Occurrence and genetic characteristics of mcr-1-positive colistin-resistant E. coli from poultry environments in Bangladesh

ABSTRACT This study aimed to investigate the genetic characteristics, antibiotic resistance patterns, and novel mechanisms involved in fluoroquinolone (FQ) resistance in commensal Escherichia coli isolates. The E. coli isolates were recovered from a previous clinical study and subjected to antimicrobial susceptibility testing and molecular typing. Known mechanisms of FQ resistance (target site mutations, plasmid-mediated quinolone resistance [PMQR] genes, relative expression levels of efflux pumps and porins) were detected using DNA sequencing of PCR products and real-time quantitative PCR. Whole-genome shotgun sequencing was performed on 11 representative strains to screen for single nucleotide polymorphisms (SNPs). The function of a key SNP (A1541G) was investigated by site-directed mutagenesis and allelic exchange. The results showed that long-term enrofloxacin treatment selected multidrug-resistant (MDR) E. coli isolates in the chicken gut and that these E. coli isolates had diverse genetic backgrounds. Multiple genetic alterations, including double mutations on GyrA (S83L and D87N), a single mutation on ParC (S80I) and ParE (S458E), activation of efflux pumps, and the presence of the QnrS1 protein, contributed to the high-level FQ resistance (enrofloxacin MIC [MICENR] ≥ 128 μg/ml), while the relatively low-level FQ resistance (MICENR = 8 or 16 μg/ml) was commonly mediated by decreased expression of the porin OmpF, besides enhancement of the efflux pumps. No significant relationship was observed between resistance mechanisms and virulence genes. Introduction of the A1541G mutation on aegA was able to increase FQ susceptibility by 2-fold. This study contributes to a better understanding of the development of MDR and the differences underlying the mechanisms of high-level and low-level FQ resistance in E. coli.

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Escherichia coli Producing Extended-Spectrum β-lactamases (ESBL) from Domestic Camels in the Canary Islands: A One Health Approach

Animals ◽

10.3390/ani10081295 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1295

Author(s):

Isabel Carvalho ◽

María Teresa Tejedor-Junco ◽

Margarita González-Martín ◽

Juan Alberto Corbera ◽

Vanessa Silva ◽

...

Keyword(s):

Escherichia Coli ◽

Canary Islands ◽

Tetracycline Resistance ◽

Phylogenetic Groups ◽

Esbl Producer ◽

Carriage Rate ◽

Genetic Characteristics ◽

Disk Diffusion Test ◽

E Coli ◽

Specific Pcr

Objective: This work aimed to determine the carriage rate of ESBL-producing Escherichia coli as well as their genetic characteristics in camels from the Canary Islands, Spain. Methods: Fecal samples were recovered from 58 healthy camels from Gran Canaria (n = 32) and Fuerteventura Islands (n = 26) during July 2019. They were seeded on MacConkey (MC) agar no supplemented and supplemented (MC + CTX) with cefotaxime (2 µg/mL). Antimicrobial susceptibility was determined by disk diffusion test (CLSI, 2018). The presence of blaCTX-M, blaSHV, blaTEM,blaCMY-2 and blaOXA-1/48 genes was tested by PCR/sequencing. Furthermore, the mcr-1 (colistin resistance), tetA/tetB (tetracycline resistance), int1 (integrase of class 1 integrons) and stx1,2 genes were analyzed. Phylogenetic groups and sequence types were determined by specific-PCR/sequencing for selected isolates. Results: E. coli was obtained from all the 58 camels in MC media (100%) and in five of them in MC + CTX media (8.6%). Furthermore, 63.8% of E. coli isolates recovered from MC agar were susceptible to all the antibiotics tested. The five E. coli isolates recovered from MC + CTX media were characterized and two of them were ESBL-producers (3.4%). Both ESBL-producer isolates carried the blaCTX-M-15 gene and belonged to the lineages ST3018 (phylogroup A) and ST69 (phylogroup B1). The 3 ESBL-negative isolates recovered from MC-CTX plates were ascribed to phylogroup-B1. Conclusions: Camels can be a source of ESBL-producer bacteria, containing the widespread blaCTX-M-15 gene associated with the lineages ST3018 and ST69.

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Prevalence of Carriage of Shiga Toxin-Producing Escherichia coli Serotypes O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28 among Slaughtered Adult Cattle in France

Applied and Environmental Microbiology ◽

10.1128/aem.03315-14 ◽

2014 ◽

Vol 81 (4) ◽

pp. 1397-1405 ◽

Cited By ~ 26

Author(s):

Delphine Bibbal ◽

Estelle Loukiadis ◽

Monique Kérourédan ◽

Franck Ferré ◽

Françoise Dilasser ◽

...

Keyword(s):

Escherichia Coli ◽

Dairy Cows ◽

Shiga Toxin ◽

Beef Cows ◽

Adult Cattle ◽

Genetic Characteristics ◽

Content Type ◽

E Coli ◽

Beef Bulls ◽

Dairy Bulls

ABSTRACTThe main pathogenic enterohemorrhagicEscherichia coli(EHEC) strains are defined as Shiga toxin (Stx)-producingE. coli(STEC) belonging to one of the following serotypes: O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28. Each of these five serotypes is known to be associated with a specific subtype of the intimin-encoding gene (eae). The objective of this study was to evaluate the prevalence of bovine carriers of these “top five” STEC in the four adult cattle categories slaughtered in France. Fecal samples were collected from 1,318 cattle, including 291 young dairy bulls, 296 young beef bulls, 337 dairy cows, and 394 beef cows. A total of 96E. coliisolates, including 33 top five STEC and 63 atypical enteropathogenicE. coli(aEPEC) isolates, with the same genetic characteristics as the top five STEC strains except that they lacked anstxgene, were recovered from these samples. O157:H7 was the most frequently isolated STEC serotype. The prevalence of top five STEC (all serotypes included) was 4.5% in young dairy bulls, 2.4% in young beef bulls, 1.8% in dairy cows, and 1.0% in beef cows. It was significantly higher in young dairy bulls (P< 0.05) than in the other 3 categories. The basis for these differences between categories remains to be elucidated. Moreover, simultaneous carriage of STEC O26:H11 and STEC O103:H2 was detected in one young dairy bull. Lastly, the prevalence of bovine carriers of the top five STEC, evaluated through a weighted arithmetic mean of the prevalence by categories, was estimated to 1.8% in slaughtered adult cattle in France.

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Virulence Determinants and Plasmid-Mediated Colistin Resistance mcr Genes in Gram-Negative Bacteria Isolated From Bovine Milk

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.761417 ◽

2021 ◽

Vol 11 ◽

Author(s):

Yasmine H. Tartor ◽

Rasha M. A. Gharieb ◽

Norhan K. Abd El-Aziz ◽

Hend M. El Damaty ◽

Shymaa Enany ◽

...

Keyword(s):

Virulence Genes ◽

Raw Milk ◽

Subclinical Mastitis ◽

Clinical Mastitis ◽

Gram Negative Bacteria ◽

Colistin Resistance ◽

Genetic Characteristics ◽

Gram Negative ◽

E Coli ◽

Resistant Strains

A major increase of bacterial resistance to colistin, a last-resort treatment for severe infections, was observed globally. Using colistin in livestock rearing is believed to be the ground of mobilized colistin resistance (mcr) gene circulation and is of crucial concern to public health. This study aimed to determine the frequency and virulence characteristics of colistin-resistant Gram-negative bacteria from the milk of mastitic cows and raw unpasteurized milk in Egypt. One hundred and seventeen strains belonging to Enterobacteriaceae (n = 90), Pseudomonas aeruginosa (n = 10), and Aeromonas hydrophila (n = 17) were screened for colistin resistance by antimicrobial susceptibility testing. The genetic characteristics of colistin-resistant strains were investigated for mcr-1–9 genes, phylogenetic groups, and virulence genes. Moreover, we evaluated four commonly used biocides in dairy farms for teat disinfection toward colistin-resistant strains. Multidrug-resistant (MDR) and extensive drug-resistant (XDR) phenotypes were detected in 82.91% (97/117) and 3.42% (4/117) of the isolates, respectively. Of the 117 tested isolates, 61 (52.14%) were colistin resistant (MIC >2 mg/L), distributed as 24/70 (34.29%) from clinical mastitis, 10/11 (90.91%) from subclinical mastitis, and 27/36 (75%) from raw milk. Of these 61 colistin-resistant isolates, 47 (19 from clinical mastitis, 8 from subclinical mastitis, and 20 from raw milk) harbored plasmid-borne mcr genes. The mcr-1 gene was identified in 31.91%, mcr-2 in 29.79%, mcr-3 in 34.04%, and each of mcr-4 and mcr-7 in 2.13% of the colistin-resistant isolates. Among these isolates, 42.55% (20/47) were E. coli, 21.28% (10/47) A. hydrophila, 19.12% (9/47) K. pneumoniae, and 17.02% (8/47) P. aeruginosa. This is the first report of mcr-3 and mcr-7 in P. aeruginosa. Conjugation experiments using the broth-mating technique showed successful transfer of colistin resistance to E. coli J53-recipient strain. Different combinations of virulence genes were observed among colistin-resistant isolates with almost all isolates harboring genes. Hydrogen peroxide has the best efficiency against all bacterial isolates even at a low concentration (10%). In conclusion, the dissemination of mobile colistin resistance mcr gene and its variants between MDR- and XDR-virulent Gram-negative isolates from dairy cattle confirms the spread of mcr genes at all levels; animals, humans, and environmental, and heralds the penetration of the last-resort antimicrobial against MDR bacteria. Consequently, a decision to ban colistin in food animals is urgently required to fight XDR and MDR bacteria.

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Comparative analysis of genetic characterization of β-lactam-resistant Escherichia coli from bulk tank milk in Korea

Irish Veterinary Journal ◽

10.1186/s13620-021-00203-4 ◽

2021 ◽

Vol 74 (1) ◽

Author(s):

Hye-Ri Jung ◽

Koeun Kim ◽

Young Ju Lee

Keyword(s):

Escherichia Coli ◽

Clinical Mastitis ◽

Phylogenetic Groups ◽

Bulk Tank Milk ◽

Genetic Characteristics ◽

E Coli ◽

Intestinal Infections ◽

Antimicrobial Resistance Genes ◽

Bulk Tank ◽

Genotypic Characteristics

Abstract Background This study was conducted to analyze the genetic characteristics of 41 β-lactam-resistant Escherichia coli isolates, which are one of the common causes of environmental mastitis, isolated from the bulk tank milk of 290 dairy farms in five factories operated by three dairy companies in Korea. Results Analysis of the phenotypic and genotypic characteristics of β-lactam-resistant E. coli isolates revealed differences between factories even within the same company. Isolates from factory A1 and C1 showed high resistance to cephalothin (76.9 and 100%, respectively), which is a first-generation cephalosporins, whereas resistance to tetracycline was showed by only the isolates from factories B1 (60.0%), C2 (66.7%), and C3 (100%). Although all the 41 β-lactam-resistant E. coli isolates were positive for blaOXA-1, blaTEM-1 was highly prevalent in isolates from factories C2 (100%) and C3 (100%). Among 17 isolates resistant to both β-lactams and aminoglycosides, the most common multilocus sequence type was ST399 (13isolates, 76.5%). Furthermore, 2 (11.8%) and 12 (70.6%) isolates belonged to the phylogenetic groups B2 and D, respectively, which are invasive strains that cause intestinal infections, respectively. The predominant serogroup was O15 (70.6%), which is a globally distributed extraintestinal pathogen. Interestingly, one isolate from factory A1 belonged to O157 and carried six virulence genes, simultaneously. Conclusions Although E. coli isolates were isolated from bulk tank milk, and not the clinical mastitis samples, the presence of the phylogenetic groups B2 and D, and the serogroups O15 and O157, which harbor antimicrobial resistance genes and virulence factors, can pose a threat to public health.

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Plasmidic resistance to colistin mediated by mcr-1 gene in Escherichia coli clinical isolates in Argentina: A retrospective study, 2012–2018

Revista Panamericana de Salud Pública ◽

10.26633/rpsp.2020.55 ◽

2020 ◽

Vol 44 ◽

pp. 1

Author(s):

Diego Faccone ◽

Melina Rapoport ◽

Ezequiel Albornoz ◽

Federico Celaya ◽

Juan De Mendieta ◽

...

Keyword(s):

Escherichia Coli ◽

Retrospective Study ◽

Genetic Relatedness ◽

Horizontal Transmission ◽

Wide Distribution ◽

Clinical Isolates ◽

Genetic Characteristics ◽

Minimal Inhibitory Concentrations ◽

E Coli ◽

Standard Polymerase Chain Reaction

Objective. To describe the resistance profile and the genetic characteristics of Escherichia coli isolates that harbor the mobilizable colistin resistance gene mcr-1 in Argentina. Methods. This was a retrospective study of 192 E. coli isolates positive for mcr-1 obtained from 69 hospitals of Buenos Aires City and 14 Argentinean provinces in 2012 – 2018. The antimicrobial susceptibility was performed by agar diffusion, broth macrodilution, and/or agar dilution. Standard polymerase chain reaction (PCR) was performed to detect resistance genes and incompatibility groups; specific PCR was applied to discriminate between blaCTX-M allelic groups and mcr-1.5 variant. The genetic relatedness among isolates was evaluated by XbaI-pulsed field gel electrophoresis and multilocus sequence typing in a subset of isolates. Results. All E. coli isolates showed minimal inhibitory concentrations to colistin = 4µg/mL; nearly 50% were resistant to third-generation cephalosporins, with CTX-M-2 being the main extended-spectrum β-lactamase detected. Five E. coli were carbapenemase-producers (3 NDM, 2 KPC). The mcr-1.5 variant was detected in 13.5% of the isolates. No genetic relationship was observed among the mcr-1-positive E. coli clinical isolates, but a high proportion (164/192; 85.4%) of IncI2 plasmids was detected. Conclusions. The presence of IncI2 plasmids among highly diverse E. coli clones suggests that the mcr-1 gene’s wide distribution in Argentina may be driven by the horizontal transmission of IncI2 plasmids.

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MOLECULAR-GENETIC CHARACTERISTICS OF SHIGELLA SONNEI-2013 STRAIN ISOLATED DURING THE OUTBREAK IN DYSENTERY IN THE REPUBLIC ABKHAZIA IN 2013

Journal of microbiology epidemiology immunobiology ◽

10.36233/0372-9311-2018-1-72-76 ◽

2018 ◽

pp. 72-76

Author(s):

O. V. Vasileva ◽

A. S. Volynkina ◽

I. V. Kuznetsova ◽

S. V. Pisarenko ◽

A. N. Kulichenko

Keyword(s):

Nucleotide Sequence ◽

Molecular Genetic ◽

Housekeeping Genes ◽

Shigella Sonnei ◽

Personal Genome ◽

Virulence Plasmid ◽

Genetic Characteristics ◽

E Coli ◽

Type Iv ◽

The Republic

Aim. Study of molecular-genetic properties of Shigella sonnei-2013 strain isolated during the outbreak in dysentery in the republic Abkhazia in 2013. Materials and methods. Genetic typing of the tested strains using multilocus sequence typing (MLST). Analyzed of nucleotide sequence fragments 7 of conservative «housekeeping» genes adk, fumC, icd, mdh, purA, recA, gyrB. Sequenced of DNA fragments compared with reference sequences from database of Escherichia coli MLST. Phylogenetic analysis was performed using UPGMA method and computer program START 2. Whole-genome sequencing performed on a genetic analyzer Ion Torrent Personal Genome Machine (PGM™) using fragment libraries (shot-gun). Aligning reads have been carried out with the program GS Reference Mapper. Results. Defined sequence - type of the studied strain - ST-152, one of the most common genotypes for S. sonnei. Demonstrated the high degree of similarity obtained contig to the sequences of the chromosome and plasmids А, В, С и E strains S. sonnei 53G and S. sonnei Ss046. Identified contigs with a high percentage similarity to the sequence of virulence plasmid p026-Vir of E. coli 026:H11 (H30). In the genomic S. sonnei-2013 revealed nucleotide sequence of 136 genes were found located on the p026-Vir strain of E. coli 026:Н11 (НЗО). Discovered genes controlling biosynthesis of type IV pili involved in adhesion to abiotic surfaces and biofilm formation. Conclusion. Identified structural peculiarities of strain induced by fragments of virulence plasmid p026-Vir strain E. coli 026:H 11 (H30).

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Analyzing the Genetic Characteristics of a Tryptophan-overproducing Escherichia Coli

10.21203/rs.3.rs-122063/v1 ◽

2020 ◽

Author(s):

Dongqin Ding ◽

Danyang Bai ◽

Jinlong Li ◽

Zhitao Mao ◽

Yaru Zhu ◽

...

Keyword(s):

Escherichia Coli ◽

Genetic Background ◽

Great Influence ◽

Random Mutagenesis ◽

Underlying Structure ◽

Carbon Utilization ◽

Genetic Characteristics ◽

E Coli ◽

Long Time ◽

Dynamics Simulations

Abstract Background: L-tryptophan (L-trp) production in Escherichia coli has been developed by employing random mutagenesis and selection for a long time, but this approach produces an unclear genetic background. Results: We generated the L-trp overproducer TPD5 by combining an intracellular L-trp biosensor and fluorescence-activated cell sorting (FACS) in E. coli, and succeeded in elucidating the genetic basis for L-trp overproduction. The most significant identified positive mutations affected TnaA (deletion), AroG (S211F), TrpE (A63V), and RpoS (nonsense mutation Q33*). The underlying structure-function relationships of the feedback-resistant AroG (S211F) and TrpE (A63V) mutants were uncovered based on protein structure modeling and molecular dynamics simulations, respectively. According to transcriptomic analysis, the global regulator RpoS not only has a great influence on cell growth and morphology, but also on carbon utilization and the direction of carbon flow. Finally, by balancing the concentrations of the L-trp precursors serine and glutamine based on the above analysis, we further increased the titer of L-trp to 3.18 g/L with a yield of 0.18 g/g. Conclusions: The analysis of the genetic characteristics of an L-trp overproducing E. coli provides valuable information on L-trp synthesis and elucidates the phenotype and complex cellular properties in a high-yielding strain, which opens the possibility to transfer beneficial mutations and reconstruct an overproducer with a clean genetic background.

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Hybrid Atypical Enteropathogenic and Extraintestinal Escherichia coli (aEPEC/ExPEC) BA1250 Strain: A Draft Genome

Pathogens ◽

10.3390/pathogens10040475 ◽

2021 ◽

Vol 10 (4) ◽

pp. 475

Author(s):

Danielle D. Munhoz ◽

Fernanda F. Santos ◽

Thais Mitsunari ◽

Paulo A. Schüroff ◽

Waldir P. Elias ◽

...

Keyword(s):

Escherichia Coli ◽

Evolutionary Biology ◽

Draft Genome ◽

Hybrid Strain ◽

Genetic Characteristics ◽

E Coli ◽

Severe Diarrhea ◽

Diarrheagenic Escherichia Coli ◽

Intestinal Infections ◽

Genome Content

Diarrheagenic Escherichia coli is the major bacterial etiological agent of severe diarrhea and a major concern of public health. These pathogens have acquired genetic characteristics from other pathotypes, leading to unusual and singular genetic combinations, known as hybrid strains and may be more virulent due to a set of virulence factors from more than one pathotype. One of the possible combinations is with extraintestinal E. coli (ExPEC), a leading cause of urinary tract infection, often lethal after entering the bloodstream and atypical enteropathogenic E. coli (aEPEC), responsible for death of thousands of people every year, mainly children under five years old. Here we report the draft genome of a strain originally classified as aEPEC (BA1250) isolated from feces of a child with acute diarrhea. Phylogenetic analysis indicates that BA1250 genome content is genetically closer to E. coli strains that cause extraintestinal infections, other than intestinal infections. A deeper analysis showed that in fact this is a hybrid strain, due to the presence of a set of genes typically characteristic of ExPEC. These genomic findings expand our knowledge about aEPEC heterogeneity allowing further studies concerning E. coli pathogenicity and may be a source for future comparative studies, virulence characteristics, and evolutionary biology.

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