The level of antimicrobial resistance of sewage isolates is higher than that of river isolates in different Escherichia coli lineages

Abstract The dissemination of antimicrobial-resistant bacteria in environmental water is an emerging concern in medical and industrial settings. Here, we analysed the antimicrobial resistance of Escherichia coli isolates from river water and sewage by the use of a combined experimental phenotypic and whole-genome-based genetic approach. Among the 283 tested strains, 52 were phenotypically resistant to one or more antimicrobial agents. The E. coli isolates from the river and sewage samples were phylogenetically indistinguishable, and the antimicrobial-resistant strains were dispersedly distributed in a whole-genome-based phylogenetic tree. The prevalence of antimicrobial-resistant strains as well as the number of antimicrobials to which they were resistant were higher in sewage samples than in river samples. Antimicrobial resistance genes were more frequently detected in strains from sewage samples than in those from river samples. We also found that 16 river isolates that were classified as Escherichia cryptic clade V were susceptible to all the antimicrobials tested and were negative for antimicrobial resistance genes. Our results suggest that E. coli strains may acquire antimicrobial resistance genes more frequently and/or antimicrobial-resistant E. coli strains may have higher rates of accumulation and positive selection in sewage than in rivers, irrespective of their phylogenetic distribution.

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Prevalence and Antimicrobial Resistance Profiles of Salmonella Species and Escherichia coli Isolates from Poultry Feeds in Ruiru Sub - County, Kenya

10.21203/rs.3.rs-94393/v1 ◽

2020 ◽

Author(s):

Dorica Gakii Ngai ◽

Anthony Kebira Nyamache ◽

Omwoyo Ombori

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Bacterial Contamination ◽

Bacterial Load ◽

Poultry Feed ◽

Poultry Feeds ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Resistant Strains

Abstract Objectives: Contaminated poultry feeds can be a major source of E. coli and Salmonella infections in poultry. This study aimed at determining the microbial quality, prevalence and antimicrobial resistance and associated resistance genes to Salmonella and E. coli isolates from poultry feeds.Results: A total of 150 samples of different poultry feed types were randomly collected from selected sites within Ruiru Sub-County. A microbial load was determined, Salmonella and Escherichia coli were isolated and antimicrobial susceptibility test accomplished. Antimicrobial resistance genes; TEM, SHV, strB and Dfr were established. Out of analyzed samples, 58% contained Escherichia coli and 28% Salmonella. Bacterial load ranged between 3.1 x105 cfug to 3.0 x106 cfu/g. The highest resistance was found with ampicillin (41%) for Salmonella and (62%) for E. coli isolates. All the Ampicilin resistant isolates carried TEM and SHV genes. In addition, strB and Dfr drug resistance genes associated with streptomycin and Cotri-moxazole were analysed. All isolates were susceptible to chloramphenicol and ciprofloxacin. The study reveals high bacterial contamination, presence of beta-lactamase, aminoglycoside and sulphonamide resistance genes across isolates from poultry feeds. Therefore, contaminated poultry feeds with bacteria are likely to lead to increase and spread of antimicrobial resistant strains across the community.

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Antimicrobial Resistance Genes in Escherichia coli Isolates Recovered from a Commercial Beef Processing Plant†

Journal of Food Protection ◽

10.4315/0362-028x-72.5.1089 ◽

2009 ◽

Vol 72 (5) ◽

pp. 1089-1093 ◽

Cited By ~ 17

Author(s):

MUEEN ASLAM ◽

MOUSSA S. DIARRA ◽

CARA SERVICE ◽

HEIDI REMPEL

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Resistant Bacteria ◽

Processing Plant ◽

Ground Meat ◽

E Coli ◽

Beef Processing ◽

Antimicrobial Resistance Genes ◽

Meat Samples

The goal of this study was to assess the distribution of antimicrobial resistance (AMR) genes in Escherichia coli isolates recovered from a commercial beef processing plant. A total of 123 antimicrobial-resistant E. coli isolates were used: 34 from animal hides, 10 from washed carcasses, 27 from conveyers for moving carcasses and meat, 26 from beef trimmings, and 26 from ground meat. The AMR genes for β-lactamase (blaCMY, blaSHV, and blaTEM), tetracycline (tet(A), tet(B), and tet(C)), sulfonamides (sul1, sul2, and sul3), and aminoglycoside (strA and strB) were detected by PCR assay. The distribution of tet(B), tet(C), sul1, blaTEM, strA, and strB genes was significantly different among sample sources. E. coli isolates positive for the tet(B) gene and for both strA and strB genes together were significantly associated with hide, washed carcass, and ground meat samples, whereas sul1 gene was associated with washed carcass and beef trimming samples. The blaTEM gene was significantly associated with ground meat samples. About 50% of tetracycline-resistant E. coli isolates were positive for tet(A) (14%), tet(B) (15%), or tet(C) (21%) genes or both tet(B) and tet(C) genes together (3%). The sul2 gene or both sul1 and sul2 genes were found in 23% of sulfisoxazole-resistant E. coli isolates, whereas the sul3 gene was not found in any of the E. coli isolates tested. The majority of streptomycin-resistant E. coli isolates (76%) were positive for the strA and strB genes together. The blaCMY, blaTEM, and blaSHV genes were found in 12, 56, and 4%, respectively, of ampicillin-resistant E. coli isolates. These data suggest that E. coli isolates harboring AMR genes are widely distributed in meat processing environments and can create a pool of transferable resistance genes for pathogens. The results of this study underscore the need for effective hygienic and sanitation procedures in meat plants to reduce the risks of contamination with antimicrobial-resistant bacteria.

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Diverse Commensal Escherichia coli Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador

mSphere ◽

10.1128/msphere.00316-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 4

Author(s):

Liseth Salinas ◽

Paúl Cárdenas ◽

Timothy J. Johnson ◽

Karla Vasco ◽

Jay Graham ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Multidrug Resistant ◽

Domestic Animals ◽

Whole Genome ◽

Content Type ◽

Phenotypic Resistance ◽

E Coli ◽

Antimicrobial Resistance Genes

ABSTRACT The increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts on human medicine. Many of the multidrug-resistant (multiresistant) Enterobacteriaceae found in humans are community acquired, and some of them are possibly linked to food animals (i.e., livestock raised for meat and dairy products). In this study, we examined whether numerically dominant commensal Escherichia coli strains from humans (n = 63 isolates) and domestic animals (n = 174 isolates) in the same community and with matching phenotypic AMR patterns were clonally related or shared the same plasmids. We identified 25 multiresistant isolates (i.e., isolates resistant to more than one antimicrobial) that shared identical phenotypic resistance patterns. We then investigated the diversity of E. coli clones, AMR genes, and plasmids carrying the AMR genes using conjugation, replicon typing, and whole-genome sequencing. All of the multiresistant E. coli isolates (from children and domestic animals) analyzed had at least 90 or more whole-genome SNP differences between one another, suggesting that none of the strains was recently transferred. While the majority of isolates shared the same antimicrobial resistance genes and replicons, DNA sequencing indicated that these genes and replicons were found on different plasmid structures. We did not find evidence of the clonal spread of AMR in this community: instead, AMR genes were carried on diverse clones and plasmids. This presents a significant challenge for understanding the movement of AMR in a community. IMPORTANCE Even though Escherichia coli strains may share nearly identical phenotypic AMR profiles and AMR genes and overlap in space and time, the diversity of clones and plasmids challenges research that aims to identify sources of AMR. Horizontal gene transfer appears to play a more significant role than clonal expansion in the spread of AMR in this community.

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Prevalence and antimicrobial resistance profiles of Salmonella species and Escherichia coli isolates from poultry feeds in Ruiru Sub-County, Kenya

BMC Research Notes ◽

10.1186/s13104-021-05456-4 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Dorica Gakii Ngai ◽

Anthony Kebira Nyamache ◽

Omwoyo Ombori

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Bacterial Load ◽

Microbial Load ◽

Poultry Feed ◽

Poultry Feeds ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Resistant Strains

Abstract Objectives Contaminated poultry feeds can be a major source of E. coli and Salmonella infections in poultry. This study aimed at determining microbial load, prevalence and antimicrobial resistance profiles of Salmonella sp. and E. coli and associated resistance genes among isolates from poultry feeds. Results A total of 150 samples of different poultry feed types were randomly collected from selected sites within Ruiru Sub-County. The microbial load was determined, Salmonella sp. and Escherichia coli were isolated and antimicrobial susceptibility test carried out. Antimicrobial resistance genes were also screened among the resistant isolates. Out of analyzed samples, 58% and 28% contained Escherichia coli and Salmonella sp. respectively. Bacterial load ranged between 3.1 × 105 and 3.0 × 106 cfu/g. Highest resistance was against ampicillin (41%) for Salmonella sp. and (62%) for E. coli isolates. Ampicillin resistant isolates carried TEM and SHV genes. In addition, strB and Dfr resistance genes associated with streptomycin and cotri-moxazole were detected. All the isolates were susceptible to chloramphenicol and ciprofloxacin. The study reveals high bacterial contamination, presence of beta-lactamase, aminoglycoside and sulphonamide resistance genes across isolates from poultry feeds. Therefore, contaminated poultry feeds with bacteria are likely to lead to increase in antimicrobial resistant strains across the community.

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Phenotypic and genotypic characterization of mcr-1-positive multidrug-resistant Escherichia coli ST93, ST117, ST156, ST10, and ST744 isolated from poultry in Poland

Brazilian Journal of Microbiology ◽

10.1007/s42770-021-00538-8 ◽

2021 ◽

Author(s):

Katarzyna Ćwiek ◽

Anna Woźniak-Biel ◽

Magdalena Karwańska ◽

Magdalena Siedlecka ◽

Christine Lammens ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Bacterial Resistance ◽

Antimicrobial Agents ◽

Genetic Relatedness ◽

Multidrug Resistant ◽

E Coli ◽

Antimicrobial Resistance Genes

Abstract Background A plasmid-mediated mechanism of bacterial resistance to polymyxin is a serious threat to public health worldwide. The present study aimed to determine the occurrence of plasmid-mediated colistin resistance genes and to conduct the molecular characterization of mcr-positive Escherichia coli strains isolated from Polish poultry. Methods In this study, 318 E. coli strains were characterized by the prevalence of mcr1–mcr5 genes, antimicrobial susceptibility testing by minimal inhibitory concentration method, the presence of antimicrobial resistance genes was screened by PCR, and the biofilm formation ability was tested using the crystal violet staining method. Genetic relatedness of mcr-1-positive E. coli strains was evaluated by multilocus sequence typing method. Results Among the 318 E. coli isolates, 17 (5.35%) harbored the mcr-1 gene. High antimicrobial resistance rates were observed for ampicillin (100%), tetracycline (88.24%), and chloramphenicol (82.35%). All mcr-1-positive E. coli strains were multidrug-resistant, and as many as 88.24% of the isolates contained the blaTEM gene, tetracycline (tetA and tetB), and sulfonamide (sul1, sul2, and sul3) resistance genes. Additionally, 41.18% of multidrug-resistant, mcr-1-positive E. coli isolates were moderate biofilm producers, while the rest of the strains showed weak biofilm production. Nine different sequence types were identified, and the dominant ST was ST93 (29.41%), followed by ST117 (17.65%), ST156 (11.76%), ST 8979 (11.76%), ST744 (5.88%), and ST10 (5.88%). Moreover, the new ST was identified in this study. Conclusions Our results showed a low occurrence of mcr-1-positive E. coli strains isolated from Polish poultry; however, all the isolated strains were resistant to multiple antimicrobial agents and were able to form biofilms at low or medium level.

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Molecular Characterization of Multidrug-Resistant Escherichia coli Isolates from Edible Offal in Korea

Journal of Food Protection ◽

10.4315/0362-028x.jfp-18-458 ◽

2019 ◽

Vol 82 (7) ◽

pp. 1183-1190

Author(s):

SE HYUN SON ◽

KWANG WON SEO ◽

YEONG BIN KIM ◽

HYE YOUNG JEON ◽

EUN BI NOH ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Virulence Genes ◽

Antimicrobial Agents ◽

Food Product ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Class 1

ABSTRACT Edible offal, which is the nonmuscular part of the livestock, is a popular food product in many countries. However, it can be easily contaminated by bacteria, such as Escherichia coli, during slaughter and processing and regarded as a reservoir for transfer of antimicrobial-resistant bacteria to humans. This study aimed to investigate prevalence and characteristics of antimicrobial-resistant E. coli isolates from edible offal in Korea. A total of 320 chicken offal samples, 540 pig offal samples, and 560 cattle offal samples were collected. Among the 118 E. coli isolates obtained, resistance to at least one antimicrobial agent was revealed in 32 (100%), 46 (95.8%), and 26 (68.4%) isolates of chicken, pig, and cattle offals, respectively, with an overall prevalence of 88.1% (104 of 118). The isolates from chicken offal showed highest resistance to most antimicrobial agents, with the exception of higher ampicillin resistance for isolates from pig offal. In the distribution of antimicrobial resistance genes of 69 (58.5%) multidrug-resistant (MDR) E. coli, blaTEM-1 (97.1%), tetA (76.6%), sul2 (70.6%), and cmlA (57.4%) were most prevalent. Class 1 and class 2 integrons were detected in 82.6 and 2.9% of the MDR isolates, respectively. In total, seven virulence genes (eaeA, escV, astA, fimH, papC, sfa/focDE, and iucC) were also identified in the MDR isolates. The fimH gene was the most frequent (91.3%). Overall, 52 isolates from chicken (24 isolates, 96.0%), pig (16 isolates, 55.2%) and cattle (12 isolates, 80.0%) offals among MDR isolates were found to have some plasmid replicons. Frep (38 isolates) and FIB (27 isolates) replicons were more prevalent than other replicon types. The results suggest that edible offal can become a relevant reservoir of E. coli strains carrying various antimicrobial resistance and virulence genes. HIGHLIGHTS

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Antimicrobial resistance genes and virulence gene encoding intimin in Escherichia coli and Enterococcus isolated from wild rabbits (Oryctolagus cuniculus) in Tunisia

Acta Veterinaria Hungarica ◽

10.1556/004.2019.047 ◽

2019 ◽

Vol 67 (4) ◽

pp. 477-488 ◽

Cited By ~ 1

Author(s):

Laila Ben Said ◽

Ahlem Jouini ◽

Ismail Fliss ◽

Carmen Torres ◽

Naouel Klibi

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Molecular Typing ◽

Oryctolagus Cuniculus ◽

Animal Health ◽

Virulence Gene ◽

Resistant Bacteria ◽

E Coli ◽

Antimicrobial Resistance Genes

The spread of antimicrobial-resistant bacteria in wildlife must be viewed as a major concern with serious implications for human and animal health. Escherichia coli and enterococcal isolates were recovered from faecal samples of 49 wild rabbits (Oryctolagus cuniculus) on specific media and were characterised using biochemical and molecular tests. For all isolates, antimicrobial susceptibility testing was performed, and resistance genes were detected by PCR. Molecular typing of isolates was carried out by pulsed-field gel-electrophoresis, and E. coli strains were also tested for the presence of intimin (eae) gene characteristic of rabbit enteropathogenic E. coli. A total of 34 E. coli and 36 enterococci [E. hirae (52.8%) and E. faecalis (47.2%)] were obtained. For E. coli, resistance to tetracycline (94%), streptomycin (62%), ciprofloxacin (47%), trimethoprim-sulphamethoxazole (35%) and chloramphenicol (6%) was observed. Resistance to third-generation cephalosporins was detected in one E. coli strain that carried the blaCMY-2 and blaTEM-1 genes. Class 1 integrons were detected in eight isolates. For enterococci, resistance to tetracycline (63.9%), erythromycin (30.5%), streptomycin (18.2%), and chloramphenicol (5.5%) was detected. The tet(M)+tet(L), erm(B) and ant (6)-Ia genes were identified in thirteen, seven and three resistant Enterococcus strains, respectively. Molecular typing showed a high diversity among our strains. Wild rabbits could represent a reservoir of E. coli, and enterococci carrying antimicrobial resistance genes and E. coli additionally carrying the eae gene of enteropathogenic pathotypes could both contaminate the environment. our finding seems to represent the first report of eae-positive E. coli in wild rabbits.

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Genotyping and antimicrobial resistance in Escherichia coli from pig carcasses

Pesquisa Veterinária Brasileira ◽

10.1590/s0100-736x2017001100010 ◽

2017 ◽

Vol 37 (11) ◽

pp. 1253-1260 ◽

Cited By ~ 1

Author(s):

Caroline Pissetti ◽

Gabriela Orosco Werlang ◽

Jalusa Deon Kich ◽

Marisa Cardoso

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Antimicrobial Agents ◽

Commensal Bacteria ◽

Pfge Analysis ◽

Gene Detection ◽

E Coli ◽

Antimicrobial Resistance Profile ◽

Resistant Strains ◽

Pig Carcasses

ABSTRACT: The increasing antimicrobial resistance observed worldwide in bacteria isolated from human and animals is a matter of extreme concern and has led to the monitoring of antimicrobial resistance in pathogenic and commensal bacteria. The aim of this study was to evaluate the antimicrobial resistance profile of Escherichia coli isolated from pig carcasses and to assess the occurrence of relevant resistance genes. A total of 319 E. coli isolates were tested for antimicrobial susceptibility against different antimicrobial agents. Moreover, the presence of extended-spectrum β-lactamase (ESBL) and inducible ampC-β-lactamase producers was investigated. Eighteen multi-resistant strains were chosen for resistance gene detection and PFGE characterization. The study showed that resistance to antimicrobials is widespread in E. coli isolated from pig carcasses, since 86.2% of the strains were resistant to at least one antimicrobial and 71.5% displayed multi-resistance profiles. No ampC-producing isolates were detected and only one ESBL-producing E. coli was identified. Genes strA (n=15), floR (n=14), aac(3)IVa (n=13), tetB (n=13), sul2 (n=12), tetA (n=11), aph(3)Ia (n=8) and sul3 (n=5) were detected by PCR. PFGE analysis of these multi-resistant E. coli strains showed less than 80% similarity among them. We conclude that antimicrobial multi-resistant E. coli strains are common on pig carcasses and present highly diverse genotypes and resistance phenotypes and genotypes.

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Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

10.1101/2020.02.19.952366 ◽

2020 ◽

Author(s):

B Constantinides ◽

KK Chau ◽

TP Quan ◽

G Rodger ◽

M Andersson ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Bacterial Infections ◽

Wide Spectrum ◽

Klebsiella Oxytoca ◽

Clinical Disease ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Wide Range

ABSTRACTEscherichia coli and Klebsiella spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant E. coli and Klebsiella spp., particularly in the context of outbreaks of resistant strains amongst patients. Without focusing exclusively on resistance markers or a clinical outbreak, we demonstrate that many hospital sink drains are abundantly and persistently colonised with diverse populations of E. coli, Klebsiella pneumoniae and Klebsiella oxytoca, including both antimicrobial-resistant and susceptible strains. Using whole genome sequencing (WGS) of 439 isolates, we show that environmental bacterial populations are largely structured by ward and sink, with only a handful of lineages, such as E. coli ST635, being widely distributed, suggesting different prevailing ecologies which may vary as a result of different inputs and selection pressures. WGS of 46 contemporaneous patient isolates identified one (2%; 95% CI 0.05-11%) E. coli urine infection-associated isolate with high similarity to a prior sink isolate, suggesting that sinks may contribute to up to 10% of infections caused by these organisms in patients on the ward over the same timeframe. Using metagenomics from 20 sink-timepoints, we show that sinks also harbour many clinically relevant antimicrobial resistance genes including blaCTX-M, blaSHV and mcr, and may act as niches for the exchange and amplification of these genes. Our study reinforces the potential role of sinks in contributing to Enterobacterales infection and antimicrobial resistance in hospital patients, something that could be amenable to intervention.IMPORTANCEEscherichia coli and Klebsiella spp. cause a wide range of bacterial infections, including bloodstream, urine and lung infections. Previous studies have shown that sink drains in hospitals may be part of transmission chains in outbreaks of antimicrobial-resistant E. coli and Klebsiella spp., leading to colonisation and clinical disease in patients. We show that even in non-outbreak settings, contamination of sink drains by these bacteria is common across hospital wards, and that many antimicrobial resistance genes can be found and potentially exchanged in these sink drain sites. Our findings demonstrate that the colonisation of handwashing sink drains by these bacteria in hospitals is likely contributing to some infections in patients, and that additional work is needed to further quantify this risk, and to consider appropriate mitigating interventions.

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Impact of UV and Peracetic Acid Disinfection on the Prevalence of Virulence and Antimicrobial Resistance Genes in Uropathogenic Escherichia coli in Wastewater Effluents

Applied and Environmental Microbiology ◽

10.1128/aem.00418-14 ◽

2014 ◽

Vol 80 (12) ◽

pp. 3656-3666 ◽

Cited By ~ 24

Author(s):

Basanta Kumar Biswal ◽

Ramzi Khairallah ◽

Kareem Bibi ◽

Alberto Mazza ◽

Ronald Gehr ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Peracetic Acid ◽

Content Type ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Antimicrobial Resistance Gene ◽

Municipal Wastewaters ◽

The Impact

ABSTRACTWastewater discharges may increase the populations of pathogens, includingEscherichia coli, and of antimicrobial-resistant strains in receiving waters. This study investigated the impact of UV and peracetic acid (PAA) disinfection on the prevalence of virulence and antimicrobial resistance genes in uropathogenicEscherichia coli(UPEC), the most abundantE. colipathotype in municipal wastewaters. Laboratory disinfection experiments were conducted on wastewater treated by physicochemical, activated sludge, or biofiltration processes; 1,766E. coliisolates were obtained for the evaluation. The target disinfection level was 200 CFU/100 ml, resulting in UV and PAA doses of 7 to 30 mJ/cm2and 0.9 to 2.0 mg/liter, respectively. The proportions of UPECs were reduced in all samples after disinfection, with an average reduction by UV of 55% (range, 22% to 80%) and by PAA of 52% (range, 11% to 100%). Analysis of urovirulence genes revealed that the decline in the UPEC populations was not associated with any particular virulence factor. A positive association was found between the occurrence of urovirulence and antimicrobial resistance genes (ARGs). However, the changes in the prevalence of ARGs in potential UPECs were different following disinfection, i.e., UV appears to have had no effect, while PAA significantly reduced the ARG levels. Thus, this study showed that both UV and PAA disinfections reduced the proportion of UPECs and that PAA disinfection also reduced the proportion of antimicrobial resistance gene-carrying UPEC pathotypes in municipal wastewaters.

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