Hotspot Dosages of Most Rapid Antibiotic Resistance Evolution

We treated Escherichia coli with the antibiotic erythromycin from zero to high dosages to determine how the evolutionary dynamics of antibiotic resistant phenotypes and genotypes depend on dose. The most rapid increase in resistance was observed just below erythromycin’s minimal inhibitory concentration (MIC) and genotype-phenotype correlations determined from whole genome sequencing revealed the molecular basis of this: simultaneous selection for copy number variation in 3 resistance mechanisms which shared an ‘inverted-U’ pattern of dose-dependent selection with several insertion sequences and an integron. Many genes did not conform to this pattern, however, because of changes in selection as dose increased: media adaptation at zero-to-low dosages gave way to drug target (ribosomal RNA operon) amplification at mid dosages whereas prophage-mediated drug efflux dominated at higher dosages where population densities were lowest. All dosages saw E. coli amplify the efflux operons acr and emrE at rates that correlated strongly with changes in population density that exhibited an inverted-U geometry too. However, we show by example that inverted-U geometries are not a universal feature of dose-resistance relationships.

Download Full-text

A trimethoprim derivative impedes antibiotic resistance evolution

Nature Communications ◽

10.1038/s41467-021-23191-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Madhu Sudan Manna ◽

Yusuf Talha Tamer ◽

Ilona Gaszek ◽

Nicole Poulides ◽

Ayesha Ahmed ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistant Bacteria ◽

Gene Encoding ◽

Antibiotic Resistant ◽

E Coli ◽

Resistance Evolution ◽

Evolutionary Trajectories ◽

Evolution Of Resistance

AbstractThe antibiotic trimethoprim (TMP) is used to treat a variety of Escherichia coli infections, but its efficacy is limited by the rapid emergence of TMP-resistant bacteria. Previous laboratory evolution experiments have identified resistance-conferring mutations in the gene encoding the TMP target, bacterial dihydrofolate reductase (DHFR), in particular mutation L28R. Here, we show that 4’-desmethyltrimethoprim (4’-DTMP) inhibits both DHFR and its L28R variant, and selects against the emergence of TMP-resistant bacteria that carry the L28R mutation in laboratory experiments. Furthermore, antibiotic-sensitive E. coli populations acquire antibiotic resistance at a substantially slower rate when grown in the presence of 4’-DTMP than in the presence of TMP. We find that 4’-DTMP impedes evolution of resistance by selecting against resistant genotypes with the L28R mutation and diverting genetic trajectories to other resistance-conferring DHFR mutations with catalytic deficiencies. Our results demonstrate how a detailed characterization of resistance-conferring mutations in a target enzyme can help identify potential drugs against antibiotic-resistant bacteria, which may ultimately increase long-term efficacy of antimicrobial therapies by modulating evolutionary trajectories that lead to resistance.

Download Full-text

Combining antibiotics with antivirulence compounds can have synergistic effects and reverse selection for antibiotic resistance in Pseudomonas aeruginosa

10.1101/861799 ◽

2019 ◽

Author(s):

Chiara Rezzoagli ◽

Martina Archetti ◽

Ingrid Mignot ◽

Michael Baumgartner ◽

Rolf Kümmerli

Keyword(s):

Pseudomonas Aeruginosa ◽

Antibiotic Resistance ◽

Synergistic Effects ◽

Rapid Evolution ◽

Resistance Mechanisms ◽

Interaction Patterns ◽

Systematic Analysis ◽

Antibiotic Resistant ◽

Drug Concentrations ◽

Selection For

AbstractAntibiotics are losing efficacy due to the rapid evolution and spread of resistance. Treatments targeting bacterial virulence factors have been considered as alternatives because they target virulence instead of pathogen viability, and should therefore exert weaker selection for resistance than conventional antibiotics. However, antivirulence treatments rarely clear infections, which compromises their clinical applications. Here, we explore the potential of combining antivirulence drugs with antibiotics against the opportunistic human pathogen Pseudomonas aeruginosa. We combined two antivirulence compounds (gallium, a siderophore-quencher, and furanone C-30, a quorum sensing-inhibitor) together with four clinically relevant antibiotics (ciprofloxacin, colistin, meropenem, tobramycin) in 9×9 drug concentration matrices. We found that drug-interaction patterns were concentration dependent, with promising levels of synergies occurring at intermediate drug concentrations for certain drug pairs. We then tested whether antivirulence compounds are potent adjuvants, especially when treating antibiotic resistant clones. We found that the addition of antivirulence compounds to antibiotics could restore growth inhibition for most antibiotic resistant clones, and even abrogate or reverse selection for resistance in five drug combination cases. Molecular analyses suggest that selection against resistant clones occurs when resistance mechanisms involve restoration of protein synthesis, but not when efflux pumps are upregulated. Altogether, our work provides a first systematic analysis of antivirulence-antibiotic combinatorial treatments and suggests that such combinations have a high potential to be both effective in treating infections and in limiting the spread of antibiotic resistance.

Download Full-text

Different evolutionary trends form the twilight zone of the bacterial pan-genome

10.1101/2021.02.15.431222 ◽

2021 ◽

Author(s):

Gal Horesh ◽

Alyce Taylor-Brown ◽

Stephanie McGimpsey ◽

Florent Lassalle ◽

Jukka Corander ◽

...

Keyword(s):

Population Structure ◽

Evolutionary Dynamics ◽

Bacterial Species ◽

Resistance Mechanisms ◽

E Coli ◽

Pan Genome ◽

Metabolic Versatility ◽

Species Population ◽

Genome Analyses ◽

Uneven Sampling

AbstractThe pan-genome is defined as the combined set of all genes in the gene pool of a species. Pan-genome analyses have been very useful in helping to understand different evolutionary dynamics of bacterial species: an open pan-genome often indicates a free-living lifestyle with metabolic versatility, while closed pan-genomes are linked to host-restricted, ecologically specialised bacteria. A detailed understanding of the species pan-genome has also been instrumental in tracking the phylodynamics of emerging drug resistance mechanisms and drug resistant pathogens. However, current approaches to analyse a species’ pan-genome do not take the species population structure into account, nor do they account for the uneven sampling of different lineages, as is commonplace due to over-sampling of clinically relevant representatives. Here we present the application of a population structure-aware approach for classifying genes in a pan-genome based on within-species distribution. We demonstrate our approach on a collection of 7,500 E. coli genomes, one of the most-studied bacterial species used as a model for an open pan-genome. We reveal clearly distinct groups of genes, clustered by different underlying evolutionary dynamics, and provide a more biologically informed and accurate description of the species’ pan-genome.

Download Full-text

Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities

10.1101/323634 ◽

2018 ◽

Cited By ~ 1

Author(s):

Aimee K. Murray ◽

Lihong Zhang ◽

Xiaole Yin ◽

Tong Zhang ◽

Angus Buckling ◽

...

Keyword(s):

Antibiotic Resistance ◽

Microbial Communities ◽

Single Species ◽

Dependent Manner ◽

Opportunistic Pathogens ◽

Antibiotic Resistant ◽

Naturally Occurring ◽

Selection For ◽

Antibiotic Degradation ◽

Dose Dependent

ABSTRACTRecent research has demonstrated selection for antibiotic resistance occurs at very low antibiotic concentrations in single species experiments, but the relevance of these findings when species are embedded in complex microbial communities is unclear. We show the strength of selection for naturally occurring resistance alleles in a complex community remains constant from low sub-inhibitory to above clinically relevant concentrations. Selection increases with antibiotic concentration before reaching a plateau where selection remains constant over a two order magnitude concentration range. This is likely to be due to cross-protection of the susceptible bacteria in the community following rapid extracellular antibiotic degradation by the resistant population, shown experimentally through a combination of chemical quantification and bacterial growth experiments. Metagenome and 16S rRNA analyses on sewage-derived bacterial communities evolved under cefotaxime exposure show preferential enrichment forblaCTX-Mgenes over all other beta-lactamase genes, as well as positive selection and co-selection for antibiotic resistant, opportunistic pathogens. These findings have far reaching implications for our understanding of the evolution of antibiotic resistance, by challenging the long-standing assumption that selection occurs in a dose-dependent manner.

Download Full-text

Combatting antibiotic resistant septicemic E. coli

10.26226/morressier.5f3641d698fd876311f7b3a8 ◽

2020 ◽

Author(s):

Eliora Ron

Keyword(s):

Antibiotic Resistant ◽

E Coli

Download Full-text

Relationship of antibiotic resistance to results of treatment in sepsis patients in Hue Central Hospital 2017 – 2018

Journal of Medicine and Pharmacy ◽

10.34071/jmp.2019.5.7 ◽

2019 ◽

pp. 48-54

Author(s):

Duy Binh Nguyen ◽

Trung Tien Phan ◽

Trong Hanh Hoang ◽

Van Tuan Mai ◽

Xuan Chuong Tran

Keyword(s):

Antibiotic Resistance ◽

Bacterial Infection ◽

Resistant Bacteria ◽

Central Hospital ◽

International Consensus ◽

Antibiotic Resistant ◽

E Coli ◽

Results Of Treatment ◽

Amoxicillin Clavulanic Acid ◽

Relationship Of

Sepsis is a serious bacterial infection. The main treatment is using antibiotics. However, the rate of antibiotic resistance is very high and this resistance is related to the outcome of treatment. Objectives: To evaluate the situation of antibiotic resistance of some isolated bacteria in sepsis patients treated at Hue Central Hospital; to evaluate the relationship of antibiotic resistance to the treatment results in patients with sepsis. Subjects and methods: prospective study of 60 sepsis patients diagnosed according to the criteria of the 3rd International Consensus-Sepsis 3 and its susceptibility patterns from April 2017 to August 2018. Results and Conclusions: The current agents of sepsis are mainly S. suis, Burkhoderiae spp. and E. coli. E. coli is resistant to cephalosporins 3rd, 4th generation and quinolone group is over 75%; resistance to imipenem 11.1%; the ESBL rate is 60%. S. suis resistant to ampicilline 11.1%; no resistance has been recorded to ceftriaxone and vancomycine. Resistance of Burkholderiae spp. to cefepime and amoxicillin/clavulanic acid was 42.9% and 55.6%, resistant to imipenem and meropenem is 20%, resistance to ceftazidime was not recorded. The deaths were mostly dued to E. coli and K. pneumoniae. The mortality for patients infected with antibiotic-resistant bacteria are higher than for sensitive groups. Key words: Sepsis, bacterial infection, antibiotics

Download Full-text

Multiresistant Bacteria Isolated from Intestinal Faeces of Farm Animals in Austria

Antibiotics ◽

10.3390/antibiotics10040466 ◽

2021 ◽

Vol 10 (4) ◽

pp. 466

Author(s):

Herbert Galler ◽

Josefa Luxner ◽

Christian Petternel ◽

Franz F. Reinthaler ◽

Juliana Habib ◽

...

Keyword(s):

Meat Products ◽

Animal Husbandry ◽

Multidrug Resistant ◽

Farm Animals ◽

Resistant Bacteria ◽

Antibiotic Resistant Bacteria ◽

Antibiotic Resistant ◽

E Coli ◽

Multiresistant Bacteria ◽

Vancomycin Resistant

In recent years, antibiotic-resistant bacteria with an impact on human health, such as extended spectrum β-lactamase (ESBL)-containing Enterobacteriaceae, methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE), have become more common in food. This is due to the use of antibiotics in animal husbandry, which leads to the promotion of antibiotic resistance and thus also makes food a source of such resistant bacteria. Most studies dealing with this issue usually focus on the animals or processed food products to examine the antibiotic resistant bacteria. This study investigated the intestine as another main habitat besides the skin for multiresistant bacteria. For this purpose, faeces samples were taken directly from the intestines of swine (n = 71) and broiler (n = 100) during the slaughter process and analysed. All samples were from animals fed in Austria and slaughtered in Austrian slaughterhouses for food production. The samples were examined for the presence of ESBL-producing Enterobacteriaceae, MRSA, MRCoNS and VRE. The resistance genes of the isolated bacteria were detected and sequenced by PCR. Phenotypic ESBL-producing Escherichia coli could be isolated in 10% of broiler casings (10 out of 100) and 43.6% of swine casings (31 out of 71). In line with previous studies, the results of this study showed that CTX-M-1 was the dominant ESBL produced by E. coli from swine (n = 25, 83.3%) and SHV-12 from broilers (n = 13, 81.3%). Overall, the frequency of positive samples with multidrug-resistant bacteria was lower than in most comparable studies focusing on meat products.

Download Full-text

Prevalence and Characterization of Extended-Spectrum β-Lactamase-Producing Antibiotic-Resistant Escherichia coli and Klebsiella pneumoniae in Ready-to-Eat Street Foods

Antibiotics ◽

10.3390/antibiotics10070850 ◽

2021 ◽

Vol 10 (7) ◽

pp. 850

Author(s):

Shobha Giri ◽

Vaishnavi Kudva ◽

Kalidas Shetty ◽

Veena Shetty

Keyword(s):

Escherichia Coli ◽

Food Safety ◽

Klebsiella Pneumoniae ◽

Rural Areas ◽

Significant Risk ◽

Microbiological Quality ◽

Resistant Bacteria ◽

Antibiotic Resistant ◽

E Coli ◽

Extended Spectrum

As the global urban populations increase with rapid migration from rural areas, ready-to-eat (RTE) street foods are posing food safety challenges where street foods are prepared with less structured food safety guidelines in small and roadside outlets. The increased presence of extended-spectrum-β-lactamase (ESBL) producing bacteria in street foods is a significant risk for human health because of its epidemiological significance. Escherichia coli and Klebsiella pneumoniae have become important and dangerous foodborne pathogens globally for their relevance to antibiotic resistance. The present study was undertaken to evaluate the potential burden of antibiotic-resistant E. coli and K. pneumoniae contaminating RTE street foods and to assess the microbiological quality of foods in a typical emerging and growing urban suburb of India where RTE street foods are rapidly establishing with public health implications. A total of 100 RTE food samples were collected of which, 22.88% were E. coli and 27.12% K. pneumoniae. The prevalence of ESBL-producing E. coli and K. pneumoniae was 25.42%, isolated mostly from chutneys, salads, paani puri, and chicken. Antimicrobial resistance was observed towards cefepime (72.9%), imipenem (55.9%), cefotaxime (52.5%), and meropenem (16.9%) with 86.44% of the isolates with MAR index above 0.22. Among β-lactamase encoding genes, blaTEM (40.68%) was the most prevalent followed by blaCTX (32.20%) and blaSHV (10.17%). blaNDM gene was detected in 20.34% of the isolates. This study indicated that contaminated RTE street foods present health risks to consumers and there is a high potential of transferring multi-drug-resistant bacteria from foods to humans and from person to person as pathogens or as commensal residents of the human gut leading to challenges for subsequent therapeutic treatments.

Download Full-text

1443. Activity of Ceftazidime-Avibactam against Carbapemenase-negative Carbapenem-resistant Enterobacterales (CRE) Isolates from US Hospitals

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.1624 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S725-S725

Author(s):

Mariana Castanheira ◽

Timothy B Doyle ◽

Cory Hubler ◽

Rodrigo E Mendes ◽

Helio S Sader

Keyword(s):

Resistance Mechanisms ◽

Chemical Diversity ◽

Services Research ◽

New Agents ◽

E Coli ◽

Department Of Health ◽

Carbapenem Resistant ◽

Center Research ◽

Research Grant

Abstract Background Most CRE isolates in US hospitals produce KPC enzymes, but some do not carry carbapenemases. We investigated the prevalence, resistance mechanisms and activity of ceftazidime-avibactam and comparator agents against CRE that did not carry carbapenemase genes from US hospitals. Additionally, meropenem-resistant isolates were tested for meropenem-vaborbactam. Methods A total of 28,904 Enterobacterales isolates were collected in 70 US hospitals during 2016-2018, and susceptibility tested by reference broth microdilution. Meropenem-vaborbactam was tested using lyophilized panels following the manufacturer’s instructions. CRE isolates were submitted to whole genome sequencing for the screening of b-lactamase genes, multilocus sequence typing, changes in outer membrane protein (OMP) genes and AmpC expression levels. Results A total of 304 (1.1%) CREs were observed in the study period and 45 (14.8%) isolates did not carry carbapenemases. These isolates were mainly Klebsiella aerogenes, Enterobacter cloacae and Klebsiella pneumoniae (11, 11 and 10 isolates, respectively), but also included 5 other species. Acquired b-lactamase genes were detected among 17 isolates and blaCTX-M-15 was the most common (13 isolates). All K. aerogenes and 10 E. cloacae did not carry acquired b-lactamase genes. Ceftazidime-avibactam (100% susceptible) inhibited all isolates at the current breakpoint, followed by tigecycline and amikacin (> 80% susceptible). Other comparators were not active against non-carbapenemase-producing CRE. Nine of 35 meropenem-resistant isolates displayed meropenem-vaborbactam MIC values of ≥ 8 mg/L (nonsusceptible). Further analysis showed that 23 isolates had disruption of OmpC/OmpK36, 4 had disrupted OmpF/OmpK35 and 13 had both OMP genes disrupted. Additionally, 7 isolates had elevated AmpC expression among 17 isolates tested. Among 7 E. coli, 4 were ST131 and only 2 of 10 K. pneumoniae were clonal complex 11. Conclusion Therapy options for treatment of infections caused by CRE were very limited until recent approval of new agents with activity against these isolates. Ceftazidime-avibactam demonstrated full in vitro activity against all carbapenemase-negative CRE carrying multiple resistance mechanisms. Disclosures Mariana Castanheira, PhD, 1928 Diagnostics (Research Grant or Support)A. Menarini Industrie Farmaceutiche Riunite S.R.L. (Research Grant or Support)Allergan (Research Grant or Support)Allergan (Research Grant or Support)Amplyx Pharmaceuticals (Research Grant or Support)Cidara Therapeutics (Research Grant or Support)Cidara Therapeutics (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Fox Chase Chemical Diversity Center (Research Grant or Support)GlaxoSmithKline (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Merck (Research Grant or Support)Merck (Research Grant or Support)Merck & Co, Inc. (Research Grant or Support)Merck & Co, Inc. (Research Grant or Support)Paratek Pharma, LLC (Research Grant or Support)Pfizer (Research Grant or Support)Qpex Biopharma (Research Grant or Support) Timothy B. Doyle, Allergan (Research Grant or Support)Allergan (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Pfizer (Research Grant or Support)Qpex Biopharma (Research Grant or Support) Cory Hubler, Allergan (Research Grant or Support) Rodrigo E. Mendes, PhD, A. Menarini Industrie Farmaceutiche Riunite S.R.L. (Research Grant or Support)Allergan (Research Grant or Support)Allergan (Research Grant or Support)Basilea Pharmaceutica International, Ltd (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Department of Health and Human Services (Research Grant or Support)GlaxoSmithKline (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Merck (Research Grant or Support)Merck (Research Grant or Support)Pfizer (Research Grant or Support) Helio S. Sader, MD, PhD, A. Menarini Industrie Farmaceutiche Riunite S.R.L. (Research Grant or Support)Allergan (Research Grant or Support)Allergan (Research Grant or Support)Allergan (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Melinta (Research Grant or Support)Merck (Research Grant or Support)Merck (Research Grant or Support)Paratek Pharma, LLC (Research Grant or Support)Pfizer (Research Grant or Support)

Download Full-text

Antimicrobial activity of Syzygium aromaticum L. essential oil on extended-spectrum beta-lactamases-producing Escherichia coli

Bulletin of the National Research Centre ◽

10.1186/s42269-020-00458-x ◽

2020 ◽

Vol 44 (1) ◽

Author(s):

E. L. Mejía-Argueta ◽

J. G. Santillán-Benítez ◽

M. M. Canales-Martinez ◽

A. Mendoza-Medellín

Keyword(s):

Escherichia Coli ◽

Essential Oil ◽

Genetic Material ◽

Gastrointestinal Diseases ◽

Syzygium Aromaticum ◽

Antibiotic Resistant ◽

Plant Essential Oils ◽

E Coli ◽

Extended Spectrum ◽

Tract Infections

Abstract Background To test the antimicrobial potential of clove essential oil that has been less investigated on antimicrobial-resistant organisms (extended-spectrum β-lactamase-ESBL-producing Escherichia coli), we collected 135 ESBL-producing Escherichia coli strains given that E. coli is the major organism increasingly isolated as a cause of complicated urinary and gastrointestinal tract infections, which remains an important cause of therapy failure with antibiotics for the medical sector. Then, in this study, we evaluated the relationship between the antibacterial potential activity of Syzygium aromaticum essential oil (EOSA) and the expression of antibiotic-resistant genes (SHV-2, TEM-20) in plasmidic DNA on ESBL-producing E. coli using RT-PCR technique. Results EOSA was obtained by hydrodistillation. Using Kirby-Baüer method, we found that EOSA presented a smaller media (mean = 15.59 mm) in comparison with chloramphenicol (mean = 17.73 mm). Thus, there were significant differences (p < 0.0001). Furthermore, EOSA had an antibacterial activity, particularly on ECB132 (MIC: 10.0 mg/mL and MBC: 80.0 mg/mL), and a bacteriostatic effect by bactericidal kinetic. We found that the expression of antibiotic-resistant gene blaTEM-20 was 23.52% (4/17 strains) and no expression of blaSHV-2. EOSA presented such as majority compounds (eugenol, caryophyllene) using the GC–MS technique. Conclusions Plant essential oils and their active ingredients have potentially high bioactivity against a different target (membranes, cytoplasm, genetic material). In this research, EOSA might become an important adjuvant against urinary and gastrointestinal diseases caused by ESBL-producing E. coli.

Download Full-text