environmental stress key to the way its resistome is expressed; intrinsic, acquired, and adaptive forms of resistant gene expression occur under different environmental pressures and lead to significant challenges in developing effective treatments in response.
135:
of drug development and maintaining public health. Human-manufactured antibiotics are not the only source of antibiotic resistant pressure in the wild, as antibiotics are present at various concentrations and function as both defense and signaling mechanisms,
114:
the exchange of antibiotic resistance genes between non-pathogenic environmental soil bacteria and clinical pathogens. The portions in the soil bacteria perfectly match the identity of several diverse human pathogens and contain resistance
401:
Dias MF, da Rocha
Fernandes G, Cristina de Paiva M, Christina de Matos Salim A, Santos AB, Amaral Nascimento AM (May 2020). "Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings".
97:
A major question surrounding the environmental resistome is: How do pathogenic bacteria acquire antibiotic resistance genes from the environment (and vice versa)? To answer this, we need to consider the mechanisms of
105:
In soil antibiotic resistant bacterial communities, resistance-conferring genes have been found on mobile genetic elements. Similarly, in an analysis of the resistome in a water treatment plant,
287:
Marathe R, Guan Z, Anandalakshmi R, Zhao H, Dinesh-Kumar SP (July 2004). "Study of
Arabidopsis thaliana resistome in response to cucumber mosaic virus infection using whole genome microarray".
574:
Manaia CM, Rocha J, Scaccia N, Marano R, Radu E, Biancullo F, et al. (June 2018). "Antibiotic resistance in wastewater treatment plants: Tackling the black box".
38:
All of the resistance genes in an organism, how they are inherited, and how their transcription levels vary to defend against pathogens like viruses and bacteria.
152:, and resistance genes within the resistome provide different functions for immune response, and are differentially transcribed. Interestingly, in one study of
156:
activated regions on the chromosome for resistance against both bacteria and viruses are clustered together, likely meaning they are co-regulated.
245:
Beutler B, Crozat K, Koziol JA, Georgel P (February 2005). "Genetic dissection of innate immunity to infection: the mouse cytomegalovirus model".
793:"Assessing the Risk of Antibiotic Resistance Transmission from the Environment to Humans: Non-Direct Proportionality between Abundance and Risk"
78:â. It is a resource intended to create a better understanding of the resistome and links healthcare, environmental, agricultural datasets.
1061:
692:"Determining the antibiotic resistance potential of the indigenous oral microbiota of humans using a metagenomic approach"
961:
Breidenstein EB, de la Fuente-NĂșñez C, Hancock RE (August 2011). "Pseudomonas aeruginosa: all roads lead to resistance".
733:"Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples"
148:
The resistome also refers to an inherited set of genes used to resist infections. This concept is also referred to as
99:
71:
110:
49:
731:
Cuadrat, Rafael R C; Sorokina, Maria; Andrade, Bruno G; Goris, Tobias; DĂĄvila, Alberto M R (2020-05-01).
85:
was published in 2020 to store the Global Ocean
Resistome ., based on the metagenomics samples from the
25:
1009:
917:
860:
643:
583:
471:
411:
352:
149:
102:(HGT) and the various opportunities for contact between environmental bacteria and human pathogens.
998:"The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units"
343:
D'Costa VM, McGrann KM, Hughes DW, Wright GD (January 2006). "Sampling the antibiotic resistome".
667:
607:
495:
435:
376:
312:
220:
119:
462:
MartĂnez JL (July 2008). "Antibiotics and antibiotic resistance genes in natural environments".
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genes from whole- or partial-genome sequence data, including unannotated raw sequence assembly
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Diaz-Torres ML, Villedieu A, Hunt N, McNab R, Spratt DA, Allan E, et al. (May 2006).
1013:
921:
864:
647:
587:
522:
McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, et al. (July 2013).
475:
415:
356:
1032:
997:
938:
905:
881:
848:
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548:
523:
1055:
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Forsberg KJ, Patel S, Gibson MK, Lauber CL, Knight R, Fierer N, Dantas G (May 2014).
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300:
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Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MO, Dantas G (August 2012).
756:
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160:
32:
929:
655:
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182:
183:"The antibiotic resistome: the nexus of chemical and genetic diversity"
106:
849:"The shared antibiotic resistome of soil bacteria and human pathogens"
75:
28:
906:"Bacterial phylogeny structures soil resistomes across habitats"
20:
has been used to describe to two similar yet separate concepts:
48:
had been confined to the laboratory. Increased availability of
66:
82:
62:
before the introduction of human-synthesized antibiotics.
31:
in communities of both pathogenic and non-pathogenic
632:"Antibacterial drug discovery in the resistance era"
685:
683:
681:
524:"The comprehensive antibiotic resistance database"
338:
336:
334:
332:
330:
328:
326:
67:Comprehensive Antibiotic Research Database (CARD)
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8:
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880:
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764:
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547:
198:
173:
996:Aguirre de CĂĄrcer D (September 2018).
528:Antimicrobial Agents and Chemotherapy
159:Comparing different mutations in the
7:
630:Brown ED, Wright GD (January 2016).
14:
709:10.1111/j.1574-6968.2006.00221.x
181:Wright, Gerard D. (March 2007).
1:
247:Current Opinion in Immunology
596:10.1016/j.envint.2018.03.044
424:10.1016/j.watres.2020.115630
749:10.1093/gigascience/giaa046
187:Nature Reviews Microbiology
1083:
1023:10.1038/s41598-018-32221-8
43:Discovery and Current Data
975:10.1016/j.tim.2011.04.005
810:10.1016/j.tim.2016.11.014
696:FEMS Microbiology Letters
576:Environment International
301:10.1007/s11103-004-0439-0
259:10.1016/j.coi.2004.11.004
109:and other protein-coding
1062:Antimicrobial resistance
791:Manaia CM (March 2017).
100:horizontal gene transfer
873:10.1126/science.1220761
484:10.1126/science.1159483
365:10.1126/science.1120800
289:Plant Molecular Biology
111:mobile genetic elements
963:Trends in Microbiology
797:Trends in Microbiology
128:Pseudomonas aeruginosa
120:classes of antibiotics
154:Arabidopsis thaliana,
72:antibiotic resistance
26:antibiotic resistance
540:10.1128/AAC.00419-13
144:Infection resistance
1014:2018NatSR...814069A
930:10.1038/nature13377
922:2014Natur.509..612F
865:2012Sci...337.1107F
656:10.1038/nature17042
648:2016Natur.529..336B
588:2018EnInt.115..312M
476:2008Sci...321..365M
416:2020WatRe.17415630D
357:2006Sci...311..374D
200:10.1038/nrmicro1614
87:Tara Oceans Project
1002:Scientific Reports
70:identification of
859:(6098): 1107â11.
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642:(7586): 336â43.
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150:innate immunity
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582:: 312â324.
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59:metagenomic
54:metagenomic
1056:Categories
410:: 115630.
168:References
757:2047-217X
440:211556937
209:1740-1526
137:selecting
116:cassettes
18:resistome
1067:Genomics
1042:30232462
983:21664819
948:24847883
891:22936781
819:28012687
775:32391909
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432:32105997
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373:16424339
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161:germline
107:plasmids
33:bacteria
24:All the
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1010:Bibcode
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861:Bibcode
853:Science
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612:4686577
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412:Bibcode
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317:7460917
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