scholarly journals Raw wastewater irrigation for urban agriculture in three African cities increases the abundance of transferable antibiotic resistance genes in soil, including those encoding extended spectrum β-lactamases (ESBLs)

2020 ◽  
Vol 698 ◽  
pp. 134201 ◽  
Author(s):  
B.P. Bougnom ◽  
S. Thiele-Bruhn ◽  
V. Ricci ◽  
C. Zongo ◽  
L.J.V. Piddock
Keyword(s):  
Antibiotic Resistance ◽  
Urban Agriculture ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Wastewater Irrigation ◽  
African Cities ◽  
Extended Spectrum ◽  
Raw Wastewater

scholarly journals Raw wastewater irrigation for urban agriculture in Africa increases the diversity of transferable antibiotic resistances genes in soil, including those encoding ESBLs

2019 ◽  
Author(s):  
B. P. Bougnom ◽  
S. Thiele-Bruhn ◽  
V. Ricci ◽  
C. Zongo ◽  
L.J.V Piddock
Keyword(s):  
Antibiotic Resistance ◽  
Urban Agriculture ◽  
Resistance Genes ◽  
Bacterial Resistance ◽  
Antibiotic Resistance Genes ◽  
Wastewater Irrigation ◽  
Antibiotic Residues ◽  
Soil Microbial Diversity ◽  
The Impact ◽  
Raw Wastewater

AbstractA metagenomic study was conducted to investigate the impact of raw wastewater use for irrigation in urban agriculture on the development of bacterial resistance in soil. Soil samples were collected in two African countries, from three different cities (each with irrigated and non-irrigated plots). Basic physical and chemical analysis were conducted, and the presence of selected antibiotic residues was assessed. Microbial DNA was extracted, quantified and sequenced. Microbial population structure and function, presence of horizontally transferable antibiotic resistance genes andEnterobacteriaceaeplasmids replicons were analysed using bioinformatics. The relative prevalence ofProteobacteriaandBacteroidetesand sequence reads coding for microbial adaptation and growth were higher in irrigated fields; 33 and 26 transferable ARGs were found in irrigated and non-irrigated fields sequence reads, respectively. Extended spectrum β-lactam genes identified in irrigated fields includedblaCARB-3,blaOXA-347,blaOXA-5 andblaRm3. Concentration of sulfamethoxazole, ciprofloxacin and enrofloxacin in soils influenced the selection of antibiotic resistance genes encoding resistance against amphenicol, β-lactams, and tetracyclines. TenEnterobacteriaceaeplasmid amplicon groups were identified in the fields, five were common to both, two (IncW and IncP1) and three (IncY, IncFIB and IncFIA) were found in irrigated and non-irrigated fields, respectively.In conclusion, wastewater irrigation affected both soil microbial diversity and functions. Irrigated fields have more diverse transferable antibiotic resistance genes, including ESBL genes that encode resistance to β-lactams antibiotics, except cephamycins and carbapenems. Even more, critical concentrations of antibiotic residues select for multiple and cross resistance. The findings from African cities show that wastewater irrigation in urban agriculture presents a serious public health risk for farmworkers and consumers by spread of bacterial resistance.

scholarly journals Comparative Genomics of Klebsiella pneumoniae Strains with Different Antibiotic Resistance Profiles

2011 ◽  
Vol 55 (9) ◽  
pp. 4267-4276 ◽  
Author(s):  
Vinod Kumar ◽  
Peng Sun ◽  
Jessica Vamathevan ◽  
Yong Li ◽  
Karen Ingraham ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Susceptible Strain ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Content Type ◽  
Extended Spectrum

ABSTRACTThere is a global emergence of multidrug-resistant (MDR) strains ofKlebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. While the epidemiology ofK. pneumoniaestrains and occurrences of specific antibiotic resistance genes, such as plasmid-borne extended-spectrum β-lactamases (ESBLs), have been extensively studied, only four complete genomes ofK. pneumoniaeare available. To better understand the multidrug resistance factors inK. pneumoniae, we determined by pyrosequencing the nearly complete genome DNA sequences of two strains with disparate antibiotic resistance profiles, broadly drug-susceptible strain JH1 and strain 1162281, which is resistant to multiple clinically used antibiotics, including extended-spectrum β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, and sulfamethoxazoles. Comparative genomic analysis of JH1, 1162281, and other publishedK. pneumoniaegenomes revealed a core set of 3,631 conserved orthologous proteins, which were used for reconstruction of whole-genome phylogenetic trees. The close evolutionary relationship between JH1 and 1162281 relative to otherK. pneumoniaestrains suggests that a large component of the genetic and phenotypic diversity of clinical isolates is due to horizontal gene transfer. Using curated lists of over 400 antibiotic resistance genes, we identified all of the elements that differentiated the antibiotic profile of MDR strain 1162281 from that of susceptible strain JH1, such as the presence of additional efflux pumps, ESBLs, and multiple mechanisms of fluoroquinolone resistance. Our study adds new and significant DNA sequence data onK. pneumoniaestrains and demonstrates the value of whole-genome sequencing in characterizing multidrug resistance in clinical isolates.

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

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.

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

2018 ◽  
Vol 81 (8) ◽  
pp. 1339-1345 ◽  
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.

scholarly journals Molecular Identification of Extended-Spectrum β-lactamase and Integron Genes in Klebsiella pneumonia

2016 ◽  
Vol 54 (202) ◽  
pp. 72-78 ◽  
Author(s):  
Ehsan Estabraghi ◽  
Taghi Zahraei Salehi ◽  
Kumarss Amini ◽  
Mahmoud Jamshidian
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Dna Amplification ◽  
Clinical Samples ◽  
Klebsiella Pneumonia ◽  
High Morbidity ◽  
Extended Spectrum ◽  
Class 1 ◽  
Amoxicillin Clavulanate

Introduction: Infections caused by Gram negative bacteria, producing extended-spectrum β-lactamase, including Klebsiella pneumoniae are increasing all over the world with high morbidity and mortality. The aim of the present study was determined antimicrobial profile susceptibility and the prevalence of antibiotic resistance genes by multiplex PCR. Methods: In the present study, we obtained one-hundred isolates of K. pneumoniae from different clinical samples. The antibiotic susceptibility testing was done in thirteen antibiotic and, therefore, M-PCRs were conducted using the DNA amplification for detection of ESBLs (blaTEM, blaCTX-M, blaSHV) and int (I, II, III) genes. Results: The results of resistance to amoxicillin/clavulanate, ciprofloxacin, amikacin, trimethoprim-sulfamethoxazole, cefotaxime, ampicillin, aztreonam, imipenem, gentamicin, ceftazidime, Cefepime, ceftriaxone and levofloxacin were obtained 37%, 37%, 93%, 84%, 52%, 87%, 59%, 8%, 24%, 67%, 52%, 43% and 26%, respectively. The frequency of the extended-spectrum β-lactamase K. pneumoniae was obtained 37%. The prevalence of resistance genes of ESBLs in the M-PCR method showed that the blaTEM, blaCTX and blaSHV were 38%, 24% and 19%, respectively, however, only 8 (8%) out of 100 isolates were found to have positive outcomes for the existence of class 1 integrons and there were no detected class 2 or class 3 integrons. Conclusions: Our results recommend the likely co-carriage of some ESBLs genes and antibiotic resistance integrons on the same plasmids harboring the MDR genes. Keywords: fKlebsiella pneumonia, integrons, drug resistance. | PubMed

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

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.

scholarly journals Molecular detection of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolates of chicken origin from East Java, Indonesia

2019 ◽  
Vol 12 (4) ◽  
pp. 578-583 ◽  
Author(s):  
Meutia Hayati ◽  
Agustin Indrawati ◽  
Ni Luh Putu Ika Mayasari ◽  
Istiyaningsih Istiyaningsih ◽  
Neneng Atikah
Keyword(s):  
Antibiotic Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Resistance Pattern ◽  
Dilution Method ◽  
Agar Dilution Method ◽  
Resistance Level ◽  
Extended Spectrum

Background and Aim: Klebsiella pneumoniae is one of the respiratory disease agents in human and chicken. This bacterium is treated by antibiotic, but this treatment may trigger antibiotic resistance. Resistance gene in K. pneumoniae may be transferred to other bacteria. One of the known resistance genes is extended-spectrum β-lactamase (ESBL). This research aimed to study K. pneumoniae isolated from chicken farms in East Java, Indonesia, by observing the antibiotic resistance pattern and detect the presence of ESBL coding gene within the isolates. Materials and Methods: A total of 11 K. pneumoniae isolates were collected from 141 chicken cloacal swabs from two regencies in East Java. All isolates were identified using the polymerase chain reaction method. Antimicrobial susceptibility was determined by agar dilution method on identified isolates, which then processed for molecular characterization to detect ESBL coding gene within the K. pneumoniae isolates found. Results: The result of antibiotic sensitivity test in 11 isolates showed highest antibiotic resistance level toward ampicillin, amoxicillin, and oxytetracycline (100%, 100%, and 90.9%) and still sensitive to gentamicin. Resistance against colistin, doxycycline, ciprofloxacin, and enrofloxacin is varied by 90.9%, 54.5%, 27.3%, and 18.2%, respectively. All isolates of K. pneumoniae were classified as multidrug resistance (MDR) bacteria. Resistance gene analysis revealed the isolates harbored as blaSHV (9.1%), blaTEM (100%), and blaCTX-M (90.9%). Conclusion: All the bacterial isolates were classified as MDR bacteria and harbored two of the transmissible ESBL genes. The presence of antibiotic resistance genes in bacteria has the potential to spread its resistance properties.

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

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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