Microbial water quality and the detection of multidrug resistant E. coli and antibiotic resistance genes in aquaculture sites of Singapore

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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Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data

Microorganisms ◽

10.3390/microorganisms9081613 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1613

Author(s):

Julian A. Paganini ◽

Nienke L. Plantinga ◽

Sergio Arredondo-Alonso ◽

Rob J. L. Willems ◽

Anita C. Schürch

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Special Focus ◽

Valuable Insight ◽

Sequencing Data ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Long Read

The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance in E. coli is often mediated by acquisition and maintenance of plasmids. The study of E. coli plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed. Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools (MOB-suite, plasmidSPAdes, gplas, FishingForPlasmids, HyAsP and SCAPP) that aim to reliably reconstruct distinct plasmids, with a special focus on plasmids carrying antibiotic resistance genes (ARGs) such as extended-spectrum beta-lactamase genes. We found that two thirds (n = 425, 66.3%) of all plasmids were correctly reconstructed by at least one of the six tools, with a range of 92 (14.58%) to 317 (50.23%) correctly predicted plasmids. However, the majority of plasmids that carried antibiotic resistance genes (n = 85, 57.8%) could not be completely recovered as distinct plasmids by any of the tools. MOB-suite was the only tool that was able to correctly reconstruct the majority of plasmids (n = 317, 50.23%), and performed best at reconstructing large plasmids (n = 166, 46.37%) and ARG-plasmids (n = 41, 27.9%), but predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes reconstructed the highest fraction of plasmids smaller than 18 kbp (n = 168, 61.54%). Large ARG-plasmids, however, were frequently merged with sequences derived from distinct replicons. Available bioinformatic tools can provide valuable insight into E. coli plasmids, but also have important limitations. This work will serve as a guideline for selecting the most appropriate plasmid reconstruction tool for studies focusing on E. coli plasmids in the absence of long-read sequencing data.

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Molecular Detection of Antibiotic Resistance Genes in Shiga toxin-producing E. coli Isolated from Different Sources

Antibiotics ◽

10.3390/antibiotics10040344 ◽

2021 ◽

Vol 10 (4) ◽

pp. 344

Author(s):

Momna Rubab ◽

Deog-Hwan Oh

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Shiga Toxin ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Foodborne Illnesses ◽

Antimicrobial Drugs ◽

E Coli ◽

Conventional Antibiotics

Shiga toxin-producing Escherichia coli (STEC) is an enteric pathogen associated with human gastroenteritis outbreaks. Extensive use of antibiotics in agriculture selects resistant bacteria that may enter the food chain and potentially causes foodborne illnesses in humans that are less likely to respond to treatment with conventional antibiotics. Due to the importance of antibiotic resistance, this study aimed to investigate the combination of phenotypic and genotypic antibiotic resistance in STEC isolates belonging to serogroups O26, O45, O103, O104, O111, O121, O145, and O157 using disc diffusion and polymerase chain reaction (PCR), respectively. All strains were phenotypically resistant to at least one antibiotic, with 100% resistance to erythromycin, followed by gentamicin (98%), streptomycin (82%), kanamycin (76%), and ampicillin (72%). The distribution of antibiotic resistance genes (ARGs) in the STEC strains was ampC (47%), aadA1 (70%), ere(A) (88%), blaSHV (19%), blaCMY (27%), aac(3)-I (90%), and tet(A) (35%), respectively. The results suggest that most of the strains were multidrug-resistant (MDR) and the most often observed resistant pattern was of aadA1, ere(A), and aac(3)-I genes. These findings indicate the significance of monitoring the prevalence of MDR in both animals and humans around the globe. Hence, with a better understanding of antibiotic genotypes and phenotypes among the diverse STEC strains obtained, this study could guide the administration of antimicrobial drugs in STEC infections when necessary.

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Characterization of Tn7-like transposons and its related antibiotic resistance among Enterobacteriaceae from livestock and poultry in China

10.21203/rs.3.rs-20496/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Juan He ◽

Cui Li ◽

Pengfei Cui ◽

Hongning Wang

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Horizontal Transmission ◽

Antibiotic Resistance Genes ◽

Variable Region ◽

Multidrug Resistant ◽

Antibiotic Resistant ◽

E Coli ◽

New Type

Abstract Background: This study was aimed to investigate the prevalence and structure of Tn7-like in Enterobacteriaceae from livestock and poultry as well as their possible role as reservoir of antibiotic resistance genes (ARGs).Methods: Polymerase chain reaction (PCR) and DNA sequencing analyses were used for the characterization of Tn7-like, associated integrons and ARGs. The antimicrobial resistance profile of the isolates was examined by using disc diffusion test.Results: Three hundred and seventy-eight Tn7-like-positive strains of Enterobacteriaceae were isolated, and included E. coli (128), Proteus(150), K. pneumonia(17), Salmonella(13), M. morganii (21) and A. baumannii(1), wherein high resistance was observed for Trimethoprim/Sulfamethoxazole and Streptomycin, and fifty percent of the strains were multidrug-resistant. Integrons class 2 were detected in all of the isolates and there are high frequency mutation sites especially in 535, a stop mutation. Variable region of class 2 integrons carried same gene cassettes, namely aadA1-sat2-dfrA1. From the 378 isolated strains, we found a new type of Tn7-like on a plasmid, named Tn6765.Conclusions: These findings proved that the Tn7-like can contribute to the horizontal transmission of antibiotic resistant genes in livestock and poultry. As potential vessels for antibiotic resistance genes (ARGs), Tn7-like could not be ignored due to their efficient transfer ability in environments.

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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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Tracking antibiotic resistance genes and class 1 integrons in Escherichia coli isolates from wastewater and agricultural fields

Water Science & Technology ◽

10.2166/wst.2021.288 ◽

2021 ◽

Author(s):

Zahra Shamsizadeh ◽

Mohammad Hassan Ehrampoush ◽

Mahnaz Nikaeen ◽

Mehdi Mokhtari ◽

Mahsa Rahimi ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Treated Wastewater ◽

E Coli ◽

Class 1 Integrons ◽

Class 1 ◽

High Concentrations

Abstract Considering high concentrations of multidrug-resistant (MDR) bacteria and antibiotic resistance genes (ARGs) in wastewater, agricultural reuse of treated wastewater may be a public health threat due to ARGs dissemination in different environmental compartments, including soil and edible parts of crops. We investigated the presence of antibiotic-resistant Escherichia coli as an indicator bacterium from secondary treated wastewater (STWW), water- or wastewater-irrigated soil and crop samples. ARGs including blaCTX-m-32, blaOXA-23, tet-W, sul1, cml-A, erm-B, along with intI1 gene in E. coli isolates were detected via molecular methods. The most prevalent ARGs in 78 E. coli isolates were sul1 (42%), followed by blaCTX-m-32 (19%), and erm-B (17%). IntI1 as a class 1 integrons gene was detected in 46% of the isolates. Cml-A was detected in STWW isolates but no E. coli isolate from wastewater-irrigated soil and crop samples contain this gene. The results also showed no detection of E. coli in water-irrigated soil and crop samples. Statistical analysis showed a correlation between sul1 and cml-A with intI1. The results suggest that agricultural reuse of wastewater may contribute to the transmission of ARB to soil and crop. Further research is needed to determine the potential risk of ARB associated with the consumption of wastewater-irrigated crops.

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Therapeutic effect of biosynthetic gold nanoparticles on multidrug-resistant Escherichia coli and Salmonella species isolated from ruminants

Veterinary World ◽

10.14202/vetworld.2021.3200-3210 ◽

2021 ◽

pp. 3200-3210

Author(s):

Abeer M. Abdalhamed ◽

Alaa A. Ghazy ◽

Eman S. Ibrahim ◽

Amany A. Arafa ◽

Gamil S. G. Zeedan

Keyword(s):

Escherichia Coli ◽

Gold Nanoparticles ◽

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Pathogenic Microorganisms ◽

Salmonella Spp ◽

Antibiotic Resistant ◽

E Coli

Background and Aim: Multidrug-resistant (MDR) pathogenic microorganisms have become a global problem in ruminants as a result of the intensive use of antibiotics, causing the development of resistance among gut microbiota. The antibiotic-resistant microorganisms can be transferred from diseased animals to humans. This study aimed to determine the prevalence of MDR Escherichia coli and Salmonella spp. isolated from cattle, buffaloes, sheep, and goats suffering from respiratory signs, diarrhea, and mastitis and to screen the antibiotic sensitivity of selected isolated bacteria. It also detected antibiotic-resistance genes by polymerase chain reaction (PCR), produced green gold nanoparticles (AuNPs) using plant extracts (Artemisia herba-alba and Morus alba), and evaluated the antimicrobial activities of these biosynthesized nanoparticles on selected pathogens (E. coli and Salmonella spp.). Materials and Methods: MDR E. coli and Salmonella spp. were investigated using fecal samples (n=408), nasal swabs (n=358), and milk samples (n=227) of cattle, buffaloes, sheep, and goats with or without clinical signs, including respiratory manifestations, pneumonia, diarrhea, and mastitis, from different governorates in Egypt. E. coli and Salmonella spp. were isolated and identified on selective media, which were confirmed by biochemical reactions and PCR. Antimicrobial susceptibility testing against 10 commonly used antibiotics was performed using the Kirby-Bauer disk diffusion method. Antibiotic resistance genes blaTEM, blaSHV, blaOXA, and blaCTX-M were detected by PCR. The antibacterial effect of the biosynthesized AuNPs was evaluated by MIC and well diffusion assay. The biosynthesized AuNPs were also characterized by ultraviolet-visible spectrophotometry and transmission electron microscopy (TEM). Results: Among all fecal samples, the prevalence of E. coli was 18.4% (183/993) and that of Salmonella spp. was 16.7% (66/408), as determined by cultural and molecular tests. All isolates of E. coli and Salmonella spp. were 100% resistant to ampicillin (AM) and amoxicillin and highly resistant to cefoxitin and AM-sulbactam. The total rate of resistance genes in E. coli was 61.2% (112/183), while that in Salmonella was 63.6% (42/66) for pathogens isolated from ruminants with respiratory manifestations, pneumonia, diarrhea, and mastitis. Among the resistance genes, blaTEM had the highest prevalence rate in E. coli (25.9%, 21/81) while blaSHV had the lowest (9.8%, 8/81) in fecal swabs. AuNPs were successfully synthesized using aqueous leaf extract of A. herba-alba and M. alba as bioreducing agents. TEM analysis showed particle size of 10-42 nm for A. herba-alba and M. alba AuNPs. The biosynthesized AuNPs showed antibacterial activity against MDR E. coli and Salmonella spp. Conclusion: Rapid and accurate diagnostic methods are the cornerstone for effective treatment to reduce the risk of antimicrobial-resistant pathogenic microorganisms. This is particularly important for overcoming the increasing rate of MDR in ruminants with respiratory manifestations, pneumonia, diarrhea, and mastitis. This can be complemented by the development of AuNPs synthesized in an environmentally friendly manner AuNPs using natural plant extracts for the treatment of antibiotic-resistant microorganisms.

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Virulence-determinants and antibiotic-resistance genes of MDR-E. coli isolated from secondary infections following FMD-outbreak in cattle

Scientific Reports ◽

10.1038/s41598-020-75914-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Abdelazeem M. Algammal ◽

Helal F. Hetta ◽

Gaber E. Batiha ◽

Wael N. Hozzein ◽

Waleed M. El Kazzaz ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Bacterial Infections ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Virulence Determinants ◽

E Coli ◽

Secondary Infections ◽

Random Samples

AbstractThis study aimed to evaluate the prevalence, multidrug-resistance traits, PCR-detection of virulence, and antibiotic-resistance genes of E. coli isolated from secondary infections following FMD-outbreak in cattle. A total of 160 random samples were gathered from private dairy farms in Damietta Province, Egypt. The specimens were subjected to bacteriological examination, serotyping, congo-red binding assay, antibiogram-testing, and PCR-monitoring of virulence-determinant genes (tsh, phoA, hly, eaeA, sta, and lt) as well as the antibiotic-resistance genes (blaTEM, blaKPC, and blaCTX). The prevalence of E. coli was 30% (n = 48) distributed in 8 serogroups (40/48, 83.3%), while 8 isolates (8/48, 16.6%) were untypable. Besides, 83.3% of the examined isolates were positive for CR-binding. The tested strains harbored the virulence genes phoA, hly, tsh, eaeA, sta, and lt with a prevalence of 100% and 50%, 45.8%, 25%, 8.4%, and 6.2%, respectively. Furthermore, 50% of the recovered strains were multidrug-resistant (MDR) to penicillins, cephalosporins, and carbapenems, and are harboring the blaTEM, blaCTX, and blaKPC genes. Moreover, 25% of the examined strains are resistant to penicillins, and cephalosporins, and are harboring the blaTEM and blaCTX genes. To the best of our knowledge, this is the first report concerning the E. coli secondary bacterial infections following the FMD-outbreak. The emergence of MDR strains is considered a public health threat and indicates complicated treatment and bad prognosis of infections caused by such strains. Colistin sulfate and levofloxacin have a promising in vitro activity against MDR-E. coli.

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Distribution of Some Antibiotics Resistance Genes in Multi-drug Resistant E. coli Isolates from the Urogenitals of Women in Port Harcourt, Nigeria

Asian Journal of Research in Infectious Diseases ◽

10.9734/ajrid/2019/v2i130091 ◽

2019 ◽

pp. 1-7

Author(s):

Josephine Anem Kpalap ◽

Easter Godwin Nwokah ◽

Moses Nnaemeka Alo

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Randomized Study ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Antibiotics Resistance ◽

Multiple Drug ◽

Drug Resistant ◽

E Coli ◽

Port Harcourt

Aim: The problem of antibiotics resistance has assumed a global emergency status. Whereas Multidrug Resistant (MDR) E. coli infection is common among human population in Port Harcourt metropolis of Nigeria, the genetic background of E. coli isolates in our locality is not well elucidated, hence this study. Study Design: This was a randomized study of women, with indications of Urogenital infections, attending Braithwaite Memorial Specialist Hospital (BMSH) Port Harcourt, Nigeria between July and December, 2017. Methodology: Ninety-Seven (97) samples comprising of urine, high vaginal swabs, end ocervical swabs were collected from patients to assess for the presence of some antibiotic resistance genes in multi-drug resistant E. coli. Samples were processed following standard microbiological protocols. Antimicrobial susceptibility test was performed on all E. coli isolates. Following this, all Multiple Drug Resistant E. coli were subjected to polymerase chain reaction (PCR) method for the detection of some antibiotic resistance-encoding genes- SHV, CTX-M, TEM. Results: Seventy-three (73) isolates, including 36 E. coli, were recovered from all the clinical specimens. Twenty-four (24) E. coli isolates were found to be multi-drug resistant. Sulphydryl Variable (SHV) was the most frequent resistant gene and was detected in 15 isolates. This was followed by Cefotaximase (CTX-M) in 10 isolates and Temoniera (TEM) in 5 isolates. Some isolates haboured more than one resistance gene. About 20% of the isolates haboured SHV/CTX-M; 2.5% haboured CTX-M/TEM, while no target was detected in one isolate. Conclusion: This present study revealed that most E. coli isolates from the urogenitals of women within our locality, possess the ESBL genes which confers on them the Multidrug resistant status and this is a major challenge to maternal health.

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