Detection of Multiple-Antimicrobial Resistance and Characterization of the Implicated Genes in Escherichia coli Isolates from Foods of Animal Origin in Tunis

Phenotypic and genotypic characterization of antimicrobial resistance was conducted for 98 Escherichia coli isolates recovered from 40 food samples of animal origin (poultry, sheep, beef, fish, and others) obtained in supermarkets and local butcheries in Tunis during 2004 and 2005. Susceptibility to 15 antimicrobial agents was tested by disk diffusion and agar dilution methods, the mechanisms of resistance were evaluated using PCR and sequencing methods, and the clonal relationship among isolates was evaluated using pulsed-field gel electrophoresis. High resistance was detected to tetracycline, sulphonamides, nalidixic acid, ampicillin, streptomycin, and trimethoprim-sulfamethoxazole (29 to 43% of isolates), but all isolates were susceptible to cefotaxime, ceftazidime, cefoxitin, azthreonam, and amikacin. One-third of the isolates had multiresistant phenotypes (resistance to at least five different families of antimicrobial agents). Different variants of blaTEM, tet, sul, dfrA, aadA, and aac(3) genes were detected in most of the strains resistant to ampicillin, tetracycline, sulphonamide, trimethoprim, streptomycin, and gentamicin, respectively. The presence of class 1 and class 2 integrons was studied in 15 sulphonamide-resistant unrelated E. coli strains, and 14 of these strains harbored class 1 integrons with five different arrangements of gene cassettes, and a class 2 integron with the dfrA1 + sat + aadA1 arrangement was found in one strain. This study revealed the high diversity of antimicrobial resistance genes, some of them included in integrons, in E. coli isolates of food origin.

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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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Impact of Feed Supplementation with Antimicrobial Agents on Growth Performance of Broiler Chickens, Clostridium perfringens and Enterococcus Counts, and Antibiotic Resistance Phenotypes and Distribution of Antimicrobial Resistance Determinants in Escherichia coli Isolates

Applied and Environmental Microbiology ◽

10.1128/aem.01086-07 ◽

2007 ◽

Vol 73 (20) ◽

pp. 6566-6576 ◽

Cited By ~ 103

Author(s):

Moussa S. Diarra ◽

Fred G. Silversides ◽

Fatoumata Diarrassouba ◽

Jane Pritchard ◽

Luke Masson ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Broiler Chickens ◽

Antimicrobial Agents ◽

Growth Promoters ◽

Feed Supplementation ◽

E Coli ◽

Resistance Determinants ◽

Class 1

ABSTRACT The effects of feed supplementation with the approved antimicrobial agents bambermycin, penicillin, salinomycin, and bacitracin or a combination of salinomycin plus bacitracin were evaluated for the incidence and distribution of antibiotic resistance in 197 commensal Escherichia coli isolates from broiler chickens over 35 days. All isolates showed some degree of multiple antibiotic resistance. Resistance to tetracycline (68.5%), amoxicillin (61.4%), ceftiofur (51.3%), spectinomycin (47.2%), and sulfonamides (42%) was most frequent. The levels of resistance to streptomycin, chloramphenicol, and gentamicin were 33.5, 35.5, and 25.3%, respectively. The overall resistance levels decreased from day 7 to day 35 (P < 0.001). Comparing treatments, the levels of resistance to ceftiofur, spectinomycin, and gentamicin (except for resistance to bacitracin treatment) were significantly higher in isolates from chickens receiving feed supplemented with salinomycin than from the other feeds (P < 0.001). Using a DNA microarray analysis capable of detecting commonly found antimicrobial resistance genes, we characterized 104 tetracycline-resistant E. coli isolates from 7- to 28-day-old chickens fed different growth promoters. Results showed a decrease in the incidence of isolates harboring tet(B), bla TEM, sulI, and aadA and class 1 integron from days 7 to 35 (P < 0.01). Of the 84 tetracycline-ceftiofur-resistant E. coli isolates, 76 (90.5%) were positive for bla CMY-2. The proportions of isolates positive for sulI, aadA, and integron class 1 were significantly higher in salinomycin-treated chickens than in the control or other treatment groups (P < 0.05). These data demonstrate that multiantibiotic-resistant E. coli isolates can be found in broiler chickens regardless of the antimicrobial growth promoters used. However, the phenotype and the distribution of resistance determinants in E. coli can be modulated by feed supplementation with some of the antimicrobial agents used in broiler chicken production.

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Molecular characterisation of antimicrobial resistance and virulence genes in Escherichia coli strains isolated from diarrhoeic and healthy rabbits in Tunisia

World Rabbit Science ◽

10.4995/wrs.2020.10879 ◽

2020 ◽

Vol 28 (2) ◽

pp. 81

Author(s):

Raouia Ben Rhouma ◽

Ahlem Jouini ◽

Amira Klibi ◽

Safa Hamrouni ◽

Aziza Boubaker ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Virulence Genes ◽

Antimicrobial Agents ◽

Antibiotic Resistance Genes ◽

Virulence Gene ◽

Diffusion Method ◽

Class 1 Integron ◽

E Coli ◽

Class 1

The purpose of this study was to identify Escherichia coli isolates in diarrhoeic and healthy rabbits in Tunisia and characterise their virulence and antibiotic resistance genes. In the 2014-2015 period, 60 faecal samples from diarrhoeic and healthy rabbits were collected from different breeding farms in Tunisia. Susceptibility to 14 antimicrobial agents was tested by disc diffusion method and the mechanisms of gene resistance were evaluated using polymerase chain reaction and sequencing methods. Forty E. coli isolates were recovered in selective media. High frequency of resistance to tetracycline (95%) was detected, followed by different levels of resistance to sulphonamide (72.5%), streptomycin (62.5%), trimethoprim-sulfamethoxazole (60%), nalidixic acid (32.5%), ampicillin (37.5%) and ticarcillin (35%). E. coli strains were susceptible to cefotaxime, ceftazidime and imipenem. Different variants of blaTEM, tet, sul genes were detected in most of the strains resistant to ampicillin, tetracycline and sulphonamide, respectively. The presence of class 1 integron was studied in 29 sulphonamide-resistant E. coli strains from which 15 harboured class 1 integron with four different arrangements of gene cassettes, dfrA17+aadA5 (n=9), dfrA1 + aadA1 (n=4), dfrA12 + addA2 (n=1), dfrA12+orf+addA2 (n=1). The qnrB gene was detected in six strains out of 13 quinolone-resistant E. coli strains. Seventeen E. coli isolates from diarrhoeic rabbits harboured the enteropathogenic eae genes associated with different virulence genes tested (fimA, cnf1, aer), and affiliated to B2 (n=8) and D (n=9) phylogroups. Isolated E. coli strains from healthy rabbit were harbouring fim A and/or cnf1 genes and affiliated to A and B1 phylogroups. This study showed that E. coli strains from the intestinal tract of rabbits are resistant to the widely prescribed antibiotics in medicine. Therefore, they constitute a reservoir of antimicrobial-resistant genes, which may play a significant role in the spread of antimicrobial resistance. In addition, the eae virulence gene seemed to be implicated in diarrhoea in breeder rabbits in Tunisia.

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Antimicrobial Resistance and Association with Class 1 Integrons in Escherichia coli Isolated from Turkey Meat Products

Journal of Food Protection ◽

10.4315/0362-028x-71.8.1679 ◽

2008 ◽

Vol 71 (8) ◽

pp. 1679-1684 ◽

Cited By ~ 5

Author(s):

M. L. KHAITSA ◽

J. OLOYA ◽

D. DOETKOTT ◽

R. KEGODE

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Antimicrobial Agents ◽

Population Attributable Fraction ◽

Meat Products ◽

Resistance Mechanisms ◽

E Coli ◽

Class 1 Integrons ◽

Turkey Meat ◽

Class 1

The objective of this study was to quantify the role of class 1 integrons in antimicrobial resistance in Escherichia coli isolated from turkey meat products purchased from retail outlets in the Midwestern United States. Of 242 E. coli isolates, 41.3% (102 of 242) tested positive for class 1 integrons. A significant association was shown between presence of class 1 integrons in E. coli isolates and the resistance to tetracycline, ampicillin, streptomycin, gentamicin, sulfisoxazole, and trimethoprim-sulfamethoxazole. Attributable risk analysis revealed that for every 100 E. coli isolates carrying class 1 integrons, resistance was demonstrated for ampicillin (22%), gentamycin (48%), streptomycin (29%), sulfisoxazole (40%), trimethoprimsulfamethoxazole (7%), and tetracycline (26%). Non–integron-related antimicrobial resistance was demonstrated for ampicillin (65%), gentamycin (16.9%), streptomycin (42.1%), sulfisoxazole (35.8%), and tetracycline (49.7%). Population-attributable fraction analysis showed that class 1 integrons accounted for the following resistances: gentamycin, 71% (50 of 71), amoxicillin–clavulanic acid, 19.6% (6 of 33), nalidixic acid, 34% (7 of 21), streptomycin, 28% (30 of 107), sulfisoxazole, 38% (40 of 106), and tetracycline, 14%, (26 of 185). In conclusion, although class 1 integrons have been implicated in resistance to antimicrobial agents, other non–integron resistance mechanisms seem to play an important part.

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Characterization of commensal Escherichia coli isolates from slaughtered sheep in Mexico

The Journal of Infection in Developing Countries ◽

10.3855/jidc.14001 ◽

2021 ◽

Vol 15 (11) ◽

pp. 1755-1760

Author(s):

Jorge Acosta-Dibarrat ◽

Edgar Enriquez-Gómez ◽

Martín Talavera-Rojas ◽

Edgardo Soriano-Vargas ◽

Armando Navarro ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Multidrug Resistant ◽

Phylogenetic Group ◽

Phylogenetic Groups ◽

E Coli ◽

New Information ◽

Antimicrobial Resistance Genes ◽

Uremic Syndrome

Introduction: Commensal Escherichia coli is defined as bacteria without known virulence factors that could be playing a specific role in some diseases; however, they could be responsible to disseminate antimicrobial resistance genes to other microorganisms. This study aimed to characterize the commensal E. coli isolates obtained from slaughtered sheep in the central region of Mexico. Methodology: Isolates were classified as commensal E. coli when distinctive genes related to diarrheagenic pathotypes (stx1, stx2, eae, bfp, LT, stp, ipaH, and aggR) were discarded by PCR. Identification of serotype, phylogenetic group, and antimicrobial resistance was also performed. Results: A total of 41 isolates were characterized. The phylogenetic groups found were B1 in 37 isolates (90.2%), A in 2 (4.8%), and 1 isolate (2.4%) for C and D groups. Serotypes associated with diarrhea in humans (O104:H2 and O154:NM) and hemolytic uremic syndrome (O8:NM) were detected. Thirty-three isolates (80%) were resistant to ceftazidime, 23 (56%), to tetracycline 8 (19.5%) to ampicillin, and 1 to amikacin. Six isolates (14.6%) were multidrug-resistant. Conclusions: This study provides new information about commensal E. coli in slaughtered sheep, high percentages of resistance to antibiotics, and different profiles of antimicrobial resistance were found, their dissemination constitute a risk factor towards the consuming population.

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Characterization of Integrons and Antimicrobial Resistance in Escherichia coli Sequence Type 131 Isolates

Canadian Journal of Infectious Diseases and Medical Microbiology ◽

10.1155/2020/3826186 ◽

2020 ◽

Vol 2020 ◽

pp. 1-8 ◽

Cited By ~ 2

Author(s):

Jiangqing Huang ◽

Fangjun Lan ◽

Yanfang Lu ◽

Bin Li

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Sequence Type ◽

Broth Culture ◽

Gene Cassettes ◽

E Coli ◽

Class 1

Background. Escherichia coli sequence type 131 (ST131) is an important multidrug-resistant extraintestinal pathogen, which can cause many kinds of infections. Integrons may play a crucial role in the dissemination of antibiotic resistance genes. The purpose of this study was to characterize the prevelance of integrons among E. coli ST131 strains in China. Methods. Eighty-three E. coli ST131 isolates were used in this study. The antibiotic susceptibility test was performed by the disk diffusion method. The presence and characterization of class 1, 2, and 3 integrons, as well as promotor of gene cassettes and other antimicrobial resistance genes, were detected by PCR and DNA sequencing. Transfer of integrons was carried out using a broth culture mating method. Clonal relatedness of E. coli ST131 isolates was analyzed by PFGE. Results. Overall, 26.5% (22/83) of the E. coli ST131 isolates carried class 1 integrons. Class 2 and 3 integrons were not found in this study. Two types of gene cassette arrays were demonstrated in this study and were as follows: dfrA17-aadA5 and aac(6′)-Ib-cr-cmlA5. Only one type of Pc promoter variant was detected among 22 integron-positive isolates (PcW). In vivo transfer of integron was successful for 9 of integron-positive E. coli ST131 isolates harboring resistance gene cassettes. Results of PFGE demonstrated that the integron-positive E. coli ST131 isolates were grouped into 12 different PFGE clusters. Conclusions. Our study showed a low prevalence of integrons was detected in E. coli ST131. Continued surveillance of this mobile genetic element should be performed to study the evolution of antibiotic resistance among E. coli ST131.

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Characterization of extended-spectrum and CMY-2 ß-lactamases, and associated virulence genes in Escherichia coli from food of animal origin in México

British Food Journal ◽

10.1108/bfj-02-2018-0104 ◽

2018 ◽

Vol 120 (7) ◽

pp. 1457-1473 ◽

Cited By ~ 1

Author(s):

Edwin Barrios-Villa ◽

Gerardo Cortés-Cortés ◽

Patricia Lozano Zarain ◽

Sergio Romero-Romero ◽

Norarizbeth Lara Flores ◽

...

Keyword(s):

Escherichia Coli ◽

Virulence Genes ◽

Food Samples ◽

Animal Origin ◽

Content Type ◽

E Coli ◽

Extended Spectrum ◽

Food Of Animal Origin ◽

Cephalosporin Resistance

Purpose Broad-spectrum cephalosporin resistance is rapidly increasing in Escherichia coli, representing a food safety problem. The purpose of this paper is to characterize eight extended-spectrum-ß-lactamase (ESBL) and acquired AmpC ß-lactamase-producing E. coli isolates and virotypes associated, obtained from chicken and pork food samples in Puebla, Mexico. Design/methodology/approach Samples (36 from chicken and 10 from pork) were cultured on Levine agar plates supplemented with cefotaxime (2 mg/L) for isolation of cefotaxime-resistant (CTXR) E. coli. CTXR-E. coli isolates were detected in 33 of 46 samples (72 percent), and one isolate/sample was characterized (28 from chicken and 5 from pork), for ESBL production, phylogenetic group, sequence typing, resistance and virulence genes by PCR and sequencing. Findings Results showed 16 ESBL-E. coli (35 percent) (12/16 belonging to phylogroup B1) and 8 CMY-2-E. coli (17 percent). ESBL detected were as follows (number of isolates): CTX-M-2 (8); CTX-M-1 (2); CTX-M-15 (1); SHV-2a (4) and TEM-52c (1). In total, 20 different sequence types (STs) were identified among the ESBL- or CMY-2-producing E. coli strains, which included four new ones. The CTX-M-15 β-lactamase was detected in one E. coli ST617-ST10 Cplx-B1 strain that also carried ibeA gene. One CMY-2-positive strain of lineage ST224-B2 was detected and it carried the qnrA1 gene. Originality/value In this study, a ST131-based virotyping scheme for strains from food of animal origin was established since this kind of strains constitutes an important vehicle of virulent ESBL- and CMY-2-producing E. coli isolates, which could be transmitted to humans by direct contact or through the food chain.

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Antimicrobial Resistance of Escherichia coli from Broilers, Pigs, and Cattle in the Greater Kumasi Metropolis, Ghana

International Journal of Microbiology ◽

10.1155/2021/5158185 ◽

2021 ◽

Vol 2021 ◽

pp. 1-7

Author(s):

Rita Ohene Larbi ◽

Linda Aurelia Ofori ◽

Augustina Angelina Sylverken ◽

Matilda Ayim-Akonor ◽

Kwasi Obiri-Danso

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Animal Origin ◽

Diffusion Method ◽

Antimicrobial Drugs ◽

Phenotypic Resistance ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Routine Surveillance ◽

Antimicrobial Resistance Genes

Globally, resistance to antimicrobial drugs in food animals is on the rise. Escherichia coli of livestock, though commensal in nature, serves as reservoir for antimicrobial resistance genes with the potential of disseminating them. This study sought to examine the antimicrobial resistance profiles of Escherichia coli in broilers, pigs, and cattle in the Kumasi Metropolis and undertake molecular characterisation of the resistances. Faecal E. coli isolates (n = 48) were obtained from 10 broiler farms, (n = 43) from 15 pig farms, and (n = 42) from cattle from the Kumasi Abattoir using standard bacteriological techniques. The Kirby–Bauer disc diffusion method was employed in testing the sensitivities of 133 E. coli isolates to 15 antimicrobials. All 48 isolates from broilers presented no resistance to amoxicillin/clavulanic acid and ceftiofur. A 100% resistance to meropenem was observed in pig and cattle isolates. Multidrug resistance (MDR) across animal groups was 95.8% (n = 46), 95.3% (n = 41), and 64.3% (n = 27) for broilers, pigs, and cattle, respectively. Twenty-eight isolates presenting phenotypic resistance to aminopenicillins and cephalosporins were screened for the presence of extended-spectrum beta-lactamase (ESBL) genes by PCR. One isolate from poultry and another from cattle tested positive for the blaCTX-M ESBL gene. There were no positives for the blaTEM and blaSHV ESBL genes. Commensal E. coli of food animal origin represents an important reservoir of antimicrobial resistance that transfers resistance to pathogenic and nonpathogenic microbes affecting humans and animals. There is an urgent need to institute routine surveillance for the establishment of the mechanisms and molecular orientation of resistance in these organisms.

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

Scientific Reports ◽

10.1038/s41598-020-75065-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Yoshitoshi Ogura ◽

Takuya Ueda ◽

Kei Nukazawa ◽

Hayate Hiroki ◽

Hui Xie ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Antimicrobial Agents ◽

Environmental Water ◽

Resistant Bacteria ◽

Whole Genome ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Resistant Strains

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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