scholarly journals Open Waste Canals as Potential Sources of Antimicrobial Resistance Genes in Aerosols in Urban Kanpur, India

2021 ◽  
Author(s):  
Olivia Ginn ◽  
David Berendes ◽  
Anna Wood ◽  
Aaron Bivins ◽  
Lucas Rocha-Melogno ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Ambient Air ◽  
Control Site ◽  
Urban Environments ◽  
Air Samples ◽  
Gene Copies ◽  
Antimicrobial Resistance Genes ◽  
Class 1 ◽  
Control Samples

Understanding the movement of antimicrobial resistance genes (ARGs) in the environment is critical to managing their spread. To assess potential ARG transport through the air via urban bioaerosols in cities with poor sanitation, we quantified ARGs and a mobile integron (MI) in ambient air over periods spanning rainy and dry seasons in Kanpur, India (n = 53), where open wastewater canals (OCWs) are prevalent. Gene targets represented major antibiotic groups—tetracyclines (tetA), fluoroquinolines (qnrB), and beta-lactams (blaTEM)—and a class 1 mobile integron (intI1). Over half of air samples located near, and up to 1 km from OCWs with fecal contamination (n = 45) in Kanpur had detectable targets above the experimentally determined limits of detection (LOD): most commonly intI1 and tetA (56% and 51% of samples, respectively), followed by blaTEM (8.9%) and qnrB (0%). ARG and MI densities in these positive air samples ranged from 6.9 × 101 to 5.2 × 103 gene copies/m3 air. Most (7/8) control samples collected 1 km away from OCWs were negative for any targets. In comparing experimental samples with control samples, we found that intI1 and tetA densities in air are significantly higher (P = 0.04 and P = 0.01, respectively, alpha = 0.05) near laboratory-confirmed fecal contaminated waters than at the control site. These data suggest increased densities of ARGs and MIs in bioaerosols in urban environments with inadequate sanitation. In such settings, aerosols may play a role in the spread of AR.

scholarly journals Metagenomic Quantification of Genes with Internal Standards

mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Emily Crossette ◽  
Jordan Gumm ◽  
Kathryn Langenfeld ◽  
Lutgarde Raskin ◽  
Melissa Duhaime ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Tetracycline Resistance ◽  
Dairy Manure ◽  
Molecular Techniques ◽  
Gene Copy ◽  
Gene Quantification ◽  
Gene Copies ◽  
Antimicrobial Resistance Genes ◽  
Metagenomic Approach

ABSTRACT We demonstrate that an assembly-independent and spike-in facilitated metagenomic quantification approach can be used to screen and quantify over 2,000 genes simultaneously, while delivering absolute gene concentrations comparable to those for quantitative PCR (qPCR). DNA extracted from dairy manure slurry, digestate, and compost was spiked with genomic DNA from a marine bacterium and sequenced using the Illumina HiSeq4000. We compared gene copy concentrations, in gene copies per mass of sample, of five antimicrobial resistance genes (ARGs) generated with (i) our quantitative metagenomic approach, (ii) targeted qPCR, and (iii) a hybrid quantification approach involving metagenomics and qPCR-based 16S rRNA gene quantification. Although qPCR achieved lower quantification limits, the metagenomic method avoided biases caused by primer specificity inherent to qPCR-based methods and was able to detect orders of magnitude more genes than is possible with qPCR assays. We used the approach to simultaneously quantify ARGs in the Comprehensive Antimicrobial Resistance Database (CARD). We observed that the total abundance of tetracycline resistance genes was consistent across different stages of manure treatment on three farms, but different samples were dominated by different tetracycline resistance gene families. IMPORTANCE qPCR and metagenomics are central molecular techniques that have offered insights into biological processes for decades, from monitoring spatial and temporal gene dynamics to tracking ARGs or pathogens. Still needed is a tool that can quantify thousands of relevant genes in a sample as gene copies per sample mass or volume. We compare a quantitative metagenomic approach with traditional qPCR approaches in the quantification of ARG targets in dairy manure samples. By leveraging the benefits of nontargeted community genomics, we demonstrate high-throughput absolute gene quantification of all known ARG sequences in environmental samples.

Diversity of antimicrobial resistance genes and class-1-integrons in phylogenetically related porcine and human Escherichia coli

2012 ◽  
Vol 160 (3-4) ◽  
pp. 403-412 ◽  
Author(s):  
Christina Susanne Hölzel ◽  
Katrin Susanne Harms ◽  
Johann Bauer ◽  
Ilse Bauer-Unkauf ◽  
Stefan Hörmansdorfer ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Class 1 Integrons ◽  
Antimicrobial Resistance Genes ◽  
Class 1

Distribution of Antimicrobial Resistance Genes and Class 1 Integron Gene Cassette Arrays in Motile Aeromonas spp. Isolated from Goldfish (Carassius auratus)

2018 ◽  
Vol 24 (8) ◽  
pp. 1217-1225 ◽  
Author(s):  
Sabrina Hossain ◽  
Benthotage Chamara Jayasankha De Silva ◽  
Sudu Hakuruge Madusha Pramud Wimalasena ◽  
Hansani Nilupama Kumari Senarath Pathirana ◽  
Pasan Sepala Dahanayake ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Carassius Auratus ◽  
Gene Cassette ◽  
Class 1 Integron ◽  
Goldfish Carassius Auratus ◽  
Antimicrobial Resistance Genes ◽  
Class 1

Characterization and Horizontal Transfer of Antimicrobial Resistance Genes and Integrons in Bacteria Isolated from Cooked Meat Products in China

2017 ◽  
Vol 80 (12) ◽  
pp. 2048-2055 ◽  
Author(s):  
Tao Yu ◽  
Xiaobing Jiang ◽  
Yu Liang ◽  
Yanping Zhu ◽  
Jinhe Tian ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Meat Products ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Integrase Gene ◽  
Antimicrobial Resistance Genes ◽  
Class 1 ◽  
Cooked Meat ◽  
Cooked Meat Products

ABSTRACT The aim of this study was to investigate antimicrobial resistance and the presence and transferability of corresponding resistance genes and integrons in bacteria isolated from cooked meat samples in the People's Republic of China. A total of 150 isolates (22 species belonging to 15 genera) were isolated from 49 samples. Resistance of these isolates to antimicrobials was commonly observed; 42.7, 36.0, and 25.3% of the isolates were resistant to tetracycline, streptomycin, and ampicillin, respectively. Multidrug resistance was observed in 41 (27.3%) of the isolates. Sixteen resistance genes, i.e., blaTEM-1 and blaCTX-M-14 (β-lactams), aac(3)-IIa (gentamicin), strA and strB (streptomycin), qnrB and qnrS (fluoroquinolone), sul1, sul2, and sul3 (sulfamethoxazole), cat1 and cat2 (chloramphenicol), and tetM, tetA, tetS, and tetB (tetracycline), were found in 54 isolates. One isolate of Pseudomonas putida carried qnrB, and sequence analysis of the PCR product revealed 96% identity to qnrB2. The qnr genes were found coresiding and were cotransferred with bla genes in two isolates. Twelve isolates were positive for the class 1 integrase gene, and four isolates carried the class 2 integrase gene. However, no class 3 integrase gene was detected. One isolate of Proteus mirabilis carried dfrA32-ereA-aadA2, and this unusual array could be transferred to Escherichia coli. Nonclassic class 1 integrons lacking qacEΔ1 and sul1 genes were found in 2 of the 12 intI1-positive isolates. Our results revealed the presence of multidrug-resistant bacteria in cooked meats and the presence and transferability of resistance genes in some isolates, suggesting that cooked meat products may act as reservoirs of drug-resistant bacteria and may facilitate the spread of resistance genes.

Antimicrobial resistance genes and class 1 integrons in MDR Salmonella strains isolated from swine lymph nodes

Food Control ◽  
2021 ◽  
Vol 128 ◽  
pp. 108190
Author(s):  
Fábio Sossai Possebon ◽  
Marcus Vinicius Niz Alvarez ◽  
Leila Sabrina Ullmann ◽  
João Pessoa Araújo Jr
Keyword(s):  
Antimicrobial Resistance ◽  
Lymph Nodes ◽  
Resistance Genes ◽  
Class 1 Integrons ◽  
Antimicrobial Resistance Genes ◽  
Class 1

scholarly journals Zoo Animals as Reservoirs of Gram-Negative Bacteria Harboring Integrons and Antimicrobial Resistance Genes

2007 ◽  
Vol 73 (20) ◽  
pp. 6686-6690 ◽  
Author(s):  
Ashraf M. Ahmed ◽  
Yusuke Motoi ◽  
Maiko Sato ◽  
Akito Maruyama ◽  
Hitoshi Watanabe ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Class 1 ◽  
Zoo Animals ◽  
Hiroshima Prefecture ◽  
Lactamase Gene

ABSTRACT A total of 232 isolates of gram-negative bacteria were recovered from mammals, reptiles, and birds housed at Asa Zoological Park, Hiroshima prefecture, Japan. Forty-nine isolates (21.1%) showed multidrug resistance phenotypes and harbored at least one antimicrobial resistance gene. PCR and DNA sequencing identified class 1 and class 2 integrons and many β-lactamase-encoding genes, in addition to a novel AmpC β-lactamase gene, bla CMY-26. Furthermore, the plasmid-mediated quinolone resistance genes qnr and aac(6′)-Ib-cr were also identified.

scholarly journals In Silico Detection of Antimicrobial Resistance Integrons in Salmonella enterica Isolates from Countries of the Andean Community

Antibiotics ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1388
Author(s):  
Lilibeth Torres-Elizalde ◽  
David Ortega-Paredes ◽  
Karen Loaiza ◽  
Esteban Fernández-Moreira ◽  
Marco Larrea-Álvarez
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
In Silico ◽  
Salmonella Enterica ◽  
Antimicrobial Resistance Genes ◽  
In Silico Studies ◽  
Class 1 ◽  
Surveillance Programs ◽  
Resistant Strains ◽  
Andean Community

Antimicrobial resistance genes are often associated with integrons, which promote their movement between and within DNA molecules. IntFinder 1.0 and I-VIP v1.2 were used for the detection of integrons and their associated resistance genes in assembled sequences and raw reads. A dataset comprising 1688 sequenced Salmonella enterica isolates from countries of the Andean Community was developed. A total of 749 and 680 integrons were identified by IntFinder 1.0 and I-VIP v1.2, respectively; class 2 integrons were the most abundant followed by class 1, whereas no class 3 integrons 3 were detected. These elements were mainly associated with isolates from animal sources. S. Infantis ST32 contained the majority of integrons. Trimethoprim resistance genes (dfrA) were found in greater numbers than others, including aadA and bla genes. The presence of these resistance integrons may come as a response to antibiotic misuse, especially of co-trimoxazole. This represents a public health risk as novel resistant strains might appear due to gene dissemination. The information gathered from in silico studies not only contributes to our understanding of integron dynamics in pathogenic Salmonella, but also helps identify potential emergent patterns of resistance in the region, which is fundamental for developing pertinent antibiotic surveillance programs.

Sign in / Sign up

Export Citation Format

Share Document