Functional Antibiotic Resistance Genes Research Articles

Identification of a Novel Plasmid-Borne Gentamicin Resistance Gene in Nontyphoidal Salmonella Isolated from Retail Turkey.

The spread of antibiotic-resistant bacteria presents a global health challenge. Efficient surveillance of bacteria harboring antibiotic resistance genes (ARGs) is a critical aspect to controlling the spread. Increased access to microbial genomic data from many diverse populations informs this surveillance but only when functional ARGs are identifiable within the data set. Current, homology-based approaches are effective at identifying the majority of ARGs within given clinical and nonclinical data sets for several pathogens, yet there are still some whose identities remain elusive. By coupling phenotypic profiling with genotypic data, these unknown ARGs can be identified to strengthen homology-based searches. To prove the efficacy and feasibility of this approach, a published data set from the U.S. National Antimicrobial Resistance Monitoring System (NARMS), for which the phenotypic and genotypic data of 640 Salmonella isolates are available, was subjected to this analysis. Six isolates recovered from the NARMS retail meat program between 2011 and 2013 were identified previously as phenotypically resistant to gentamicin but contained no known gentamicin resistance gene. Using the phenotypic and genotypic data, a comparative genomics approach was employed to identify the gene responsible for the observed resistance in all six of the isolates. This gene, grdA, is harbored on a 9,016-bp plasmid that is transferrable to Escherichia coli, confers gentamicin resistance to E. coli, and has never before been reported to confer gentamicin resistance. Bioinformatic analysis of the encoded protein suggests an ATP binding motif. This work demonstrates the advantages associated with coupling genomics technologies with phenotypic data for novel ARG identification.

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes

BackgroundAntibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect diverse bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate.ResultsWe evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and β-lactamases, were identified. In particular, when a lenient threshold of e value of ≤ 1 × e−5 and query coverage of ≥ 60% were employed in the Resfams database, the novel β-lactamases blaHRV-1 and blaHRVM-1 were found. These genes had unique sequences, forming distinct clades of class A and subclass B3 β-lactamases, respectively. Minimum inhibitory concentration analyses for E. coli strains harboring blaHRV-1 and blaHRVM-1 and catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow- and extended-spectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating that they were harbored by actively infecting phages.ConclusionOur results showed that viruses in the environment carry as-yet-unreported functional ARGs, albeit in small quantities. We thereby suggest that environmental bacteriophages could be reservoirs of widely variable, unknown ARGs that could be disseminated via virus-host interactions.4ZRryVp6ySP7-sdMyhXuoSVideo abstract.

Genesis of Antibiotic (Ab) Resistance (AR) XXXVI: “Hormesis Activate resident AR Genes (ARG) to Functional Antibiotic Resistance Genes (FARG) in Yanomami Amerindians (YA) During Swarming”.

YA are mountain people who were first contacted in the mid‐1960s, and who continue to live seminomadic hunter‐gatherer lifestyles in the Amazon jungle of Venezuela. YA harbor bacteria that carry FARG, including those that confer resistance to synthetic antibiotics and are syntenic with mobilization elements (verbatim) (Sci Adv. 2015 Apr 3; 1(3)). An effort has been made to provide the rationale for the presence of FRAG in YA genome even in the absence of exposure to commercial antibiotics. I. Acquiring the ARG from the soil commensal bacteria and activated upon exposure to Ab became FRAG, II. Having a diverse group of resident bacterial colonies with ARG upon exposure to Ab, the bacteria became adapted to form FRAG, III. Induction of ARG to FRAG by active metabolic compounds acquired from herbal remedies to the active form, IV. Horizontal Gene transfer mediated acquirement of ARG or FRAG from the gold miners referred as “Garimpeiros” through microevolution, V. Exposure/Inhalation of Particulate Matter (PM) (EHP. 2015 Apr;123(4):337–43.) induced “Cline” (cline is a steady change in certain characteristics present by members of the same population of the same species). During a cline, a species deals with mutations and variation, to be better adapted to the new environment, but their bacteria is also dealing with mutations and variations which will make it resistant to most forces. Yanomami's never actually knew they were having contact or taking antibiotics because they took them unknowingly. This could have also happened because the bacteria could have had silent antibiotics in them. So when the Yanomami's where exposed to bacteria, they were also being exposed to antibiotics, IV. Through “Persistence, V. Through intrinsic resistance is when the bacteria have the ability to protect it from the attacks of the antibiotics (Nature. 2016; 533:212–6. Hormesis ‐ Int J Mol Sci. 2017 Jan 15; 18(1). In essence, due to the fact that YA is nomadic (Hunter‐Gatherer) mode of life moving from one location to other location in the deep forest in groups are constantly exposed to low dose of the PM in the air. At the initial stage there may have been causality (Altruistic Death) conferring survival advantage to YA transforming a sensitive state to more tolerant to PM, through “Hormesis” enabling the inactive ARG to adapt and form FRAG by a process known as Collective Antibiotic Resistance (CAT) (Nat Chem Biol. 2015 Mar; 11:182–188). It is speculated that the resident bacteria in the gastrointestinal tract (GI) of YA may have evolved “swarming” state (surface growth) while initiating “quorum sensing (QS), forming a biofilm on the skin surface as well as GI. Swarming phenotype of bacteria has been shown to confer survival advantage via the altruistic death of initial population directly exposed to antibiotic and subsequent increase in the density of Ab tolerant and/or resistant pathogenic bacteria (J.Bac. 2003; 185:3111; PNAS. 2010; 107:3776). It is also a strong possibility that as inhabitants of the “Amazon River” basin, could have acquired water‐borne bacterial pathogen with FRAG in the form of consumption, irrigation and sewage disposal. Taken together, YA does not have to be consuming antibiotics or infected by AR pathogens to become resistant and engender FRAG. As per our hypothetical scheme, all of the above mechanisms could be contributing to the intrinsic AR. The degree of FARG in the genome of YA and resident commensal microbiome of YA directly proportional to extent of the exposure and tolerance to PM.Support or Funding InformationSupported by Professional Development funds to Subburaj KannanThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.