Modeling the Emergence of Antibiotic Resistance in Bacterial Populations

2018 ◽  
Vol 80 (3) ◽  
pp. 214-220 ◽  
Author(s):  
Michelle A. Williams ◽  
Patricia J. Friedrichsen ◽  
Troy D. Sadler ◽  
Pamela J. B. Brown
Keyword(s):  
Antibiotic Resistance ◽  
Coli Strain ◽  
Science Standards ◽  
Evolutionary Mechanisms ◽  
Resistance Level ◽  
Random Mutation ◽  
Bacterial Populations ◽  
E Coli ◽  
Disk Diffusion Assay ◽  
High School Classroom

Since antibiotics have become routinely used to treat infections, antibiotic resistance is now an emerging concern for public health. To understand how bacteria become resistant to antibiotics, many students draw from the common misconception that bacteria gain resistance upon antibiotic exposure. We have designed models and a corresponding lab that explores how a population of bacteria can evolve antibiotic resistance, with emphasis on dispelling common misconceptions surrounding the mechanism of antibiotic resistance. Using an antibiotic disk diffusion assay, students compare the antibiotic resistance level of a harmless E. coli strain of bacteria over time. Then, students compare their lab data to the models, which together illustrate the roles that initial genetic variation and random mutation play in the evolution of antibiotic resistance. In this guided investigation, basic microbiology concepts and techniques are made accessible to students in a high school classroom. The models developed here are in line with the practices of the Next Generation Science Standards (NGSS). The models, together with the lab, are used to guide students through the process of argumentation using a claim, evidence, and reasoning (CER) format to explain the evolutionary mechanisms of antibiotic resistance.

Surveillance of Antibiotic Resistance Among Enterobacteriaceae Strains Isolated in an Infectious Diseases Hospital from Romania

2018 ◽  
Vol 69 (5) ◽  
pp. 1240-1243
Author(s):  
Manuela Arbune ◽  
Mioara Decusara ◽  
Luana Andreea Macovei ◽  
Aurelia Romila ◽  
Alina Viorica Iancu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Infectious Diseases ◽  
Salmonella Spp ◽  
Resistance Level ◽  
E Coli ◽  
Bacterial Genus ◽  
Antibiotic Resistance Profile ◽  
Carbapenem Resistant ◽  
Invasive Infections ◽  
Klebsiella Spp

The aim of the present study was to characterize the antibiotic resistance profile of enterobacteriaceae strains isolated in Infectious Diseases Hospital Galati, Romania, during 2016, in order to guide the local antibiotic stewardship strategy. There are 597 biological samples with positive cultures for enterobacteriaceae, related to invasive and non-invasive infections. The main bacterial genus were E. coli 62%, Klebsiella spp 15%, Proteus spp 11% and Salmonella spp 6%. Over a half of isolated strains have one or more antibiotic resistance. The resistance level depends on bacterial genus, with highest level found among the rare isolates: Enterobacter spp, Citrobacter spp, Morganella spp and Serratia spp. The rate of MDR was 17.,6% for E. coli, 40.9% for Klebsiella spp and 50.7% for Proteus spp. while the rate of strains producing Extended Spectrum of Beta Lactamase are 7.2% for E. coli, 28.4% for Klebsiella spp and 12.3% for Proteus spp. The carbapenem resistant strains were found in 1.1% cases.

scholarly journals 609. Differing Genotypic Contexts Between E. coli and A. baumannii Modulate the Role of blaADC-7 in the Development of Antibiotic Collateral Sensitivity

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S284-S285
Author(s):  
Erin McClure ◽  
Julia Newman ◽  
Nikhil Krishnan ◽  
Joseph Rutter ◽  
Andrea M Hujer ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Fold Increase ◽  
Protein Product ◽  
Coli Strain ◽  
Fourth Generation ◽  
Clinical Strain ◽  
Health Crisis ◽  
E Coli ◽  
Collateral Sensitivity ◽  
Resistance Evolution

Abstract Background Antibiotic resistance is a global health crisis. While persistent drug discovery of novel antibiotics has previously been relied upon to thwart resistance, evolution inevitably perseveres. While genes conferring antibiotic resistance have previously been characterized, it is unclear how varying genetic contexts can change the antibiotic resistance phenotype a given gene confers. Methods The DH10B strain of E. coli was transformed with a blaADC-7 plasmid. In 12 evolutionary replicates, the modified E. coli strain and a clinical strain of A. baumannii containing the same resistance gene were passaged daily for 10 days on cefepime gradient agar plates with gradually increasing concentrations of cefepime. MICs of cefepime and a diverse set of 15 other drugs were determined for the parental strains and after the final passage passage. MIC of cefepime after intermediary passages were determined for select replicates. Lastly the blaADC-7 gene after the final passage was sequenced. Results At the end of 10 passages, collateral sensitivity in A. baumannii was observed to tigecycline and fosfomycin in 5 and 6 replicates respectively, out of 12 total. 4 out of 12 E. coli replicates displayed collateral sensitivity to minocycline (Figure 1). In the third E. coli replicate, Sanger sequencing revealed a novel S286R mutation in blaADC-7 appearing in passage seven which preceded a several log fold increase in the MIC of cefepime (Figures 2 and 3). No additional mutations were found in the other evolutionary replicates. Conclusion Patterns of resistance varied among antibiotics of the same class, (e.g., tetracyclines, fourth-generation cephalosporins) in both E. coli and A. baumannii; however, A. baumannii expressed less widespread collateral resistance than E. coli. A previously undiscovered S286R mutation in blaADC-7 coincided with a pronounced increased in resistance to cefepime. Further studies are required to determine whether this mutation gives rise to a structural change in the protein product. Given that no other mutations were found, resistance to cefepime and subsequent collateral resistance to other antibiotics may have developed due to epigenetic changes or mutations outside the blaADC-7 genes. Indeed, future experiments with whole-genome sequencing may reveal such changes. Disclosures All authors: No reported disclosures.

scholarly journals Genomic and Proteomic Characterization of the Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli Strain CCUG 73778: A Virulent, Nosocomial Outbreak Strain

2020 ◽  
Vol 8 (6) ◽  
pp. 893 ◽  
Author(s):  
Daniel Jaén-Luchoro ◽  
Antonio Busquets ◽  
Roger Karlsson ◽  
Francisco Salvà-Serra ◽  
Christina Åhrén ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Coli Strain ◽  
University Hospital ◽  
Hospital Environment ◽  
Resistance Factors ◽  
E Coli ◽  
Extended Spectrum ◽  
Liquid Chromatography Tandem Mass

Escherichia coli strain CCUG 78773 is a virulent extended-spectrum β-lactamase (ESBL)-producing ST131-O25b type strain isolated during an outbreak at a regional university hospital. The complete and closed genome sequence, comprising one chromosome (5,076,638 bp) and six plasmids (1718–161,372 bp), is presented. Characterization of the genomic features detected the presence of 59 potential antibiotic resistance factors, including three prevalent β-lactamases. Several virulence associated elements were determined, mainly related with adherence, invasion, biofilm formation and antiphagocytosis. Twenty-eight putative type II toxin-antitoxin systems were found. The plasmids were characterized, through in silico analyses, confirming the two β-lactamase-encoding plasmids to be conjugative, while the remaining plasmids were mobilizable. BLAST analysis of the plasmid sequences showed high similarity with plasmids in E. coli from around the world. Expression of many of the described virulence and AMR factors was confirmed by proteomic analyses, using bottom-up, liquid chromatography-tandem mass spectrometry (LC-MS/MS). The detailed characterization of E. coli strain CCUG 78773 provides a reference for the relevance of genetic elements, as well as the characterization of antibiotic resistance and the spread of bacteria harboring ESBL genes in the hospital environment.

scholarly journals American Crows as Carriers of Extra Intestinal Pathogenic E. coli and Avian Pathogenic-Like E. coli and Their Potential Impact on a Constructed Wetland

2020 ◽  
Vol 8 (10) ◽  
pp. 1595
Author(s):  
Keya Sen ◽  
Vaughn Shepherd ◽  
Tanner Berglund ◽  
Alexa Quintana ◽  
Shnia Puim ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Surface Water ◽  
Constructed Wetland ◽  
Coli Strain ◽  
Medical Community ◽  
Poultry Industry ◽  
Wetland Area ◽  
E Coli ◽  
American Crows ◽  
Potential Impact

The study examines whether crows are carriers of extraintestinal pathogenic E. coli (ExPEC) and avian pathogenic E. coli (APEC)-like strains, and if wetland roost areas contribute to their spread. A total of 10 crow feces (n = 71) and 15 water E. coli isolates (n = 134) from a wetland area could be characterized as potentially ExPEC based on the presence of ≥2 of the five cardinal genes iutA, kpsMT2, papEF, pap A/C, papG, sfa/foc, and afa/dra, while six fecal and 14 water isolates could be characterized as potentially APEC-like based on the presence of plasmid associated genes: iutA, episomal iss, ompT, hlyF and iroN. A total of 32 fecal and 27 water isolates tested carried plasmids based on incompatibility typing. Plasmids from 34 of 38 isolates tested could be transferred to another E. coli strain by conjugation with the antibiotic resistance (AR) profile being transferred, indicating their potential to be transferred to indigenous and non-pathogenic strains in the wetland. APEC-like plasmids could be transferred in six of eight isolates tested. Pathogenic E. coli of importance to the medical community and poultry industry may be detected in high levels in surface water due to corvid activity. Regardless of their role in health or disease, water in wetlands and streams can serve as a media for the dissemination of AR and virulence traits of bacteria, with corvids acting as potential vectors for farther dissemination.

Characterization of antibiotic-resistant and potentially pathogenic Escherichia coli from soil fertilized with litter of broiler chickens fed antimicrobial-supplemented diets

2012 ◽  
Vol 58 (9) ◽  
pp. 1084-1098 ◽  
Author(s):  
Laura E. Merchant ◽  
Heidi Rempel ◽  
Tom Forge ◽  
Tissa Kannangara ◽  
Shabtai Bittman ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Broiler Chickens ◽  
Antimicrobial Agents ◽  
Soil Samples ◽  
Plate Count ◽  
Virulence Determinants ◽  
Resistance Level ◽  
Antibiotic Resistant ◽  
E Coli

The objective of this study was to characterize antimicrobial resistance and virulence determinants of Escherichia coli from soil amended with litter from 36-day-old broiler chickens ( Gallus gallus domesticus ) fed with diets supplemented with a variety of antimicrobial agents. Soil samples were collected from plots before and periodically after litter application in August to measure E. coli numbers. A total of 295 E. coli were isolated from fertilized soil samples between August and March. Antibiotic susceptibility was determined by Sensititre, and polymerase chain reaction was performed to detect the presence of resistance and virulence genes. The results confirmed that E. coli survived and could be quantified by direct plate count for at least 7 months in soil following litter application in August. The effects of feed supplementation were observed on E. coli numbers in November and January. Among the 295 E. coli, the highest antibiotic resistance level was observed against tetracycline and β-lactams associated mainly with the resistance genes tetB and blaCMY-2, respectively. Significant treatment effects were observed for phylogenetic groups, antibiotic resistance profiles, and virulence gene frequencies. Serotyping, phylogenetic grouping, and pulsed-field gel electrophoresis confirmed that multiple-antibiotic-resistant and potentially pathogenic E. coli can survive in soil fertilized with litter for several months regardless of antimicrobials used in the feed.

scholarly journals Temporal Dynamics and Impact of Manure Storage on Antibiotic Resistance Patterns and Population Structure of Escherichia coli Isolates from a Commercial Swine Farm

2007 ◽  
Vol 73 (17) ◽  
pp. 5486-5493 ◽  
Author(s):  
Patrick Duriez ◽  
Edward Topp
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Population Structure ◽  
Temporal Dynamics ◽  
Swine Farm ◽  
Bacterial Populations ◽  
E Coli ◽  
Resistance Patterns ◽  
Fresh Feces ◽  
Antibiotic Resistance Patterns

ABSTRACT Many confined-livestock farms store their wastes for several months prior to use as a fertilizer. Storing manure for extended periods could significantly bias the composition of enteric bacterial populations subsequently released into the environment. Here, we compared populations of Escherichia coli isolated from fresh feces and from the manure-holding tank (stored manure) of a commercial swine farm, each sampled monthly for 6 months. The 4,668 confirmed E. coli isolates were evaluated for resistance to amikacin, ampicillin, cephalothin, chloramphenicol, kanamycin, nalidixic acid, streptomycin, sulfamethoxazole, tetracycline, trimethoprim, and trimethoprim plus sulfamethoxazole. A subset of 1,687 isolates was fingerprinted by repetitive extragenic palindromic PCR (rep-PCR) with the BOXA1R primer to evaluate the diversity and the population structure of the collection. The population in the stored manure was generally more diverse than that in the fresh feces. Half of the genotypes detected in the stored manure were never detected in the fresh fecal material, and only 16% were detected only in the fresh feces. But the majority of the isolates (84%) were assigned to the 34% of genotypes shared between the two environments. The structure of the E. coli population showed important monthly variations both in the extent and distribution of the diversity of the observed genotypes. The frequency of detection of resistance to specific antibiotics was not significantly different between the two collections and varied importantly between monthly samples. Resistance to multiple antibiotics was much more temporally dynamic in the fresh feces than in the stored manure. There was no relationship between the distribution of rep-PCR fingerprints and the distribution of antibiotic resistance profiles, suggesting that specific antibiotic resistance determinants were dynamically distributed within the population.

scholarly journals Carriage of Carbapenem-Resistant Enterobacterales in Adult Patients Admitted to a University Hospital in Italy

Antibiotics ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 61
Author(s):  
Pamela Barbadoro ◽  
Daniela Bencardino ◽  
Elisa Carloni ◽  
Enrica Omiccioli ◽  
Elisa Ponzio ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Resistance Rate ◽  
Coli Strain ◽  
Adult Patients ◽  
University Hospital ◽  
E Coli ◽  
Genetic Features ◽  
Phenotypic Tests

The emerging spread of carbapenemase-producing Enterobacterales (CPE) strains, in particular, Klebsiella pneumoniae and Escherichia coli, has become a significant threat to hospitalized patients. Carbapenemase genes are frequently located on plasmids than can be exchanged among clonal strains, increasing the antibiotic resistance rate. The aim of this study was to determine the prevalence of CPE in patients upon their admission and to analyze selected associated factors. An investigation of the antibiotic resistance and genetic features of circulating CPE was carried out. Phenotypic tests and molecular typing were performed on 48 carbapenemase-producing strains of K. pneumoniae and E. coli collected from rectal swabs of adult patients. Carbapenem-resistance was confirmed by PCR detection of resistance genes. All strains were analyzed by PCR-based replicon typing (PBRT) and multilocus sequence typing (MLST) was performed on a representative isolate of each PBRT profile. More than 50% of the strains were found to be multidrug-resistant, and the blaKPC gene was detected in all the isolates with the exception of an E. coli strain. A multireplicon status was observed, and the most prevalent profile was FIIK, FIB KQ (33%). MLST analysis revealed the prevalence of sequence type 512 (ST512). This study highlights the importance of screening patients upon their admission to limit the spread of CRE in hospitals.

scholarly journals Antimicrobial Susceptibility Profile of Several Bacteria Species Identified in the Peritoneal Exudate of Cows Affected by Parietal Fibrinous Peritonitis after Caesarean Section

2021 ◽  
Vol 8 (12) ◽  
pp. 295
Author(s):  
Salem Djebala ◽  
Julien Evrard ◽  
Fabien Gregoire ◽  
Calixte Bayrou ◽  
Linde Gille ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Caesarean Section ◽  
Antimicrobial Susceptibility ◽  
Multidrug Resistant ◽  
Drug Resistant ◽  
E Coli ◽  
Extensively Drug Resistant ◽  
Antimicrobial Susceptibility Profile ◽  
Disk Diffusion Assay ◽  
Diffusion Assay

The aim of this study was to identify the species and antimicrobial susceptibility of bacteria involved in parietal fibrinous peritonitis (PFP). We studied 156 peritoneal fluid samples from cows presenting PFP after caesarean section. Bacteria were cultured in selective media and their antimicrobial susceptibility was tested by disk diffusion assay. Bacteria were isolated in the majority (129/156; 83%) of samples. The majority (82/129; 63%) of positive samples contained one dominant species, while two or more species were cultured in 47/129 (36%) samples. Trueperella pyogenes (T. Pyogenes) (107 strains) was the most identified species, followed by Escherichia coli (E. coli) (38 strains), Proteus mirabilis (P. mirabilis) (6 strains), and Clostridium perfringens (C. perfringens) (6 strains). Several other species were sporadically identified. Antimicrobial susceptibility was tested in 59/185 strains, predominantly E. coli (38 strains) and P. mirabilis (6 strains). Antibiotic resistance, including resistance to molecules of critical importance, was commonly observed; strains were classified as weakly drug resistant (22/59; 37%), multidrug resistant (24/59; 41%), extensively drug resistant (12/59; 20%), or pan-drug resistant (1/59; 2%). In conclusion, extensive antibiotic resistance in the isolated germs might contribute to treatment failure. Ideally, antimicrobial therapy of PFP should be based upon bacterial culture and susceptibility testing.

scholarly journals Rapid decline of bacterial drug-resistance in an antibiotic-free environment through phenotypic reversion

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Anett Dunai ◽  
Réka Spohn ◽  
Zoltán Farkas ◽  
Viktória Lázár ◽  
Ádám Györkei ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Antibiotic Resistance ◽  
Practical Importance ◽  
Rapid Decline ◽  
Resistance Mutations ◽  
Resistance Level ◽  
Bacterial Populations ◽  
Bacterial Drug Resistance ◽  
Free Environment ◽  
Phenotypic Reversion

Antibiotic resistance typically induces a fitness cost that shapes the fate of antibiotic-resistant bacterial populations. However, the cost of resistance can be mitigated by compensatory mutations elsewhere in the genome, and therefore the loss of resistance may proceed too slowly to be of practical importance. We present our study on the efficacy and phenotypic impact of compensatory evolution in Escherichia coli strains carrying multiple resistance mutations. We have demonstrated that drug-resistance frequently declines within 480 generations during exposure to an antibiotic-free environment. The extent of resistance loss was found to be generally antibiotic-specific, driven by mutations that reduce both resistance level and fitness costs of antibiotic-resistance mutations. We conclude that phenotypic reversion to the antibiotic-sensitive state can be mediated by the acquisition of additional mutations, while maintaining the original resistance mutations. Our study indicates that restricting antimicrobial usage could be a useful policy, but for certain antibiotics only.

scholarly journals Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Alfonso Santos-Lopez ◽  
Christopher W Marshall ◽  
Michelle R Scribner ◽  
Daniel J Snyder ◽  
Vaughn S Cooper
Keyword(s):  
Antibiotic Resistance ◽  
Experimental Evolution ◽  
Drug Targets ◽  
Evolutionary Dynamics ◽  
Selective Sweeps ◽  
Resistance Level ◽  
Bacterial Populations ◽  
Collateral Sensitivity ◽  
Genetic Mechanisms ◽  
Evolution Of Resistance

Bacterial populations vary in their stress tolerance and population structure depending upon whether growth occurs in well-mixed or structured environments. We hypothesized that evolution in biofilms would generate greater genetic diversity than well-mixed environments and lead to different pathways of antibiotic resistance. We used experimental evolution and whole genome sequencing to test how the biofilm lifestyle influenced the rate, genetic mechanisms, and pleiotropic effects of resistance to ciprofloxacin in Acinetobacter baumannii populations. Both evolutionary dynamics and the identities of mutations differed between lifestyle. Planktonic populations experienced selective sweeps of mutations including the primary topoisomerase drug targets, whereas biofilm-adapted populations acquired mutations in regulators of efflux pumps. An overall trade-off between fitness and resistance level emerged, wherein biofilm-adapted clones were less resistant than planktonic but more fit in the absence of drug. However, biofilm populations developed collateral sensitivity to cephalosporins, demonstrating the clinical relevance of lifestyle on the evolution of resistance.

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