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

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.

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Analysis of antibiotic resistance phenotypes and genes of Escherichia coli from healthy swine in Guizhou, China

Onderstepoort Journal of Veterinary Research ◽

10.4102/ojvr.v88i1.1880 ◽

2021 ◽

Vol 88 (1) ◽

Author(s):

Bo Yu ◽

Yanan Zhang ◽

Li Yang ◽

Jinge Xu ◽

Shijin Bu

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Resistance Genes ◽

Detection Rate ◽

Antimicrobial Agents ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Multiple Drug ◽

E Coli ◽

Extended Spectrum

This study was carried out to investigate the resistance phenotypes and resistance genes of Escherichia coli from swine in Guizhou, China. A total of 47 E. coli strains isolated between 2013 and 2018 were tested using the Kirby–Bauer (K–B) method to verify their resistance to 19 common clinical antimicrobials. Five classes consisting of 29 resistance genes were detected using polymerase chain reaction. The status regarding extended-spectrum β-lactamase (ESBL) and the relationship between ESBL CTX-M-type β-lactamase genes and plasmid-mediated quinolone resistance (PMQR) genes were analysed. A total of 46 strains (97.9%) were found to be multidrug resistant. Amongst them, 27 strains (57.4%) were resistant to more than eight antimicrobials, and the maximum number of resistant antimicrobial agents was 16. Twenty antibiotic resistance genes were detected, including six β-lactamase genes blaTEM (74.5%), blaCTX-M-9G (29.8%), blaDHA (17.0%), blaCTX-M-1G (10.6%), blaSHV (8.5%), blaOXA (2.1%), five aminoglycoside-modifying enzyme genes aac(3′)-IV (93.6%), aadA1 (78.7%), aadA2 (76.6%), aac(3′)-II c (55.3%), aac(6′)-Ib (2.1%) and five amphenicol resistance genes floR (70.2%), cmlA (53.2%), cat2 (10.6%), cat1 (6.4%), cmlB (2.1%), three PMQR genes qnrS (55.3%), oqxA (53.2%), qepA (27.7%) and polypeptide resistance gene mcr-1 (40.4%). The detection rate of ESBL-positive strains was 80.9% (38/47) and ESBL TEM-type was the most abundant ESBLs. The percentage of the PMQR gene in blaCTX-M-positive strains was high, and the detection rate of blaCTX-M-9G was the highest in CTX-M type. It is clear that multiple drug resistant E. coli is common in healthy swine in this study. Extended-spectrum β-lactamase is very abundant in the E. coli strains isolated from swine and most of them are multiple compound genotypes.

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Interplay between bacterial clone and plasmid in the spread of antibiotic resistance genes in the gut: lessons from a temporal study in veal calves

Applied and Environmental Microbiology ◽

10.1128/aem.01358-21 ◽

2021 ◽

Author(s):

Méril Massot ◽

Pierre Châtre ◽

Bénédicte Condamine ◽

Véronique Métayer ◽

Olivier Clermont ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Resistance Genes ◽

Molecular Mechanisms ◽

Antibiotic Resistance Genes ◽

Field Work ◽

E Coli ◽

Veal Calves ◽

Evolutionary Forces ◽

Extended Spectrum

Intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli is a frequent, increasing and worrying phenomenon, but little is known about the molecular scenario and the evolutionary forces at play. We screened 45 veal calves, known to have high prevalence of carriage, for ESBL-producing E. coli on 514 rectal swabs (one randomly selected colony per sample) collected over six months. We characterized the bacterial clones and plasmids carrying bla ESBL genes with a combination of genotyping methods, whole genome sequencing and conjugation assays. One hundred and seventy-three ESBL-producing E. coli isolates [ bla CTX-M-1 (64.7%), bla CTX-M -14 (33.5%) or bla CTX-M-15 (1.8%)] were detected, belonging to 32 bacterial clones, mostly of phylogroup A. Calves were colonized successively by different clones with a trend in decreasing carriage. The persistence of a clone in a farm was significantly associated with the number of calves colonized. Despite a high diversity of E. coli clones and bla CTX-M -carrying plasmids, few bla CTX-M gene/plasmid/chromosomal background combinations dominated, due to (i) efficient colonization of bacterial clones and/or (ii) successful plasmid spread in various bacterial clones. The scenario ‘clone vs. plasmid spread’ depended on the farm. Thus, epistatic interactions between resistance genes, plasmids and bacterial clones contribute to optimize fitness in specific environments. Importance The gut microbiota is the epicenter of the emergence of resistance. Considerable amount of knowledge on the molecular mechanisms of resistance has been accumulated but the ecological and evolutionary forces at play in nature are less studied. In this context, we performed a field work on temporal intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli in veal farms. Veal calves are animals with one of the highest levels of ESBL producing E. coli fecal carriage, due to early high antibiotic exposure. We were able to show that calves were colonized successively by different ESBL-producing E. coli clones, and that two main scenarios were at play in the spread of bla CTX-M genes among calves: efficient colonization of several calves by a few bacterial clones and successful plasmid spread in various bacterial clones. Such knowledge should help develop new strategies to fight the emergence of antibiotic-resistance.

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Carbapenemases and Extended-Spectrum β-Lactamase–Producing Multidrug-Resistant Escherichia coli Isolated from Retail Chicken in Peshawar: First Report from Pakistan

Journal of Food Protection ◽

10.4315/0362-028x.jfp-18-045 ◽

2018 ◽

Vol 81 (8) ◽

pp. 1339-1345 ◽

Cited By ~ 2

Author(s):

KAFEEL AHMAD ◽

FARYAL KHATTAK ◽

AMJAD ALI ◽

SHAISTA RAHAT ◽

SHAZIA NOOR ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Nalidixic Acid ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

E Coli ◽

Extended Spectrum ◽

Amoxicillin Clavulanate ◽

Synergy Test

ABSTRACT We report the prevalence of extended-spectrum β-lactamases and carbapenemases in Escherichia coli isolated from retail chicken in Peshawar, Pakistan. One hundred E. coli isolates were recovered from retail chicken. Antibiotic susceptibility testing was carried out against ampicillin, chloramphenicol, kanamycin, nalidixic acid, cephalothin, gentamicin, sulfamethoxazole-trimethoprim, and streptomycin. Phenotypic detection of β-lactamase production was analyzed through double disc synergy test using the antibiotics amoxicillin-clavulanate, cefotaxime, ceftazidime, cefepime, and aztreonam. Fifty multidrug-resistant isolates were screened for detection of sul1, aadA, cmlA, int, blaTEM, blaSHV, blaCTX-M, blaOXA-10, blaVIM, blaIMP, and blaNDM-1 genes. Resistance to ampicillin, nalidixic acid, kanamycin, streptomycin, cephalothin, sulfamethoxazole-trimethoprim, gentamicin, cefotaxime, ceftazidime, aztreonam, cefepime, amoxicillin-clavulanate, and chloramphenicol was 92, 91, 84, 73, 70, 67, 53, 48, 40, 39, 37, 36, and 23% respectively. Prevalence of sul1, aadA, cmlA, int, blaTEM, blaCTX-M, blaIMP, and blaNDM-1 was 78% (n = 39), 76% (n = 38), 20% (n = 10), 90% (n = 45), 74% (n = 37), 94% (n = 47), 22% (n = 11), and 4% (n = 2), respectively. blaSHV, blaOXA-10, and blaVIM were not detected. The coexistence of multiple antibiotic resistance genes in multidrug-resistant strains of E. coli is alarming. Hence, robust surveillance strategies should be developed with a focus on controlling the spread of antibiotic resistance genes via the food chain.

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Genetic Features of Extended-Spectrum β-Lactamase-Producing Escherichia coli from Poultry in Mayabeque Province, Cuba

Antibiotics ◽

10.3390/antibiotics10020107 ◽

2021 ◽

Vol 10 (2) ◽

pp. 107 ◽

Cited By ~ 1

Author(s):

Michel Baez ◽

Ivette Espinosa ◽

Alexandra Collaud ◽

Iliana Miranda ◽

Damarys de las Nieves Montano ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance Genes ◽

Generation Cephalosporin ◽

Fluoroquinolone Resistance ◽

Multiple Sources ◽

Detection Rates ◽

E Coli ◽

Extended Spectrum ◽

Genetic Features

A total of 434 poultry cloacal samples were collected from seven different farms in different years (2013–2015) in the Cuban province of Mayabeque and analyzed for the presence of third-generation cephalosporin-resistant Escherichia coli (3GC-R-Ec). Sixty-two 3GC-R-Ec isolates were recovered in total from the farms, with detection rates of 2.9% in 2013, 10.3% in 2014, and 28.7% in 2015. Characterization of 32 3GC-R-Ec isolates revealed the presence of the extended-spectrum β-lactamase (ESBL) genes blaCTX-M-1 (n = 27), blaCTX-M-15 (n = 4), and blaCTX-M-1 together with blaLAP-2 (n = 1). The isolates also contained different proportions of genes conferring decreased susceptibility to sulfonamides (sul1, sul2, sul3), trimethoprim (dfrA1, dfrA7, dfrA12, dfrA14, dfrA17), tetracyclines (tet(A), tet(B)), aminoglycosides (aac(6′)-Ib-cr, strA, strB), chloramphenicol (cmlA1, floR), macrolides (mph(A), mph(D)), and quinolones (qnrS, qnrB, aac(6′)-Ib-cr) as well as mutations in the fluoroquinolone-resistance determining regions of GyrA (S83L, D87N, D87Y) and ParC (S80I, E84G). The isolates belonged to 23 different sequence types and to phylogroups A (n = 25), B1 (n = 5), and D (n = 2), and they contained plasmid-associated incompatibility groups FII, X1, HI1, HI2, N, FIA, and FIB. These findings reveal a genetically diverse population of multiresistant ESBL-producing E. coli in poultry farms in Cuba, which suggests multiple sources of contamination and the acquisition of antibiotic resistance genes.

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Resistome characterization of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolated from wastewater treatment utilities in Oregon

10.1101/2021.11.15.21266365 ◽

2021 ◽

Author(s):

Maeghan Easler ◽

Clint Cheney ◽

Jared D Johnson ◽

Marjan Khorshidi Zadeh ◽

Jacquelynn N Nguyen ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Wastewater Treatment ◽

Virulence Factors ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Beta Lactamase ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Extended Spectrum

Infections resistant to broad spectrum antibiotics due to the emergence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae is of global concern. This study characterizes the resistome (i.e., entire ecology of resistance determinants) of 11 ESBL-producing Escherichia coli isolates collected from eight wastewater treatment utilities across Oregon. Whole genome sequencing was performed to identify the most abundant antibiotic resistance genes including ESBL-associated genes, virulence factors, as well as their sequence types. Moreover, the phenotypes of antibiotic resistance were characterized. ESBL-associated genes (i.e., blaCMY, blaCTX, blaSHV, blaTEM) were found in all but one of the isolates with five isolates carrying two of these genes (4 with blaCTX and blaTEM; 1 with blaCMY and blaTEM). The ampC gene and virulence factors were present in all the E. coli isolates. Across all the isolates, 31 different antibiotic resistance genes were identified. Additionally, all E. coli isolates harbored phenotypic resistance to beta-lactams (penicillins and cephalosporins), while eight of the 11 isolates carried multi-drug resistance phenotypes (resistance to three or more classes of antibiotics). Findings highlight the risks associated with the presence of ESBL-producing E. coli isolates in wastewater systems that have the potential to enter the environment and may pose direct or indirect risks to human health.

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Emergence of extended-spectrum beta-lactamases-producing Escherichia coli in community-acquired urinary infections in Casablanca, Morocco

The Journal of Infection in Developing Countries ◽

10.3855/jidc.1490 ◽

2011 ◽

Vol 5 (12) ◽

pp. 850-855 ◽

Cited By ~ 18

Author(s):

Fatna Bourjilat ◽

Brahim Bouchrif ◽

Noureddine Dersi ◽

Jean David Perrier Gros Claude ◽

Hamid Amarouch ◽

...

Keyword(s):

Escherichia Coli ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Beta Lactamase ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Extended Spectrum ◽

Urinary Infections ◽

Genes Encoding ◽

Tract Infections

Introduction: Extended-spectrum beta-lactamase- (ESBL)-producing Escherichia coli are an increasingly significant cause of community-acquired infection worldwide. The aim of this study was to assess the prevalence of ESBL-producing E. coli in a community, to analyze the relationship between strains studied, and to characterize the ESBL genes involved in this resistance. Methodology: ESBL production was detected by the double disk synergy test. Genes encoding ESBLs (blaTEM, blaCTM, blaSHV) were identified by PCR and DNA sequencing. Conjugation experiments were performed to check the transferability of antibiotic resistance genes. Strain inter-relationships were studied by pulsed field gel electrophoresis. Results: Seven ESBL-producing E. coli were identified among the 535 E. coli isolates. Most of them expressed a CTX-M enzyme (6/7) with a predominance of CTX-M-15 (6/6). Two strains possessed TEM in combination with CTX-M-15 or SHV-5. Plasmid content and gene transfer analysis showed that resistance genes were carried by high molecular weight conjugative plasmids. PFGE analysis showed that the strains were not clonal. Conclusions: ESBL-producing E. coli from urinary tract infections in Casablanca belong to different clones and carry mobile beta-lactamase genes. It is therefore essential to monitor the epidemiology of ESBLs in E. coli and related organisms locally to effectively combat resistance.

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Detection of Extended-Spectrum Beta-Lactamase-ProducingEscherichia coliin Market-Ready Chickens in Zambia

International Journal of Microbiology ◽

10.1155/2016/5275724 ◽

2016 ◽

Vol 2016 ◽

pp. 1-5 ◽

Cited By ~ 13

Author(s):

K. Chishimba ◽

B. M. Hang’ombe ◽

K. Muzandu ◽

S. E. Mshana ◽

M. I. Matee ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Agents ◽

Human Consumption ◽

Antibiotic Administration ◽

Beta Lactam ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Antimicrobial Sensitivity ◽

Extended Spectrum ◽

Potential Reservoir

The frequent administering of antibiotics in the treatment of poultry diseases may contribute to emergence of antimicrobial-resistant strains. The objective of this study was to detect the presence of extended-spectrumβ-lactamase- (ESBL-) producingEscherichia coliin poultry in Zambia. A total of 384 poultry samples were collected and analyzed for ESBL-producingEscherichia coli. The culturedE. coliisolates were subjected to antimicrobial susceptibility tests and the polymerase chain reaction for detection ofblaCTX-M,blaSHV, andblaTEMgenes. Overall 20.1%, 77/384, (95% CI; 43.2–65.5%) of total samples analyzed contained ESBL-producingEscherichia coli. The antimicrobial sensitivity test revealed that 85.7% (66/77; CI: 75.7–92) of ESBL-producingE. coliisolates conferred resistance to beta-lactam and other antimicrobial agents. These results indicate that poultry is a potential reservoir for ESBL-producingEscherichia coli. The presence of ESBL-producingEscherichia coliin poultry destined for human consumption requires strengthening of the antibiotic administering policy. This is important as antibiotic administration in food animals is gaining momentum for improved animal productivity in developing countries such as Zambia.

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

Microorganisms ◽

10.3390/microorganisms9020308 ◽

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.

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Mechanisms of Resistance in Multiple-Antibiotic-Resistant Escherichia coli Strains of Human, Animal, and Food Origins

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.48.10.3996-4001.2004 ◽

2004 ◽

Vol 48 (10) ◽

pp. 3996-4001 ◽

Cited By ~ 269

Author(s):

Yolanda Sáenz ◽

Laura Briñas ◽

Elena Domínguez ◽

Joaquim Ruiz ◽

Myriam Zarazaga ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Amino Acid ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Mechanisms Of Resistance ◽

Antibiotic Resistant ◽

E Coli ◽

Class 1 ◽

Human Animal

ABSTRACT Seventeen multiple-antibiotic-resistant nonpathogenic Escherichia coli strains of human, animal, and food origins showed a wide variety of antibiotic resistance genes, many of them carried by class 1 and class 2 integrons. Amino acid changes in MarR and mutations in marO were identified for 15 and 14 E. coli strains, respectively.

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Antibiotic-resistant Escherichia coli and Salmonella spp. associated with dairy cattle and farm environment having public health significance

Veterinary World ◽

10.14202/vetworld.2019.984-993 ◽

2019 ◽

Vol 12 (7) ◽

pp. 984-993 ◽

Cited By ~ 14

Author(s):

Md. Abdus Sobur ◽

Abdullah Al Momen Sabuj ◽

Ripon Sarker ◽

A. M. M. Taufiqur Rahman ◽

S. M. Lutful Kabir ◽

...

Keyword(s):

Public Health ◽

Escherichia Coli ◽

Antibiotic Resistance ◽

Resistance Genes ◽

One Health ◽

Dairy Farm ◽

Antibiotic Resistance Genes ◽

Salmonella Spp ◽

Antibiotic Resistant ◽

E Coli

Aim: The present study was carried out to determine load of total bacteria, Escherichia coli and Salmonella spp. in dairy farm and its environmental components. In addition, the antibiogram profile of the isolated bacteria having public health impact was also determined along with identification of virulence and resistance genes by polymerase chain reaction (PCR) under a one-health approach. Materials and Methods: A total of 240 samples of six types (cow dung - 15, milk - 10, milkers' hand wash - 10, soil - 10 water - 5, and vegetables - 10) were collected from four dairy farms. For enumeration, the samples were cultured onto plate count agar, eosin methylene blue, and xylose-lysine deoxycholate agar and the isolation and identification of the E. coli and Salmonella spp. were performed based on morphology, cultural, staining, and biochemical properties followed by PCR. The pathogenic strains of E. coli stx1, stx2, and rfbO157 were also identified through PCR. The isolates were subjected to antimicrobial susceptibility test against 12 commonly used antibiotics by disk diffusion method. Detection of antibiotic resistance genes ereA, tetA, tetB, and SHV were performed by PCR. Results: The mean total bacterial count, E. coli and Salmonella spp. count in the samples ranged from 4.54±0.05 to 8.65±0.06, 3.62±0.07 to 7.04±0.48, and 2.52±0.08 to 5.87±0.05 log colony-forming unit/g or ml, respectively. Out of 240 samples, 180 (75%) isolates of E. coli and 136 (56.67%) isolates of Salmonella spp. were recovered through cultural and molecular tests. Among the 180 E. coli isolates, 47 (26.11%) were found positive for the presence of all the three virulent genes, of which stx1 was the most prevalent (13.33%). Only three isolates were identified as enterohemorrhagic E. coli. Antibiotic sensitivity test revealed that both E. coli and Salmonella spp. were found highly resistant to azithromycin, tetracycline, erythromycin, oxytetracycline, and ertapenem and susceptible to gentamycin, ciprofloxacin, and imipenem. Among the four antibiotic resistance genes, the most observable was tetA (80.51-84.74%) in E. coli and Salmonella spp. and SHV genes were the lowest one (22.06-25%). Conclusion: Dairy farm and their environmental components carry antibiotic-resistant pathogenic E. coli and Salmonella spp. that are potential threat for human health which requires a one-health approach to combat the threat.

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