Whole Genome Sequencing and Characteristics of mcr-1–Harboring Plasmids of Porcine Escherichia coli Isolates Belonging to the High-Risk Clone O25b:H4-ST131 Clade B

Flament-Simon, Saskia-Camille; Toro, María de; Mora, Azucena; García, Vanesa; García-Meniño, Isidro; Díaz-Jiménez, Dafne; Blanco, Jorge

doi:10.3389/fmicb.2020.00387

Cited by 28 publications

(36 citation statements)

References 107 publications

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“…The presence of ColV plasmid in E. coli strains isolated from humans can indicate evidence of zoonotic transmission (Rodriguez-Siek et al, 2005;Liu et al, 2018). As detected in the present study, ColV plasmids can also carry multiple antimicrobial resistance genes, which is clinically relevant due to the combination of virulence and resistance determinants in a single mobile genetic element (Flament-Simon et al, 2020).…”

Section: Discussionsupporting

confidence: 68%

“…Notably, IncF [F1:A2:B20] plasmids without bla CTX−M−15, the most clinically relevant ESBL gene worldwide (Bevan et al, 2017), and IncF [F2:A1:B-] plasmids with this gene are the most frequently associated with the C1 and C2 subclades of ST131, respectively (Johnson et al, 2016;Pitout and DeVinney, 2017). In contrast, IncF [F2:A-:B1] without bla CTX−M−15 is commonly detected in clade B (Reid et al, 2019;Flament-Simon et al, 2020). Interestingly, we reported the presence of bla CTX−M−15 in clade B of ST131 in this study (Figure 1).…”

Section: Discussionmentioning

confidence: 99%

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Colistin-Resistant mcr-1-Positive Escherichia coli ST131-H22 Carrying blaCTX–M–15 and qnrB19 in Agricultural Soil

et al. 2021

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The pandemic Escherichia coli sequence type 131 (ST131) carrying plasmid-mediated colistin resistance mcr genes has emerged worldwide causing extraintestinal infections, with lineages belonging to three major clades (A, B, and C). Clade B is the most prevalent in animals, contaminating associated meat products, and can be transmitted zoonotically. However, the blaCTX–M–15 gene has only been associated with C2 subclade so far. In this study, we performed a genomic investigation of an E. coli (strain S802) isolated from a kale crop in Brazil, which exhibited a multidrug-resistant (MDR) profile to clinically significant antimicrobials (i.e., polymyxin, broad-spectrum cephalosporins, aminoglycosides, and fluoroquinolones). Whole-genome sequencing analysis revealed that the S802 strain belonged to serotype O25:H4, ST131/CC131, phylogenetic group B2, and virotype D5. Furthermore, S802 carried the clade B-associated fimH22 allele, genes encoding resistance to clinically important antimicrobials, metals, and biocides, and was phylogenetically related to human, avian, and swine ST131-H22 strains. Additionally, IncHI2-IncQ1, IncF [F2:A-:B1], and ColE1-like plasmids were identified harboring mcr-1.1, blaCTX–M–15, and qnrB19, respectively. The emergence of the E. coli ST131-H22 sublineage carrying mcr-1.1, blaCTX–M–15, and qnrB19 in agricultural soil represents a threat to food and environmental safety. Therefore, a One Health approach to genomic surveillance studies is required to effectively detect and limit the spread of antimicrobial-resistant bacteria and their resistance genes.

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Section: Discussionsupporting

confidence: 68%

Section: Discussionmentioning

confidence: 99%

Colistin-Resistant mcr-1-Positive Escherichia coli ST131-H22 Carrying blaCTX–M–15 and qnrB19 in Agricultural Soil

et al. 2021

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“…Whole-genome sequencing analysis of these mcr-1 positive E. coli strains identified 19 different STs and was consistent with previous reports documenting the ST diversity of MCRPEC (Wang et al, 2018). However, ST10, ST1146, and ST1147 were more prevalent in our isolates and ST10 is frequently found in clinical (Lin et al, 2020), animal (García-Meniño et al, 2018, and environmental samples (Flament-Simon et al, 2020). In addition, we found that the genomes of two MCRPE isolates from the same sample differed by the phylogenetic analysis.…”

Section: Isolatesupporting

confidence: 90%

Identification of the Plasmid-Mediated Colistin Resistance Gene mcr-1 in Escherichia coli Isolates From Migratory Birds in Guangdong, China

et al. 2021

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We determined the prevalence and transmission characteristics of mcr-1-positive Escherichia coli (MCRPEC) isolates from migratory birds Anser indicus in Guangdong, China. We identified 22 MCRPEC from 303 A. indicus fecal samples (7.3%) in Guangzhou, Zhaoqing, and Futian. The mcr-1 gene coexisted with 24 other types of antibiotic resistance genes (ARG), and 11 ARGs were highly prevalent at levels >50%. The MCRPEC displayed a diversity of sequence types (ST), and 19 distinct STs were identified with ST10, ST1146, and ST1147 as the most prevalent. In addition, these MCRPEC from birds were closely related phylogenetically to those from other sources in China. Whole-genome sequencing analysis demonstrated that mcr-1 was located on IncX4 (n=9, 40.9%), IncI2 (n=5, 22.7%) and IncP (n=1, 4.5%) plasmids and the latter shared an identical plasmid backbone with other sources. These results highlight the significance of migratory birds in the transmission of antibiotic resistance and provide powerful evidence that migratory birds are potential transmitters of antibiotic resistance.

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“…coli ., Moraxella spp., Klebsiella spp., Salmonella spp., Enterobacter spp. and Citrobacter spp [ 44 ]. The mcr -carrying plasmids frequently co-harbor other resistance determinants e.g.…”

Section: Discussionmentioning

confidence: 99%

Whole genome sequencing and characteristics of Escherichia coli with co-existence of ESBL and mcr genes from pigs

Trongjit

Chuanchuen

2021

PLoS ONE

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This study aimed to analyze three ESBL-producing E. coli co-harboring mcr and ESBL genes from a healthy fattening pig (E. 431) and two sick pigs (ECP.81 and ECP.82) in Thailand using Whole Genome Sequencing (WGS) using either Illumina MiSeq or HiSeq PE150 platforms to determine their genome and transmissible plasmids. E. 431 carrying mcr-2.1 and mcr-3.1 belonged to serotype O142:H31 with ST29 sequence type. ECP.81 and ECP.82 from sick pigs harboring mcr-1.1 and mcr-3.1 were serotype O9:H9 with ST10. Two mcr-1.1 gene cassettes from ECP.81 and ECP.82 were located on IncI2 plasmid with 98% identity to plasmid pHNSHP45. The mcr-2.1-carrying contig in E. 431 showed 100% identity to plasmid pKP37-BE with the upstream flanking sequence of IS1595. All three mcr-3.1-carrying contigs contained the ΔTnAs2-mcr-3.1-dgkA core segment and had high nucleotide similarity (85–100%) to mcr-3.1-carrying plasmid, pWJ1. The mobile elements i.e. IS4321, ΔTnAs2, ISKpn40 and IS3 were identified in the flanking regions of mcr-3. Several genes conferring resistance to aminoglycosides (aac(3)-IIa, aadA1, aadA2b, aph(3’’)-Ib, aph(3’)-IIa and aph(6)-Id), macrolides (mdf(A)), phenicols (cmlA1), sulphonamide (sul3) and tetracycline (tet(A) and tet(M)) were located on plasmids, of which their presence was well corresponded to the host’s resistance phenotype. Amino acid substitutions S83L and D87G in GyrA and S80I and E62K in ParC were observed. The blaCTX-M-14 and blaCTX-M-55 genes were identified among these isolates additionally harbored blaTEM-1B. Co-transfer of mcr-1.1/blaTEM-1B and mcr-3.1/blaCTX-M-55 was observed in ECP.81 and ECP.82 but not located on the same plasmid. The results highlighted that application of advanced innovation technology of WGS in AMR monitoring and surveillance provide comprehensive information of AMR genotype that could yield invaluable benefits to development of control and prevention strategic actions plan for AMR.

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Whole Genome Sequencing and Characteristics of mcr-1–Harboring Plasmids of Porcine Escherichia coli Isolates Belonging to the High-Risk Clone O25b:H4-ST131 Clade B

Cited by 28 publications

References 107 publications

Colistin-Resistant mcr-1-Positive Escherichia coli ST131-H22 Carrying blaCTX–M–15 and qnrB19 in Agricultural Soil

Colistin-Resistant mcr-1-Positive Escherichia coli ST131-H22 Carrying blaCTX–M–15 and qnrB19 in Agricultural Soil

Identification of the Plasmid-Mediated Colistin Resistance Gene mcr-1 in Escherichia coli Isolates From Migratory Birds in Guangdong, China

Whole genome sequencing and characteristics of Escherichia coli with co-existence of ESBL and mcr genes from pigs

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