scholarly journals Genotypic-Phenotypic Discrepancies between Antibiotic Resistance Characteristics of Escherichia coli Isolates from Calves in Management Settings with High and Low Antibiotic Use

2011 ◽  
Vol 77 (10) ◽  
pp. 3293-3299 ◽  
Author(s):  
Margaret A. Davis ◽  
Thomas E. Besser ◽  
Lisa H. Orfe ◽  
Katherine N. K. Baker ◽  
Amelia S. Lanier ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Antibiotic Use ◽  
Dairy Calf ◽  
Bacterial Populations ◽  
Content Type ◽  
Exact Test ◽  
E Coli ◽  
Fisher’S Exact Test

ABSTRACTWe hypothesized that bacterial populations growing in the absence of antibiotics will accumulate more resistance gene mutations than bacterial populations growing in the presence of antibiotics. If this is so, the prevalence of dysfunctional resistance genes (resistance pseudogenes) could provide a measure of the level of antibiotic exposure present in a given environment. As a proof-of-concept test, we assayed field strains ofEscherichia colifor their resistance genotypes using a resistance gene microarray and further characterized isolates that had resistance phenotype-genotype discrepancies. We found a small but significant association between the prevalence of isolates with resistance pseudogenes and the lower antibiotic use environment of a beef cow-calf operation versus a higher antibiotic use dairy calf ranch (Fisher's exact test,P= 0.044). Other significant findings include a very strong association between the dairy calf ranch isolates and phenotypes unexplained by well-known resistance genes (Fisher's exact test,P< 0.0001). Two novel resistance genes were discovered inE. coliisolates from the dairy calf ranch, one associated with resistance to aminoglycosides and one associated with resistance to trimethoprim. In addition, isolates resistant to expanded-spectrum cephalosporins but negative forblaCMY-2had mutations in the promoter regions of the chromosomalE. coliampCgene consistent with reported overexpression of native AmpC beta-lactamase. Similar mutations in hospitalE. coliisolates have been reported worldwide. Prevalence or rates ofE. coliampCpromoter mutations may be used as a marker for high expanded-spectrum cephalosporin use environments.

scholarly journals Prevalence of Antimicrobial Resistance and Transfer of Tetracycline Resistance Genes in Escherichia coli Isolates from Beef Cattle

2015 ◽  
Vol 81 (16) ◽  
pp. 5560-5566 ◽  
Author(s):  
Seung Won Shin ◽  
Min Kyoung Shin ◽  
Myunghwan Jung ◽  
Kuastros Mekonnen Belaynehe ◽  
Han Sang Yoo
Keyword(s):  
Escherichia Coli ◽  
South Korea ◽  
Beef Cattle ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Tetracycline Resistance ◽  
Tetracycline Resistance Gene ◽  
Content Type ◽  
E Coli ◽  
Tetracycline Resistance Genes

ABSTRACTThe aim of this study was to investigate the prevalence and transferability of resistance in tetracycline-resistantEscherichia coliisolates recovered from beef cattle in South Korea. A total of 155E. coliisolates were collected from feces in South Korea, and 146 were confirmed to be resistant to tetracycline. The tetracycline resistance genetet(A) (46.5%) was the most prevalent, followed bytet(B) (45.1%) andtet(C) (5.8%). Strains carryingtet(A) plustet(B) andtet(B) plustet(C) were detected in two isolates each. In terms of phylogenetic grouping, 101 (65.2%) isolates were classified as phylogenetic group B1, followed in decreasing order by D (17.4%), A (14.2%), and B2 (3.2%). Ninety-one (62.3%) isolates were determined to be multidrug resistant by the disk diffusion method. MIC testing using the principal tetracyclines, namely, tetracycline, chlortetracycline, oxytetracycline, doxycycline, and minocycline, revealed that isolates carryingtet(B) had higher MIC values than isolates carryingtet(A). Conjugation assays showed that 121 (82.9%) isolates could transfer a tetracycline resistance gene to a recipient via the IncFIB replicon (65.1%). This study suggests that the high prevalence of tetracycline-resistantE. coliisolates in beef cattle is due to the transferability of tetracycline resistance genes betweenE. colipopulations which have survived the selective pressure caused by the use of antimicrobial agents.

scholarly journals Emergence of Colistin Resistance Gene mcr-1 in Cronobacter sakazakii Producing NDM-9 and in Escherichia coli from the Same Animal

2016 ◽  
Vol 61 (2) ◽  
Author(s):  
Bao-Tao Liu ◽  
Feng-Jing Song ◽  
Ming Zou ◽  
Zhi-Hui Hao ◽  
Hu Shan
Keyword(s):  
Escherichia Coli ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Cronobacter Sakazakii ◽  
Colistin Resistance ◽  
Content Type ◽  
E Coli ◽  
Carbapenem Resistant

ABSTRACT We report the presence of mcr-1 in Escherichia coli and carbapenem-resistant Cronobacter sakazakii from the same diseased chicken. The mcr-1 gene linked with ISApl1 was located on two different IncI2 plasmids, including one multidrug plasmid in E. coli, whereas fosA3-bla NDM-9 was on an IncB/O plasmid in C. sakazakii. The development of the fosA3-bla NDM-9 resistance region was mediated by IS26. The colocation of mcr-1 or bla NDM-9 with other resistance genes will accelerate the dissemination of the two genes.

scholarly journals A Novel Trimethoprim Resistance Gene, dfrA36, Characterized from Escherichia coli from Calves

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Dominik Wüthrich ◽  
Michael Brilhante ◽  
Anna Hausherr ◽  
Jens Becker ◽  
Mireille Meylan ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Multidrug Resistant ◽  
Content Type ◽  
Genetic Link ◽  
E Coli ◽  
Global Spread ◽  
Different Sources ◽  
Disinfectant Resistance

The presence of dfrA36 associated with ISCR2 in Escherichia coli from animals, as well as its presence in other E. coli strains from different sources and countries and in Acinetobacter, highlights the global spread of this gene and its potential for further dissemination. The genetic link of ISCR2-dfrA36 with other antibiotic and disinfectant resistance genes showed that multidrug-resistant E. coli may be selected and maintained by the use of either one of several antimicrobials.

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

2014 ◽  
Vol 80 (12) ◽  
pp. 3656-3666 ◽  
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.

scholarly journals Spread of NDM-5 and OXA-181 Carbapenemase-Producing Escherichia coli in Chad

2019 ◽  
Vol 63 (11) ◽  
Author(s):  
Oumar Ouchar Mahamat ◽  
Manon Lounnas ◽  
Mallorie Hide ◽  
Abelsalam Tidjani ◽  
Julio Benavides ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Healthy Volunteers ◽  
Resistance Genes ◽  
Sequence Type ◽  
Hospitalized Patients ◽  
Content Type ◽  
E Coli ◽  
First Time

ABSTRACT We detected for the first time blaNDM-5 and blaOXA-181 in Escherichia coli isolates from hospitalized patients and healthy volunteers in Chad. These resistance genes were located on IncX3 and IncF plasmids. Despite the large diversity of E. coli clones, the identified resistant intestinal isolates belonged mainly to the same sequence type.

scholarly journals F Plasmids Are the Major Carriers of Antibiotic Resistance Genes in Human-Associated Commensal Escherichia coli

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Craig Stephens ◽  
Tyler Arismendi ◽  
Megan Wright ◽  
Austin Hartman ◽  
Andres Gonzalez ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Transposable Elements ◽  
Dna Sequencing ◽  
Resistance Genes ◽  
Bacterial Pathogens ◽  
Acquired Resistance ◽  
Antibiotic Resistance Genes ◽  
Content Type ◽  
E Coli

ABSTRACT The evolution and propagation of antibiotic resistance by bacterial pathogens are significant threats to global public health. Contemporary DNA sequencing tools were applied here to gain insight into carriage of antibiotic resistance genes in Escherichia coli, a ubiquitous commensal bacterium in the gut microbiome in humans and many animals, and a common pathogen. Draft genome sequences generated for a collection of 101 E. coli strains isolated from healthy undergraduate students showed that horizontally acquired antibiotic resistance genes accounted for most resistance phenotypes, the primary exception being resistance to quinolones due to chromosomal mutations. A subset of 29 diverse isolates carrying acquired resistance genes and 21 control isolates lacking such genes were further subjected to long-read DNA sequencing to enable complete or nearly complete genome assembly. Acquired resistance genes primarily resided on F plasmids (101/153 [67%]), with smaller numbers on chromosomes (30/153 [20%]), IncI complex plasmids (15/153 [10%]), and small mobilizable plasmids (5/153 [3%]). Nearly all resistance genes were found in the context of known transposable elements. Very few structurally conserved plasmids with antibiotic resistance genes were identified, with the exception of an ∼90-kb F plasmid in sequence type 1193 (ST1193) isolates that appears to serve as a platform for resistance genes and may have virulence-related functions as well. Carriage of antibiotic resistance genes on transposable elements and mobile plasmids in commensal E. coli renders the resistome highly dynamic. IMPORTANCE Rising antibiotic resistance in human-associated bacterial pathogens is a serious threat to our ability to treat many infectious diseases. It is critical to understand how acquired resistance genes move in and through bacteria associated with humans, particularly for species such as Escherichia coli that are very common in the human gut but can also be dangerous pathogens. This work combined two distinct DNA sequencing approaches to allow us to explore the genomes of E. coli from college students to show that the antibiotic resistance genes these bacteria have acquired are usually carried on a specific type of plasmid that is naturally transferrable to other E. coli, and likely to other related bacteria.

scholarly journals ESKAPE Bacteria and Extended-Spectrum-β-Lactamase-Producing Escherichia coli Isolated from Wastewater and Process Water from German Poultry Slaughterhouses

2020 ◽  
Vol 86 (8) ◽  
Author(s):  
Mykhailo Savin ◽  
Gabriele Bierbaum ◽  
Jens Andre Hammerl ◽  
Céline Heinemann ◽  
Marijo Parcina ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Wastewater Treatment ◽  
Resistance Genes ◽  
Wastewater Treatment Plants ◽  
Process Water ◽  
Resistant Bacteria ◽  
Content Type ◽  
E Coli ◽  
Extended Spectrum ◽  
Clinically Relevant Bacteria

ABSTRACT The wastewater of livestock slaughterhouses is considered a source of antimicrobial-resistant bacteria with clinical relevance and may thus be important for their dissemination into the environment. To get an overview of their occurrence and characteristics, we investigated process water (n = 50) from delivery and unclean areas as well as wastewater (n = 32) from the in-house wastewater treatment plants (WWTPs) of two German poultry slaughterhouses (slaughterhouses S1 and S2). The samples were screened for ESKAPE bacteria (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) and Escherichia coli. Their antimicrobial resistance phenotypes and the presence of extended-spectrum-β-lactamase (ESBL), carbapenemase, and mobilizable colistin resistance genes were determined. Selected ESKAPE bacteria were epidemiologically classified using different molecular typing techniques. At least one of the target species was detected in 87.5% (n = 28/32) of the wastewater samples and 86.0% (n = 43/50) of the process water samples. The vast majority of the recovered isolates (94.9%, n = 448/472) was represented by E. coli (39.4%), the A. calcoaceticus-A. baumannii (ACB) complex (32.4%), S. aureus (12.3%), and K. pneumoniae (10.8%), which were widely distributed in the delivery and unclean areas of the individual slaughterhouses, including their wastewater effluents. Enterobacter spp., Enterococcus spp., and P. aeruginosa were less abundant and made up 5.1% of the isolates. Phenotypic and genotypic analyses revealed that the recovered isolates exhibited diverse resistance phenotypes and β-lactamase genes. In conclusion, wastewater effluents from the investigated poultry slaughterhouses exhibited clinically relevant bacteria (E. coli, methicillin-resistant S. aureus, K. pneumoniae, and species of the ACB and Enterobacter cloacae complexes) that contribute to the dissemination of clinically relevant resistances (i.e., blaCTX-M or blaSHV and mcr-1) in the environment. IMPORTANCE Bacteria from livestock may be opportunistic pathogens and carriers of clinically relevant resistance genes, as many antimicrobials are used in both veterinary and human medicine. They may be released into the environment from wastewater treatment plants (WWTPs), which are influenced by wastewater from slaughterhouses, thereby endangering public health. Moreover, process water that accumulates during the slaughtering of poultry is an important reservoir for livestock-associated multidrug-resistant bacteria and may serve as a vector of transmission to occupationally exposed slaughterhouse employees. Mitigation solutions aimed at the reduction of the bacterial discharge into the production water circuit as well as interventions against their further transmission and dissemination need to be elaborated. Furthermore, the efficacy of in-house WWTPs needs to be questioned. Reliable data on the occurrence and diversity of clinically relevant bacteria within the slaughtering production chain and in the WWTP effluents in Germany will help to assess their impact on public and environmental health.

scholarly journals Silver Resistance Genes Are Overrepresented among Escherichia coli Isolates with CTX-M Production

2014 ◽  
Vol 80 (22) ◽  
pp. 6863-6869 ◽  
Author(s):  
Susanne Sütterlin ◽  
Petra Edquist ◽  
Linus Sandegren ◽  
Marlen Adler ◽  
Thomas Tängdén ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Selective Pressure ◽  
Human Origin ◽  
Content Type ◽  
Beta Lactamases ◽  
E Coli ◽  
Genes Encoding ◽  
Extended Spectrum Beta Lactamases ◽  
M 14

ABSTRACTMembers of theEnterobacteriaceaewith extended-spectrum beta-lactamases (ESBLs) of the CTX-M type have disseminated rapidly in recent years and have become a threat to public health. In parallel with the CTX-M type expansion, the consumption and widespread use of silver-containing products has increased. To determine the carriage rates of silver resistance genes in differentEscherichia colipopulations, the presence of three silver resistance genes (silE,silP, andsilS) and genes encoding CTX-M-, TEM-, and SHV-type enzymes were explored inE. coliisolates of human (n= 105) and avian (n= 111) origin. The antibiotic profiles were also determined. Isolates harboring CTX-M genes were further characterized, and phenotypic silver resistance was examined. ThesilEgene was present in 13 of the isolates. All of them were of human origin. Eleven of these isolates harbored ESBLs of the CTX-M type (P= 0.007), and eight of them were typed as CTX-M-15 and three as CTX-M-14. None of thesilE-positive isolates was related to the O25b-ST131 clone, but 10 out of 13 belonged to the ST10 or ST58 complexes. Phenotypic silver resistance (silver nitrate MIC > 512 mg/liter) was observed after silver exposure in 12 of them, and a concomitant reduced susceptibility to piperacillin-tazobactam developed in three. In conclusion, 12% of the humanE. coliisolates but none of the avian isolates harbored silver resistance genes. This indicates another route for or level of silver exposure for humans than that caused by common environmental contamination. SincesilE-positive isolates were significantly more often found in CTX-M-positive isolates, it is possible that silver may exert a selective pressure on CTX-M-producingE. coliisolates.

scholarly journals Comparative Genomics of an IncA/C Multidrug Resistance Plasmid from Escherichia coli and Klebsiella Isolates from Intensive Care Unit Patients and the Utility of Whole-Genome Sequencing in Health Care Settings

2014 ◽  
Vol 58 (8) ◽  
pp. 4814-4825 ◽  
Author(s):  
Tracy H. Hazen ◽  
LiCheng Zhao ◽  
Mallory A. Boutin ◽  
Angela Stancil ◽  
Gwen Robinson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Health Care ◽  
Intensive Care Unit ◽  
Intensive Care ◽  
Comparative Genomics ◽  
Resistance Genes ◽  
Whole Genome ◽  
Content Type ◽  
Health Care Settings ◽  
E Coli

ABSTRACTThe IncA/C plasmids have been implicated for their role in the dissemination of β-lactamases, including gene variants that confer resistance to expanded-spectrum cephalosporins, which are often the treatment of last resort against multidrug-resistant, hospital-associated pathogens. AblaFOX-5gene was detected in 14Escherichia coliand 16Klebsiellaisolates that were cultured from perianal swabs of patients admitted to an intensive care unit (ICU) of the University of Maryland Medical Center (UMMC) in Baltimore, MD, over a span of 3 years. Four of the FOX-encoding isolates were obtained from subsequent samples of patients that were initially negative for an AmpC β-lactamase upon admission to the ICU, suggesting that the AmpC β-lactamase-encoding plasmid was acquired while the patient was in the ICU. The genomes of fiveE. coliisolates and sixKlebsiellaisolates containingblaFOX-5were selected for sequencing based on their plasmid profiles. An ∼167-kb IncA/C plasmid encoding the FOX-5 β-lactamase, a CARB-2 β-lactamase, additional antimicrobial resistance genes, and heavy metal resistance genes was identified. Another FOX-5-encoding IncA/C plasmid that was nearly identical except for a variable region associated with the resistance genes was also identified. To our knowledge, these plasmids represent the first FOX-5-encoding plasmids sequenced. We used comparative genomics to describe the genetic diversity of a plasmid encoding a FOX-5 β-lactamase relative to the whole-genome diversity of 11E. coliandKlebsiellaisolates that carry this plasmid. Our findings demonstrate the utility of whole-genome sequencing for tracking of plasmid and antibiotic resistance gene distribution in health care settings.

scholarly journals Effects of Cover Crop Species and Season on Population Dynamics of Escherichia coli and Listeria innocua in Soil

2016 ◽  
Vol 82 (6) ◽  
pp. 1767-1777 ◽  
Author(s):  
Neiunna L. Reed-Jones ◽  
Sasha Cahn Marine ◽  
Kathryne L. Everts ◽  
Shirley A. Micallef
Keyword(s):  
Escherichia Coli ◽  
Cover Crops ◽  
Cover Crop ◽  
Green Manure ◽  
Listeria Innocua ◽  
Hairy Vetch ◽  
Bacterial Populations ◽  
Content Type ◽  
E Coli ◽  
Crimson Clover

ABSTRACTCover crops provide several ecosystem services, but their impact on enteric bacterial survival remains unexplored. The influence of cover cropping on foodborne pathogen indicator bacteria was assessed in five cover crop/green manure systems: cereal rye, hairy vetch, crimson clover, hairy vetch-rye and crimson clover-rye mixtures, and bare ground. Cover crop plots were inoculated withEscherichia coliandListeria innocuain the fall of 2013 and 2014 and tilled into the soil in the spring to form green manure. Soil samples were collected and the bacteria enumerated. Time was a factor for all bacterial populations studied in all fields (P< 0.001).E. colilevels declined when soil temperatures dipped to <5°C and were detected only sporadically the following spring.L. innocuadiminished somewhat but persisted, independently of season. In an organic field, the cover crop was a factor forE. coliin year 1 (P= 0.004) and forL. innocuain year 2 (P= 0.011). In year 1,E. colilevels were highest in the rye and hairy vetch-rye plots. In year 2,L. innocualevels were higher in hairy vetch-rye (P= 0.01) and hairy vetch (P= 0.03) plots than in the rye plot. Bacterial populations grew (P< 0.05) or remained the same 4 weeks after green manure incorporation, although initial reductions inL. innocuanumbers were observed after tilling (P< 0.05). Green manure type was a factor only forL. innocuaabundance in a transitional field (P< 0.05). Overall, the impacts of cover crops/green manures on bacterial population dynamics in soil varied, being influenced by bacterial species, time from inoculation, soil temperature, rainfall, and tillage; this reveals the need for long-term studies.

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