scholarly journals Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69 Escherichia coli Strain in Italy

2020 ◽  
Vol 8 (8) ◽  
pp. 1232
Author(s):  
Vittoria Mattioni Marchetti ◽  
Ibrahim Bitar ◽  
Aurora Piazza ◽  
Alessandra Mercato ◽  
Elena Fogato ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Care Facility ◽  
Genomic Analysis ◽  
Coli Strain ◽  
Beta Lactam ◽  
Aminoglycoside Resistance ◽  
Term Care ◽  
Antimicrobial Resistance Genes

Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the blaVIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using “Microbial Assembly”. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6′)-Ib4, ant(3″)-Ia, aph(3″)-Ib, aph(3′)-XV, aph(6)-Id), beta-lactam resistance (blaSHV-12, blaVIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the blaVIM-1 gene in Italy.

Prevalence and genomic analysis of ESBL-producing Escherichia coli in retail raw meats in Singapore

2020 ◽  
Author(s):  
Siyao Guo ◽  
Kyaw Thu Aung ◽  
Pimlapas Leekitcharoenphon ◽  
Moon Y F Tay ◽  
Kelyn L G Seow ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Colistin Resistance ◽  
Aminoglycoside Resistance ◽  
Genetic Characteristics ◽  
Raw Meat ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Raw Meats

Abstract Objectives To determine the prevalence and genetic characteristics of ESBL-producing Escherichia coli in retail raw meats from Singapore markets. Methods A total of 634 raw meat (chicken, pork and beef) samples were collected from markets in Singapore during June 2017–October 2018. The samples were enriched overnight and then incubated on Brilliance™ ESBL Agar. Presumptive ESBL isolates were confirmed using the double-disc synergy test. Confirmed ESBL-producing E. coli were sent for WGS and bioinformatic analysis was performed. Results The prevalence of ESBL-producing E. coli in chicken, pork and beef meats was 51.2% (109/213), 26.9% (58/216) and 7.3% (15/205), respectively. A total of 225 ESBL-producing E. coli were isolated from 184 samples. β-Lactam resistance genes were detected in all isolates. After β-lactam resistance genes, the most common antimicrobial resistance genes detected were aminoglycoside resistance genes (92.4%). One hundred and seventy-two (76.4%), 102 (45.3%) and 52 (23.1%) isolates carried blaCTX-M genes, blaTEM genes and blaSHV genes, respectively. blaCTX-M-55 (57/225, 25.3%) and blaCTX-M-65 (40/225, 17.8%) were the most frequent ESBL genes. Colistin resistance genes (including mcr-1, mcr-3 and mcr-5) were found in 15.6% of all isolates. Conclusions This study indicates that ESBL-producing E. coli are widely found in retail raw meats, especially chicken, in Singapore. Occurrence of MDR (resistance to at least three classes of antimicrobial) and colistin resistance genes in retail raw meat suggests potential food safety and public health risks.

scholarly journals Virulence Properties of mcr-1-Positive Escherichia coli Isolated from Retail Poultry Meat

2021 ◽  
Vol 9 (2) ◽  
pp. 308
Author(s):  
Michaela Kubelová ◽  
Ivana Koláčková ◽  
Tereza Gelbíčová ◽  
Martina Florianová ◽  
Alžběta Kalová ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Poultry Meat ◽  
Human Populations ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Mlst Type ◽  
On Line ◽  
Sequence Types

The great plasticity and diversity of the Escherichia coli genome, together with the ubiquitous occurrence, make E. coli a bacterium of world-wide concern. Of particular interest are pathogenic strains and strains harboring antimicrobial resistance genes. Overlapping virulence-associated traits between avian-source E. coli and human extraintestinal pathogenic E. coli (ExPEC) suggest zoonotic potential and safety threat of poultry food products. We analyzed whole-genome sequencing (WGS) data of 46 mcr-1-positive E. coli strains isolated from retail raw meat purchased in the Czech Republic. The investigated strains were characterized by their phylogroup—B1 (43%), A (30%), D (11%), E (7%), F (4%), B2 (2%), C (2%), MLST type, and serotype. A total of 30 multilocus sequence types (STs), of which ST744 was the most common (11%), were identified, with O8 and O89 as the most prevalent serogroups. Using the VirulenceFinder tool, 3 to 26 virulence genes were detected in the examined strains and a total of 7 (15%) strains met the pathogenic criteria for ExPEC. Four strains were defined as UPEC (9%) and 18 (39%) E. coli strains could be classified as APEC. The WGS methods and available on-line tools for their evaluation enable a comprehensive approach to the diagnosis of virulent properties of E. coli strains and represent a suitable and comfortable platform for their detection. Our results show that poultry meat may serve as an important reservoir of strains carrying both virulence and antibiotic resistance genes for animal and human populations.

Antibiotic susceptibility profiles and frequency of resistance genes in clinical Shiga toxin-producing Escherichia coli isolates from Michigan over a 14-year period

2021 ◽  
Author(s):  
Sanjana Mukherjee ◽  
Heather M. Blankenship ◽  
Jose A. Rodrigues ◽  
Rebekah E. Mosci ◽  
James T. Rudrik ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Shiga Toxin ◽  
Antibiotic Susceptibility ◽  
Genetic Relatedness ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Mechanisms Of Resistance ◽  
Susceptibility Profiles

Background: Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen that contributes to over 250,000 infections in the US each year. Because antibiotics are not recommended for STEC infections, resistance in STEC has not been widely researched despite an increased likelihood for the transfer of resistance gene from STEC to opportunistic pathogens residing within the same microbial community. Methods: Between 2001 and 2014, 969 STEC isolates were collected from Michigan patients. Serotyping and antibiotic susceptibility profiles to clinically relevant antibiotics were determined using disc diffusion, while epidemiological data was used to identify factors associated with resistance. Whole genome sequencing was used to examine genetic relatedness and identify genetic determinants and mechanisms of resistance in the non-O157 isolates. Results: Increasing frequencies of resistance to at least one antibiotic was observed over the 14 years (p=0.01). While the non-O157 serogroups were more commonly resistant than O157 (Odds Ratio: 2.4; 95% Confidence Interval:1.43-4.05), the frequency of ampicillin resistance among O157 isolates was significantly higher in Michigan compared to the national average (p=0.03). Genomic analysis of 321 non-O157 isolates uncovered 32 distinct antibiotic resistance genes (ARGs). Although mutations in genes encoding resistance to ciprofloxacin and ampicillin were detected in four isolates, most of the horizontally acquired ARGs conferred resistance to aminoglycosides, β-lactams, sulfonamides and/or tetracycline. Conclusions: This study provides insight into the mechanisms of resistance in a large collection of clinical non-O157 STEC isolates and demonstrates that antibiotic resistance among all STEC serogroups has increased over time, prompting the need for enhanced surveillance.

scholarly journals Characterization and Comparative Genomics Analysis of lncFII Multi-Resistance Plasmids Carrying blaCTX–M and Type1 Integrons From Escherichia coli

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Zhou ◽  
Enbao Zhang ◽  
Jinzhi Zhou ◽  
Ze He ◽  
Yuqiao Zhou ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Antimicrobial Agents ◽  
Antibiotic Resistance Genes ◽  
Beta Lactam ◽  
Detection Rates ◽  
E Coli ◽  
Extended Spectrum ◽  
Poultry Breeding ◽  
Resistance Plasmids

This research aimed to investigate the presence and transferability of the extended-spectrum β-lactamase resistance genes to identify the genetic context of multi-drug resistant (MDR) loci in two Escherichia coli plasmids from livestock and poultry breeding environment. MICs were determined by broth microdilution. A total of 137 E. coli resistant to extended-spectrum β-lactam antibiotics were screened for the presence of the ESBL genes by PCR. Only two E. coli out of 206 strains produced carbapenemases, including strain 11011 that produced enzyme A, and strain 417957 that produced enzyme B. The genes were blaKPC and blaNDM, respectively. The plasmids containing blaCTX–M were conjugatable, and the plasmids containing carbapenem resistance gene were not conjugatable. Six extended-spectrum β-lactamase resistance genes were detected in this research, including blaTEM, blaCTX–M, blaSHV, blaOAX–1, blaKPC, and blaNDM, and the detection rates were 94.89% (130/137), 92.7% (127/137), 24.81% (34/137), 20.43% (28/137), 0.72% (1/137), and 0.72% (1/137), respectively. Two conjugative lncFII multi-resistance plasmids carrying blaCTX–M, p11011-fosA and p417957-CTXM, were sequenced and analyzed. Both conjugative plasmids were larger than 100 kb and contained three accessory modules, including MDR region. The MDR region of the two plasmids contained many antibiotic resistance genes, including blaCTX–M, mph (A), dfrA17, aadA5, sul1, etc. After transfer, both the transconjugants displayed elevated MICs of the respective antimicrobial agents. A large number of resistance genes clusters in specific regions may contribute to the MDR profile of the strains. The presence of mobile genetic elements at the boundaries can possibly facilitate transfer among Enterobacteriaceae through inter-replicon gene transfer. Our study provides beta-lactam resistance profile of bacteria, reveals the prevalence of β-lactamase resistance genes in livestock and poultry breeding environment in Zhejiang Province, and enriches the research on IncFII plasmids containing blaCTX–M.

scholarly journals Associations between Antimicrobial Resistance Genes in Fecal Generic Escherichia coli Isolates from Cow-Calf Herds in Western Canada

2008 ◽  
Vol 74 (12) ◽  
pp. 3658-3666 ◽  
Author(s):  
Sheryl P. Gow ◽  
Cheryl L. Waldner ◽  
Josee Harel ◽  
Patrick Boerlin
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Gene Selection ◽  
Western Canada ◽  
Genetic Determinants ◽  
Aminoglycoside Resistance ◽  
Antimicrobial Resistance Genes ◽  
Cow Calf ◽  
Aminoglycoside Resistance Genes

ABSTRACT The objective of this study was to examine associations among the genetic determinants of antimicrobial resistance (AMR) in 207 fecal generic Escherichia coli isolates obtained from 77 cow-calf herds in western Canada. Twenty-three resistance genes corresponding to six different antimicrobial families were assessed using DNA hybridization and PCR. The most common resistance genes in the study sample (207 isolates) were sul2 (48.3%), tet(B) (45.4%), and ant(3″)-Ia (aadA1) (19.3%). Several statistically significant associations between the examined resistance genes were detected. The strongest associations observed were those between genes for resistance to chloramphenicol (catI) and trimethoprim (dhfrI) (odds ratio [OR] = 214; P = 0.0001), sulfonamide (sul1) and chloramphenicol (catI) (OR = 96.9; P = 0.0001), streptomycin [ant(3″)-Ia (aadA1)] and trimethoprim (dhfrI) (OR = 96.2; P = 0.0001), sulfonamide (sul1) and streptomycin [ant(3″)-Ia (aadA1)] (OR = 79.3; P = 0.0001), and tetracycline [tet(B)] and sulfonamides (sul2) (OR = 25.7; P = 0.0001). At least one of the resistance genes corresponding to each nonaminoglycoside family of antimicrobials examined in this study was associated with the two aminoglycoside resistance genes ant(3″)-Ia (aadA1) and aph(3′)-Ia. The multiple, strong associations between genes and the diverse nature of the associations described in this study demonstrate the complexity of resistance gene selection in cow-calf herds and should be considered in the planning of AMR control practices for cow-calf operations.

The contribution of small cryptic plasmids to the antibiotic resistance of enteropathogenic Escherichia coli E2348/69

2009 ◽  
Vol 55 (11) ◽  
pp. 1229-1239 ◽  
Author(s):  
Cynthia L. Handford ◽  
Charma T. Stang ◽  
Tracy L. Raivio ◽  
Jonathan J. Dennis
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Dna Sequence ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Gene Clusters ◽  
Coli Strain ◽  
Enteropathogenic Escherichia Coli ◽  
E Coli ◽  
Cryptic Plasmids

Two uncharacterized small cryptic plasmids (SCPs) were isolated from enteropathogenic Escherichia coli strain E2348/69. Genomic DNA sequence analysis of both SCPs indicated that the smaller plasmid, p5217, encoded several mobilization genes, whereas the larger plasmid, p6148, encoded several putative antibiotic resistance determinants. Complementation analysis showed that p6148 encodes functional streptomycin resistance genes but, owing to the presence of several frameshift mutations, a nonfunctional sulfonamide resistance determinant. A plasmid similar to p6148 has previously been shown to confer a slight growth advantage on E. coli. However, we were unable to observe any significant growth advantage in different E. coli strains transformed with p6148. The p6148 DNA sequence is homologous in sequence and arrangement to DNA from other plasmid families, including large conjugative plasmids and SXT integrative and conjugative elements. This study suggests that gene clusters of the sul2–strAB antibiotic resistance genes are widespread and highly transferable, owing to their presence in a wide variety of mobile genetic elements.

scholarly journals Prolonged clonal spreading and dynamic changes in antimicrobial resistance of Escherichia coli ST68 among patients who stayed in a respiratory care ward

2014 ◽  
Vol 63 (11) ◽  
pp. 1531-1541 ◽  
Author(s):  
Chih-Ming Chen ◽  
Se-Chin Ke ◽  
Chia-Ru Li ◽  
Chien-Shun Chiou ◽  
Chao-Chin Chang
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Care Facility ◽  
Respiratory Care ◽  
Term Care ◽  
Long Term Care Facility ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Care Ward

From 2007 to 2009, we collected a total of 83 bacteraemic isolates of Escherichia coli with reduced susceptibility or resistance to third-generation cephalosporins (TGCs). Isolates were genotyped by PFGE and multilocus sequence typing (MLST). The PFGE patterns revealed two highly correlated clusters (cluster E: nine isolates; cluster G: 22 isolates) associated with this prolonged clonal spreading. Compared with cluster E isolates, cluster G isolates were significantly more likely to harbour aac(6')-Ib-cr (P<0.05), and most of these isolates were isolated during a later year than cluster E isolates (P<0.05). By MLST analysis, 94 % of cluster E and G isolates (29/31) were ST68. Although no time or space clustering could be identified by the conventional hospital-acquired infection monitoring system, E. coli cases caused by cluster E and G isolates were significantly associated with having stayed in our hospital’s respiratory care ward (P<0.05). Isolates obtained from patients who had stayed in the respiratory care ward had a significantly higher rate of aac(6')-Ib-cr and bla CTX-M-14 positivity, and were more likely to belong to ST68/S68-like (all P<0.05). To our knowledge, this is the first report of prolonged clonal spreading caused by E. coli ST68 associated with a stay in a long-term care facility. Using epidemiological investigations and PFGE and MLST analyses, we have identified long-term clonal spreading caused by E. coli ST68, with extra antimicrobial-resistance genes possibly acquired during the prolonged spreading period.

Molecular Characterization of Multidrug-Resistant Escherichia coli Isolated from Milk of Dairy Cows with Clinical Mastitis in Algeria

2020 ◽  
Vol 83 (12) ◽  
pp. 2173-2178
Author(s):  
SEDRATI TAHAR ◽  
MENOUERI M. NABIL ◽  
TENNAH SAFIA ◽  
EDGARTHE P. NGAIGANAM ◽  
AZZI OMAR ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Multilocus Sequence Typing ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Clinical Mastitis ◽  
Diffusion Method ◽  
Aminoglycoside Resistance ◽  
Disk Diffusion Method ◽  
Columbia Blood Agar

ABSTRACT The objective of this study was to investigate the occurrence of multidrug-resistant Escherichia coli in cows with clinical mastitis in 42 different dairy farms located in the Bordj Bou Arreridj region of Algeria. Milk samples were cultured on Columbia blood agar, and isolates were then identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry. In total, 200 samples were screened and 52 E. coli strains confirmed as causative agents were obtained. The antimicrobial susceptibility testing was performed by disk diffusion method. Antibiotic resistance genes, including those conferring resistance to extended-spectrum β-lactamases (i.e., blaTEM, blaSHV, and blaCTX-M), tetracyclines (tetA, tetB, tetC, and tetJ), aminoglycosides [aph(3′), aac(3′), aac(6′), ant, aad, and armA], and quinolones (qnrA and qnrB) were amplified by standard PCR and sequenced when positive. Transferability of resistance genes has been investigated by conjugation experiments and multilocus sequence typing. The most frequently observed resistance was to amoxicillin (86.5%), followed by tetracycline (75%), amoxicillin–clavulanic acid (59.6%), trimethoprim-sulfamethoxazole (36.5%), doxycycline (13.5%), and ciprofloxacin (13.5%). Multidrug resistance was observed in 38.4% of isolates. Genotypic characterization showed that tetA (44.2%) and blaTEM-1 (30.7%) genes were the most prevalent. Screening for plasmid-mediated quinolone resistance genes demonstrated that seven isolates (13.5%) expressed qnrB and one isolate (1.9%) harbored qnrA. In addition, aminoglycoside resistance determinants including aadA1 and aac(3)-Id were detected in seven and two isolates, respectively. Moreover, blaTEM, tetA, tetB, qnrB, and aadA1 were successfully transferred horizontally to transconjugant strains. The multilocus sequence typing revealed the presence of three different sequence types (ST162, ST371, and ST 949).

Sign in / Sign up

Export Citation Format

Share Document