Association of nanoparticles with extracellular genetic material and implications for the fate of antibiotic resistance genes in environmental systems

Bacterial resistance is a complex scientific issue. To manage this issue, we need to deeply understand the influencing factors and mechanisms. Based on the background of livestock husbandry, this paper reviews the factors that affect the acquisition of bacterial resistance. Meanwhile, the resistance mechanism is also discussed. “Survival of the fittest” is the result of genetic plasticity of bacterial pathogens, which brings about specific response, such as producing adaptive mutation, gaining genetic material or changing gene expression. To a large extent, bacterial populations acquire resistance genes directly caused by the selective pressure of antibiotics. However, mobile resistance genes may be co-selected by other existing substances (such as heavy metals and biocides) without direct selection pressure from antibiotics. This is because the same mobile genetic elements as antibiotic resistance genes can be co-located by the resistance determinants of some of these compounds. Furthermore, environmental factors are a source of resistance gene acquisition. Here, we describe some of the key measures that should be taken to mitigate the risk of antibiotic resistance. We call on the relevant governments or organizations around the world to formulate and improve the monitoring policies of antibiotic resistance, strengthen the supervision, strengthen the international cooperation and exchange, and curb the emergence and spread of drug-resistant strains.

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Implications of indoor microbial ecology and evolution on antibiotic resistance

Journal of Exposure Science & Environmental Epidemiology ◽

10.1038/s41370-019-0171-0 ◽

2019 ◽

Vol 30 (1) ◽

pp. 1-15 ◽

Cited By ~ 1

Author(s):

Sarah Ben Maamar ◽

Jinglin Hu ◽

Erica M. Hartmann

Keyword(s):

Antibiotic Resistance ◽

Built Environment ◽

Health Outcomes ◽

Resistance Genes ◽

Genetic Material ◽

Antibiotic Resistance Genes ◽

Building Design ◽

Microbial Interactions ◽

Environment Design ◽

Positive Health

Abstract The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide “healthy” building design.

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CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens

10.1101/2021.04.12.439454 ◽

2021 ◽

Author(s):

Elizabeth Pursey ◽

Tatiana Dimitriu ◽

Fernanda L. Paganelli ◽

Edze R. Westra ◽

Stineke van Houte

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Resistance Genes ◽

Bacterial Pathogens ◽

Genetic Material ◽

Antibiotic Resistance Genes ◽

Mobile Genetic Elements ◽

Genetic Elements ◽

Defence System

AbstractThe acquisition of antibiotic resistance genes via horizontal gene transfer is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of antibiotic resistance. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of antibiotic resistance. We analysed ~40,000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens including Enterococcus, Staphylococcus, Acinetobacter and Pseudomonas. We modelled the association between CRISPR-Cas and indicators of horizontal gene transfer, and found that pathogens with a CRISPR-Cas system were less likely to carry antibiotic resistance genes than those lacking this defence system. Analysis of the mobile genetic elements targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of antibiotic resistance. These results suggest a potential “immunocompromised” state for multidrug-resistant strains that may be exploited in tailored interventions that rely on mobile genetic elements, such as phage or phagemids, to treat infections caused by bacterial pathogens.

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The occurrence of specific markers of Bacteroides fragilis group, B. dorei and antibiotic-resistance genes in the wastewater treatment plants

E3S Web of Conferences ◽

10.1051/e3sconf/20184400124 ◽

2018 ◽

Vol 44 ◽

pp. 00124

Author(s):

Sebastian Niestępski ◽

Monika Harnisz ◽

Ewa Korzeniewska ◽

Adriana Osińska

Keyword(s):

Antibiotic Resistance ◽

Wastewater Treatment ◽

Resistance Genes ◽

Pathogenic Bacteria ◽

Wastewater Treatment Plants ◽

Genetic Material ◽

Bacteroides Fragilis ◽

Antibiotic Resistance Genes ◽

Genes Encoding ◽

Wastewater Samples

Wastewater treatment plants (WWTPs) are one of the main transmission sources of pathogenic bacteria and antibiotic-resistance genes in the natural environment. In this study, the presence of specific markers of Bacteroides fragilis group (BFG), B. dorei and genes encoding resistance to beta-lactams (cepA, cfxA), tetracyclines (tet(Q)), macrolides, lincosamides and streptogramins (MLS) mechanism (ermF, linA) was analyzed by standard PCR in the inflows and outflows from three wastewater treatment plants with the activated sludge process. Genetic material was isolated from wastewater samples with the use of two commercial kits for genomic DNA extraction, the Fast DNA SPIN Kit for Soil and the Genomic Micro AX Bacteria Gravity Kit. The quality of the isolated genetic material differed between the tested isolation kits. The Fast DNA SPIN Kit for Soil was more effective in detecting cfxA, ermF and linA genes. However, both extraction kits effectively identified tet(Q), bfr and HF183/BacR287 genes in all wastewater samples. The results of the study indicate that genes specific to BFG and B. dorei, and genes encoding resistance to MLS and tetracyclines are not completely eliminated during the wastewater treatment process.

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The human gut resistome

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2014.0087 ◽

2015 ◽

Vol 370 (1670) ◽

pp. 20140087 ◽

Cited By ~ 146

Author(s):

Willem van Schaik

Keyword(s):

Antibiotic Resistance ◽

Gut Microbiota ◽

Resistance Genes ◽

Horizontal Transfer ◽

Genetic Material ◽

Antibiotic Resistance Genes ◽

Strictly Anaerobic ◽

Donor Strain ◽

Human Gut ◽

Frequent Event

In recent decades, the emergence and spread of antibiotic resistance among bacterial pathogens has become a major threat to public health. Bacteria can acquire antibiotic resistance genes by the mobilization and transfer of resistance genes from a donor strain. The human gut contains a densely populated microbial ecosystem, termed the gut microbiota, which offers ample opportunities for the horizontal transfer of genetic material, including antibiotic resistance genes. Recent technological advances allow microbiota-wide studies into the diversity and dynamics of the antibiotic resistance genes that are harboured by the gut microbiota (‘the gut resistome’). Genes conferring resistance to antibiotics are ubiquitously present among the gut microbiota of humans and most resistance genes are harboured by strictly anaerobic gut commensals. The horizontal transfer of genetic material, including antibiotic resistance genes, through conjugation and transduction is a frequent event in the gut microbiota, but mostly involves non-pathogenic gut commensals as these dominate the microbiota of healthy individuals. Resistance gene transfer from commensals to gut-dwelling opportunistic pathogens appears to be a relatively rare event but may contribute to the emergence of multi-drug resistant strains, as is illustrated by the vancomycin resistance determinants that are shared by anaerobic gut commensals and the nosocomial pathogen Enterococcus faecium .

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Infectious phage particles packaging antibiotic resistance genes found in meat products and chicken feces

Scientific Reports ◽

10.1038/s41598-019-49898-0 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 10

Author(s):

Clara Gómez-Gómez ◽

Pedro Blanco-Picazo ◽

Maryury Brown-Jaque ◽

Pablo Quirós ◽

Lorena Rodríguez-Rubio ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Genetic Material ◽

Meat Products ◽

Antibiotic Resistance Genes ◽

Fecal Microbiota ◽

Phage Dna ◽

Before And After ◽

Microbiological Parameters ◽

Minced Meat

Abstract Bacteriophages can package part of their host’s genetic material, including antibiotic resistance genes (ARGs), contributing to a rapid dissemination of resistances among bacteria. Phage particles containing ARGs were evaluated in meat, pork, beef and chicken minced meat, and ham and mortadella, purchased in local retailer. Ten ARGs (blaTEM, blaCTX-M-1, blaCTX-M-9, blaOXA-48, blaVIM, qnrA, qnrS, mecA, armA and sul1) were analyzed by qPCR in the phage DNA fraction. The genes were quantified, before and after propagation experiments in Escherichia coli, to evaluate the ability of ARG-carrying phage particles to infect and propagate in a bacterial host. According to microbiological parameters, all samples were acceptable for consumption. ARGs were detected in most of the samples after particle propagation indicating that at least part of the isolated phage particles were infectious, being sul1the most abundant ARG in all the matrices followed by β-lactamase genes. ARGs were also found in the phage DNA fraction of thirty-seven archive chicken cecal samples, confirming chicken fecal microbiota as an important ARG reservoir and the plausible origin of the particles found in meat. Phages are vehicles for gene transmission in meat that should not be underestimated as a risk factor in the global crisis of antibiotic resistance.

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Genomic Analysis of Global Staphylococcus argenteus Strains Reveals Distinct Lineages With Differing Virulence and Antibiotic Resistance Gene Content

Frontiers in Microbiology ◽

10.3389/fmicb.2021.795173 ◽

2021 ◽

Vol 12 ◽

Author(s):

Cosmika Goswami ◽

Stephen Fox ◽

Matthew Holden ◽

Alistair Leanord ◽

Thomas J. Evans

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Gene ◽

Genetic Material ◽

Clinical Manifestations ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Pathogenicity Islands ◽

Type I ◽

Virulence Determinants

Infections due to Staphylococcus argenteus have been increasingly reported worldwide and the microbe cannot be distinguished from Staphylococcus aureus by standard methods. Its complement of virulence determinants and antibiotic resistance genes remain unclear, and how far these are distinct from those produced by S. aureus remains undetermined. In order to address these uncertainties, we have collected 132 publicly available sequences from fourteen different countries, including the United Kingdom, between 2005 and 2018 to study the global genetic structure of the population. We have compared the genomes for antibiotic resistance genes, virulence determinants and mobile genetic elements such as phages, pathogenicity islands and presence of plasmid groups between different clades. 20% (n = 26) isolates were methicillin resistant harboring a mecA gene and 88% were penicillin resistant, harboring the blaZ gene. ST2250 was identified as the most frequent strain, but ST1223, which was the second largest group, contained a marginally larger number of virulence genes compared to the other STs. Novel S. argenteus pathogenicity islands were identified in our isolates harboring tsst-1, seb, sec3, ear, selk, selq toxin genes, as well as chromosomal clusters of enterotoxin and superantigen-like genes. Strain-specific type I modification systems were widespread which would limit interstrain transfer of genetic material. In addition, ST2250 possessed a CRISPR/Cas system, lacking in most other STs. S. argenteus possesses important genetic differences from S. aureus, as well as between different STs, with the potential to produce distinct clinical manifestations.

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Interspecies DNA acquisition by a naturally competentAcinetobacter baumanniistrain

10.1101/308833 ◽

2018 ◽

Author(s):

German M. Traglia ◽

Kori Place ◽

Cristian Dotto ◽

Jennifer S. Fernandez ◽

Camila dos Santos Bahiense ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Genetic Material ◽

Antibiotic Resistance Genes ◽

Human Pathogen ◽

Whole Genome Analysis ◽

Resistance Level ◽

Resistance Determinants ◽

Carbapenem Resistant ◽

Multiple Resistance Genes

ABSTRACTAcinetobacter baumanniiis a human pathogen that frequently acquires antibiotic resistance genes leading to the emergence of multi-drug-resistant (MDR) strains. To investigate the role of transformation in the acquisition of resistance determinants by this species, the susceptible strain A118 was exposed to genomic DNA of carbapenem-resistantKlebsiella pneumoniae(CRKp). Resistant transformants were obtained and an increase in the resistance level to all β-lactam antibiotics was observed. Whole genome analysis of transformant clones demonstrated the acquisition of CRKp DNA. The most frequently acquired genes correspond to mobile elements, antibiotic resistance genes, and operons involved in metabolism. Bioinformatic analyses andin silicogene flow prediction strengthen our findings, showing that a continuing exchange of genetic material betweenA. baumanniiandK. pneumoniaeoccurs when they share the same niche. Our results reinforce the idea that natural transformation may play a key role in the increasing emergence ofA. baumanniiMDR.IMPORTANCESince the characterization of antibiotic resistance in the late ‘50s, antibiotic resistance propagation was classically associated with horizontal gene transfer (HGT) mediated by plasmids bearing multiple resistance genes. Here we show that, at least in the human pathogenA. baumannii, transformation also plays a major role in the acquisition of antibiotic resistance determinants. This study unravels that at least for certain pathogens the propagation of resistance genes occurs by alternative HGT mechanisms which in the past have been unappreciated.

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Quintuplex PCR to Detect Antibiotic Resistance Genes in Streptococcus pneumoniae

Journal of Clinical and Health Sciences ◽

10.24191/jchs.v2i1.5861 ◽

2016 ◽

Vol 1 (2) ◽

pp. 22 ◽

Cited By ~ 2

Author(s):

Navindra Kumari Palanisamy ◽

Parasakthi Navaratnam ◽

Shamala Devi Sekaran

Keyword(s):

Antibiotic Resistance ◽

Streptococcus Pneumoniae ◽

Resistance Genes ◽

Bacterial Pathogen ◽

Antibiotic Resistance Genes ◽

Pcr Amplification ◽

Penicillin Resistance ◽

Penicillin Binding Proteins ◽

Efflux Mechanism ◽

Mic Value

Introduction: Streptococcus pneumoniae is an important bacterial pathogen, causing respiratory infection. Penicillin resistance in S. pneumoniae is associated with alterations in the penicillin binding proteins, while resistance to macrolides is conferred either by the modification of the ribosomal target site or efflux mechanism. This study aimed to characterize S. pneumoniae and its antibiotic resistance genes using 2 sets of multiplex PCRs. Methods: A quintuplex and triplex PCR was used to characterize the pbp1A, ermB, gyrA, ply, and the mefE genes. Fifty-eight penicillin sensitive strains (PSSP), 36 penicillin intermediate strains (PISP) and 26 penicillin resistance strains (PRSP) were used. Results: Alteration in pbp1A was only observed in PISP and PRSP strains, while PCR amplification of the ermB or mefE was observed only in strains with reduced susceptibility to erythromycin. The assay was found to be sensitive as simulated blood cultures showed the lowest level of detection to be 10cfu. Conclusions: As predicted, the assay was able to differentiate penicillin susceptible from the non-susceptible strains based on the detection of the pbp1A gene, which correlated with the MIC value of the strains.

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