Genomic features of a multidrug-resistant and mercury-tolerant environmental Escherichia coli recovered after a mining dam disaster in South America

Gaeta, Natália Carrillo; Carvalho, Daniel U de; Fontana, Herrison; Sano, Elder; Moura, Quézia; Fuga, Bruna; Munoz, Patricio Montecinos; Gregory, Lílian; Lincopán, Nilton

doi:10.1016/j.scitotenv.2022.153590

Cited by 10 publications

(5 citation statements)

References 62 publications

(74 reference statements)

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“…The copyright holder for this preprint this version posted April 3, 2023. ; https://doi.org/10.1101/2023.04.03.533045 doi: bioRxiv preprint One E. coli strain in our study also harboured the mer operon on the same plasmid as the tetA, sul1, and ant(3")-Ia resistance genes. The co-location of tetracycline, sulphonamide and aminoglycoside encoding resistance genes with the mercury operon on IncF plasmids has been previously described (Gaeta et al, 2022;Souza et al, 2022;Zhao et al, 2020) and the presence of the mer operon was positively correlated with sulphonamide and aminoglycoside resistance genes, but not tetracycline resistance genes (Souza et al, 2022). Both heavy metals and disinfectants have previously been shown to co-select for resistance genes (Baker-Austin et al, 2006;Gaeta et al, 2020;Mazhar et al, 2021).…”

Section: Discussionmentioning

confidence: 87%

The characterisation of antimicrobial resistantEscherichia colifrom dairy calves

Mwenifumbo¹,

Zhao²,

Ahmed³

et al. 2023

Preprint

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Dairy calves, particularly pre-weaned calves have been identified as a common source of multidrug (MDR) resistant E. coli. However, the strains and whether their resistance genes are plasmid or chromosomally located have not been well characterised. Our study examined the phenotype and genotype of antimicrobial resistant E. coli isolated from young calves (≤ 14 days old). Recto-anal swab enrichments from 40 dairy calves located on four dairy farms were examined for tetracycline, streptomycin, ciprofloxacin, and third-generation cephalosporin resistant E. coli. Fifty-eight percent (23/40) of calves harboured antimicrobial resistant E. coli: 18/40 (45%) harboured tetracycline resistant and 25% (10/40) harboured chromosomal mediated AmpC producing E. coli. Whole genome sequencing of 27 isolates revealed five sequence types, with ST88 being the dominant ST (17/27, 63% of the sequenced isolates) followed by ST1308 (3/27, 11%), along with the extraintestinal pathogenic E. coli lineages ST69 (3/27), ST10 (2/27, 7%), and ST58 (1/27, 4%). Additionally, 16 isolates were MDR, harbouring additional resistance genes that were not tested phenotypically. Oxford Nanopore long-read sequencing technologies enabled the location of multiple resistant gene cassettes in IncF plasmids to be determined. A phylogenetic comparison of the ST10 and ST69 isolates demonstrated that the calf derived isolates were distinct from other New Zealand animal, human, and environmental isolates. and highlights the importance of understanding the sources of antimicrobial resistance.

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Section: Discussionmentioning

confidence: 87%

The characterisation of antimicrobial resistantEscherichia colifrom dairy calves

Mwenifumbo¹,

Zhao²,

Ahmed³

et al. 2023

Preprint

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“…Many studies have reported finding the HRG and ARG co-distribution in various complex environments or in single microorganisms [ 20 , 21 , 24 , 45 , 46 ]. We found that there were 1368 plasmids harboring both HRGs and ARGs, representing approximately 7.30%, 79.40%, and 22.13% of all analyzed plasmids, plasmids with HRGs, and plasmids with ARGs, respectively ( Table S4 ).…”

Section: Resultsmentioning

confidence: 99%

“…Exposure to Hg and antibiotics has led to intersecting evolutionary pressures on bacteria, leading to cross-resistant bacterial phenotypes [ 17 , 18 ]. More and more studies have reported that bacteria from both clinical and natural environments can harbor a wealth of antibiotic resistant genes (ARGs) and HRGs, and these two types of genes are closely linked [ 19 , 20 , 21 ]. This may be explained by an adaptive evolution for bacterial genomes against Hg toxicity, and ancient antimicrobial agents before antibiotics were discovered for large production and use.…”

Section: Introductionmentioning

confidence: 99%

Plasmid Genomes Reveal the Distribution, Abundance, and Organization of Mercury-Related Genes and Their Co-Distribution with Antibiotic Resistant Genes in Gammaproteobacteria

Yang

Zhang

et al. 2022

Genes

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Mercury (Hg) pollution poses human health and environmental risks worldwide, as it can have toxic effects and causes selective pressure that facilitates the spread of antibiotic resistant genes (ARGs) among microbes. More and more studies have revealed that numerous Hg-related genes (HRGs) can help to resist and transform Hg. In the present study, we systematically analyzed the HRG distribution, abundance, organization, and their co-distribution with ARGs, using 18,731 publicly available plasmid genomes isolated from a Gammaproteobacteria host. Our results revealed that there were many Hg-resistant (mer) operon genes but they were not extensively distributed across plasmids, with only 9.20% of plasmids harboring HRGs. Additionally, no hgcAB genes (which methylate Hg to create methylmercury) were identified in any of the analyzed plasmids. The host source significantly influenced the number of HRGs harbored by plasmids; plasmids isolated from humans and animals harbored a significantly smaller number of HRGs than plasmids isolated from the wastewater and sludge. HRG clusters displayed an extremely high organizational diversity (88 HRG cluster types), though incidences of more than half of the HRG cluster types was <5. This indicates the frequent rearrangement among HRGs in plasmids. The 1368 plasmids harboring both HRGs and ARGs, were dominated by Klebsiella, followed by Escherichia, Salmonella, and Enterobacter. The tightness of the HRG and ARG co-distribution in plasmids was affected by the host sources but not by pathogenicity. HRGs were more likely to co-occur with specific ARG classes (sulfonamide, macrolide-lincosamide-streptogramin, and aminoglycoside resistance genes). Collectively, our results reveal the distribution characteristics of HRGs in plasmids, and they have important implications for further understanding the environmental risks caused by the spread of ARGs through the plasmid-mediated co-transfer of ARGs and HRGs.

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“…coli strain in our study also harboured the mer operon on the same plasmid as the tetA , sul1 , and ant(3’)-Ia resistance genes. The co-location of tetracycline, sulphonamide and aminoglycoside encoding resistance genes with the mercury operon on IncF plasmids has been previously described [54, 64, 65] and the presence of the mer operon was positively correlated with sulphonamide and aminoglycoside resistance genes, but not tetracycline resistance genes [65].…”

Section: Discussionmentioning

confidence: 99%

The characterisation of antimicrobial resistant Escherichia coli from dairy calves

Mwenifumbo

Zhao

Ahmed

et al. 2023

Journal of Medical Microbiology

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Introduction. Dairy calves, particularly pre-weaned calves have been identified as a common source of multidrug resistant (MDR) Escherichia coli . Gap statement. E. coli strains isolated from dairy calves and the location of their resistance genes (plasmid or chromosomal) have not been well characterised. Aim. To characterise the phenotypic and genotypic features as well as the population structure of antimicrobial-resistant E. coli isolated from calves located on dairy farms that feed waste-milk to their replacement calves. Methodology. Recto-anal swab enrichments from 40 dairy calves (≤ 14 days old) located on four dairy farms were examined for tetracycline, streptomycin, ciprofloxacin, and third-generation cephalosporin resistant E. coli . Whole genome sequencing was performed using both short- and long-read technologies on selected antimicrobial resistant E. coli . Results. Fifty-eight percent (23/40) of calves harboured antimicrobial resistant E. coli : 43 % (17/40) harboured tetracycline resistant, and 23 % (9/40) harboured chromosomal mediated AmpC producing E. coli . Whole genome sequencing of 27 isolates revealed five sequence types, with ST88 being the dominant ST (17/27, 63 % of the sequenced isolates) followed by ST1308 (3/27, 11 %), along with the extraintestinal pathogenic E. coli lineages ST69 (3/27, 11 %), ST10 (2/27, 7 %), and ST58 (2/27, 7 %). Additionally, 16 isolates were MDR, harbouring additional resistance genes that were not tested phenotypically. Oxford Nanopore long-read sequencing technologies enabled the location of multiple resistant gene cassettes in IncF plasmids to be determined. Conclusion. Our study identified a high incidence of tetracycline and streptomycin-resistant E. coli in dairy calves, and highlighted the presence of multidrug-resistant strains, emphasising the need for further investigation into potential associations with farm management practices.

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Genomic features of a multidrug-resistant and mercury-tolerant environmental Escherichia coli recovered after a mining dam disaster in South America

Cited by 10 publications

References 62 publications

The characterisation of antimicrobial resistantEscherichia colifrom dairy calves

The characterisation of antimicrobial resistantEscherichia colifrom dairy calves

Plasmid Genomes Reveal the Distribution, Abundance, and Organization of Mercury-Related Genes and Their Co-Distribution with Antibiotic Resistant Genes in Gammaproteobacteria

The characterisation of antimicrobial resistant Escherichia coli from dairy calves

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