Antimicrobial Resistance Profile and mcr-1 Gene Detection in Salmonella Isolates from Poultry in Bangladesh: Molecular and Bioinformatics Characterization

AbstractAntimicrobial resistance gene mcr-1 has been disseminated globally since its first discovery in Southern China in late 2015. However, the mcr-1 gene had not been identified previously in Salmonella isolates from poultry in Bangladesh. Here, we aimed to explore antimicrobial resistance gene mcr-1 in Salmonella isolates. Eighty two Salmonella isolates were isolated and characterized from suspected poultry specimens received from different zones of the country. A phenotypic disc diffusion assay with 15 antimicrobial agents was performed following CLSI standard. The disk diffusion assay showed that, all of the isolates presented high resistance to colistin (92.68%), oxytetracycline (86.59%), co-trimoxazole (76.83%), ciprofloxacin (73.17%) and enrofloxacin (65.85%). Further, randomly selected 10 Salmonella isolates were analyzed by polymerase chain reaction (PCR) targeting genus-specific invA and antimicrobial (colistin) resistance mcr-1 genes. Five were confirmed for the presence of the mcr-1 gene belonging to Salmonella spp. Further, sequencing followed by phylogenetic analysis revealed divergent evolutionary relation between the LptA and MCR proteins rendering them resistant to colistin. Three-dimensional homology structures of MCR-1 proteins were constructed and verified using different bioinformatics tools. Moreover, molecular docking interactions suggested that, MCR-1 and LptA share a similar substrate binding cavity which could be validated for the functional analysis. The results represent here is the first molecular and in silico analysis of colistin resistance mcr-1 gene of Salmonella in poultry in Bangladesh, which may emphasize the importance of the study on antibiotic resistance genes requiring for national monitoring and strategic surveillance in the country.

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Metagenomics Analysis Reveals the Microbial Communities, Antimicrobial Resistance Gene Diversity and Potential Pathogen Transmission Risk of Two Different Landfills in China

Diversity ◽

10.3390/d13060230 ◽

2021 ◽

Vol 13 (6) ◽

pp. 230

Author(s):

Shan Wan ◽

Min Xia ◽

Jie Tao ◽

Yanjun Pang ◽

Fugen Yu ◽

...

Keyword(s):

Antibiotic Resistance ◽

Microbial Communities ◽

Resistance Gene ◽

Resistance Genes ◽

Gene Diversity ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Pathogen Transmission ◽

Transmission Risk ◽

Antimicrobial Resistance Gene

In this study, we used a metagenomic approach to analyze microbial communities, antibiotic resistance gene diversity, and human pathogenic bacterium composition in two typical landfills in China. Results showed that the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in the two landfills, and archaea and fungi were also detected. The genera Methanoculleus, Lysobacter, and Pseudomonas were predominantly present in all samples. sul2, sul1, tetX, and adeF were the four most abundant antibiotic resistance genes. Sixty-nine bacterial pathogens were identified from the two landfills, with Klebsiella pneumoniae, Bordetella pertussis, Pseudomonas aeruginosa, and Bacillus cereus as the major pathogenic microorganisms, indicating the existence of potential environmental risk in landfills. In addition, KEGG pathway analysis indicated the presence of antibiotic resistance genes typically associated with human antibiotic resistance bacterial strains. These results provide insights into the risk of pathogens in landfills, which is important for controlling the potential secondary transmission of pathogens and reducing workers’ health risk during landfill excavation.

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Variations in bacterial community structure and antimicrobial resistance gene abundance in cattle manure and poultry litter

Environmental Research ◽

10.1016/j.envres.2021.111011 ◽

2021 ◽

Vol 197 ◽

pp. 111011

Author(s):

Biyensa Gurmessa ◽

Amanda J. Ashworth ◽

Yichao Yang ◽

Mary Savin ◽

Philip A. Moore ◽

...

Keyword(s):

Community Structure ◽

Antimicrobial Resistance ◽

Bacterial Community ◽

Resistance Gene ◽

Bacterial Community Structure ◽

Poultry Litter ◽

Cattle Manure ◽

Gene Abundance ◽

Antimicrobial Resistance Gene

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Molecular characterisation of antimicrobial resistance and virulence genes in Escherichia coli strains isolated from diarrhoeic and healthy rabbits in Tunisia

World Rabbit Science ◽

10.4995/wrs.2020.10879 ◽

2020 ◽

Vol 28 (2) ◽

pp. 81

Author(s):

Raouia Ben Rhouma ◽

Ahlem Jouini ◽

Amira Klibi ◽

Safa Hamrouni ◽

Aziza Boubaker ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Virulence Genes ◽

Antimicrobial Agents ◽

Antibiotic Resistance Genes ◽

Virulence Gene ◽

Diffusion Method ◽

Class 1 Integron ◽

E Coli ◽

Class 1

The purpose of this study was to identify Escherichia coli isolates in diarrhoeic and healthy rabbits in Tunisia and characterise their virulence and antibiotic resistance genes. In the 2014-2015 period, 60 faecal samples from diarrhoeic and healthy rabbits were collected from different breeding farms in Tunisia. Susceptibility to 14 antimicrobial agents was tested by disc diffusion method and the mechanisms of gene resistance were evaluated using polymerase chain reaction and sequencing methods. Forty E. coli isolates were recovered in selective media. High frequency of resistance to tetracycline (95%) was detected, followed by different levels of resistance to sulphonamide (72.5%), streptomycin (62.5%), trimethoprim-sulfamethoxazole (60%), nalidixic acid (32.5%), ampicillin (37.5%) and ticarcillin (35%). E. coli strains were susceptible to cefotaxime, ceftazidime and imipenem. Different variants of blaTEM, tet, sul genes were detected in most of the strains resistant to ampicillin, tetracycline and sulphonamide, respectively. The presence of class 1 integron was studied in 29 sulphonamide-resistant E. coli strains from which 15 harboured class 1 integron with four different arrangements of gene cassettes, dfrA17+aadA5 (n=9), dfrA1 + aadA1 (n=4), dfrA12 + addA2 (n=1), dfrA12+orf+addA2 (n=1). The qnrB gene was detected in six strains out of 13 quinolone-resistant E. coli strains. Seventeen E. coli isolates from diarrhoeic rabbits harboured the enteropathogenic eae genes associated with different virulence genes tested (fimA, cnf1, aer), and affiliated to B2 (n=8) and D (n=9) phylogroups. Isolated E. coli strains from healthy rabbit were harbouring fim A and/or cnf1 genes and affiliated to A and B1 phylogroups. This study showed that E. coli strains from the intestinal tract of rabbits are resistant to the widely prescribed antibiotics in medicine. Therefore, they constitute a reservoir of antimicrobial-resistant genes, which may play a significant role in the spread of antimicrobial resistance. In addition, the eae virulence gene seemed to be implicated in diarrhoea in breeder rabbits in Tunisia.

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The global distribution and spread of the mobilized colistin resistance gene mcr-1

10.1101/220921 ◽

2017 ◽

Author(s):

Ruobing Wang ◽

Lucy van Dorp ◽

Liam Shaw ◽

Phelim Bradley ◽

Qi Wang ◽

...

Keyword(s):

Resistance Gene ◽

Antibiotic Resistance Genes ◽

Global Distribution ◽

Colistin Resistance ◽

Posterior Density ◽

Carbapenem Resistant ◽

Significant Public Health ◽

Monitoring And Surveillance ◽

Multiple Levels ◽

Carbapenem Resistant Enterobacteriaceae

AbstractColistin represents one of the very few available drugs for treating infections caused by carbapenem resistant Enterobacteriaceae (CRE). As such, the recent plasmid-mediated spread of the mobilized colistin resistance gene mcr-1 poses a significant public health threat requiring global monitoring and surveillance. In this work, we characterize the global distribution of mcr-1 using a dataset of 457 mcr-1 positive sequenced isolates consisting of currently publicly available mcr-1 carrying sequences combined with an additional 110 newly sequenced mcr-1 positive isolates from China. We find mcr-1 in a diversity of plasmid backgrounds but identify an immediate background common to all mcr-1 sequences. Our analyses establish that all mcr-1 elements in circulation descend from the same initial mobilization of mcr-1 by an ISApl1 transposon in the mid 2000s (2002-2008; 95% higher posterior density), followed by a dramatic demographic expansion, which led to its current global distribution. Our results provide the first systematic phylogenetic analysis of the origin and spread of mcr-1, and emphasize the importance of understanding the movement of mobile elements carrying antibiotic resistance genes across multiple levels of genomic organization.

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