Insights into Emergence of Antibiotic Resistance in Acid-Adapted Enterohaemorrhagic Escherichia coli

Fitness trade-offs of multidrug efflux pumps in Escherichia coli K-12 in acid or base, and with aromatic phytochemicals

Multidrug efflux pumps are the frontline defense mechanisms of Gram-negative bacteria, yet little is known of their relative fitness trade-offs under gut conditions such as low pH and the presence of antimicrobial food molecules. Low pH contributes to the proton-motive force (PMF) that drives most efflux pumps. We show how the PMF-dependent pumps AcrAB-TolC, MdtEF-TolC, and EmrAB-TolC undergo selection at low pH and in the presence of membrane-permeant phytochemicals. Competition assays were performed by flow cytometry of co-cultured Escherichia coli K-12 strains possessing or lacking a given pump complex. All three pumps showed negative selection under conditions that deplete PMF (pH 5.5 with carbonyl cyanide 3-chlorophenylhydrazone or at pH 8.0). At pH 5.5, selection against AcrAB-TolC was increased by aromatic acids, alcohols, and related phytochemicals such as methyl salicylate. The degree of fitness cost for AcrA was correlated with the phytochemical's lipophilicity (logP). Methyl salicylate and salicylamide selected strongly against AcrA, without genetic induction of drug resistance regulons. MdtEF-TolC and EmrAB-TolC each had a fitness cost at pH 5.5, but salicylate or benzoate made the fitness contribution positive. Pump fitness effects were not explained by gene expression (measured by digital PCR). Between pH 5.5 and 8.0, acrA and emrA were upregulated in the log phase, whereas mdtE expression was upregulated in the transition-to-stationary phase and at pH 5.5 in the log phase. Methyl salicylate did not affect pump gene expression. Our results suggest that lipophilic non-acidic molecules select against a major efflux pump without inducing antibiotic resistance regulons.IMPORTANCEFor drugs that are administered orally, we need to understand how ingested phytochemicals modulate drug resistance in our gut microbiome. Bacteria maintain low-level resistance by proton-motive force (PMF)-driven pumps that efflux many different antibiotics and cell waste products. These pumps play a key role in bacterial defense by conferring resistance to antimicrobial agents at first exposure while providing time for a pathogen to evolve resistance to higher levels of the antibiotic exposed. Nevertheless, efflux pumps confer energetic costs due to gene expression and pump energy expense. The bacterial PMF includes the transmembrane pH difference (ΔpH), which may be depleted by permeant acids and membrane disruptors. Understanding the fitness costs of efflux pumps may enable us to develop resistance breakers, that is, molecules that work together with antibiotics to potentiate their effect. Non-acidic aromatic molecules have the advantage that they avoid the Mar-dependent induction of regulons conferring other forms of drug resistance. We show that different pumps have distinct selection criteria, and we identified non-acidic aromatic molecules as promising candidates for drug resistance breakers.

Biocide Tolerance and Impact of Sanitizer Concentrations on the Antibiotic Resistance of Bacteria Originating from Cheese

In this study, we determined and identified the bacterial diversity of different types of artisanal and industrially produced cheese. The antibiotic (erythromycin, chloramphenicol, kanamycin, ampicillin, clindamycin, streptomycin, tetracycline, and gentamicin) and biocide (peracetic acid, sodium hypochlorite, and benzalkonium chloride) resistance of clinically relevant bacteria was determined as follows: Staphylococcus aureus, Macrococcus caseolyticus, Bacillus sp., Kocuria varians, Escherichia coli, Enterococcus faecalis, Citrobacter freundii, Citrobacter pasteurii, Klebsiella oxytoca, Klebsiella michiganensis, Enterobacter sp., Enterobacter cloacae, Enterobacter sichuanensis, Raoultella ornithinolytica, Shigella flexneri, and Salmonella enterica. Also, the effect of the sub-inhibitory concentration of three biocides on antibiotic resistance was determined. The microbiota of evaluated dairy products comprise diverse and heterogeneous groups of bacteria with respect to antibiotic and disinfectant tolerance. The results indicated that resistance was common in the case of ampicillin, chloramphenicol, erythromycin, and streptomycin. Bacillus sp. SCSSZT2/3, Enterococcus faecalis SRGT/1, E. coli SAT/1, Raoultella ornithinolytica MTT/5, and S. aureus SIJ/2 showed resistance to most antibiotics. The tested bacteria showed sensitivity to peracetic acid and a different level of tolerance to benzalkonium chloride and sodium hypochlorite. The inhibition zone diameter of antibiotics against Enterococcus faecalis SZT/2, S. aureus JS11, E. coli CSKO2, and Kocuria varians GRT/10 was affected only by the sub-inhibitory concentration of peracetic acid.

Residual chlorine persistently changes antibiotic resistance gene composition and increases the risk of antibiotic resistance in sewer systems

During the COVID-19 pandemic, excessive amounts of disinfectants and their transformation products entered sewer systems worldwide, which was an extremely rare occurrence before. The stress of residual chlorine and disinfection by-products is not only likely to promote the spread of antibiotic resistance genes (ARGs), but also leads to the enrichment of chlorine-resistant bacteria that may also be resistant to antibiotics. Therefore, the potential impact of such discharge on ARG composition should be studied and the health risks should be assessed. Thus, this study combined high-throughput 16S rRNA gene amplicon sequencing and metagenomic analysis with long-term batch tests that involved two stages of stress and recovery to comprehensively evaluate the impact of residual chlorine on the microbial community and ARG compositions in sewer systems. The tests demonstrated that the disturbance of the microbial community structure by residual chlorine was reversible, but the change in ARG composition was persistent. This study found that vertical propagation and horizontal gene transfer jointly drove ARG composition succession in the biofilm, while the driving force was mainly horizontal gene transfer in the sediment. In this process, the biocide resistance gene (BRG) subtype chtR played an important role in promoting co-selection with ARGs through plasmids and integrative and conjugative elements. Moreover, it was further shown that the addition of sodium hypochlorite increased the risk of ARGs to human health, even after discontinuation of dosing, signifying that the impact was persistent. In general, this study strengthens the co-selection theory of ARGs and BRGs, and calls for improved disinfection strategies and more environmentally friendly disinfectants.

Cumulative Antibiogram: A Rapid Method to Hinder Transmission of Resistant Bacteria to Oral Cavity of Newborn Babies

BACKGROUND

A rapid bacterial diagnostic is needed more and more in the treatment of patients, because of the emergence of antibiotic resistance. The cumulative antibiogram, an annual report that monitors antimicrobial resistance trends in health care facilities, may provide a profile of empirical therapy useful in diverse emergency situations, such as transmission of resistant bacteria to oral cavity of newborn babies. We aimed to draw a profile of antibiotic resistance encountered.

METHODS

We assessed the antibiotic resistance (ABR) profile in childbearing women and newborn babies in Ploiesti Obstetrics and Gynecology Hospital by the disk diffusion method characterizing the multidrug-resistant organisms after isolation and identification by phenotypic tests. Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-E), Carbapenem-resistant Enterobacterales (CRE), vancomycin-resistant Enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin resistant Group B Streptococcus (VR-GBS) were detected.

RESULTS

The prevalence of antibiotic resistance was 11.32% (53/468), while the prevalence of the ESBL-E, MRSA, VRE and VR-GBS strains was 8.34% (39/468). Within the bacteria isolated from fifty-three childbearing women, the prevalence of ESBL-E, MRSA, VRE and VR-GBS was 22.64% (12/53), 32.08% (17/53), 11.32% (6/53) and 7.55% (4/53). In the whole studied group, the prevalence was 2.56% (12/468), 3.63% (17/468), 1.28% (6/468) and 0.86% (4/468). Resistant bacteria were detected at birth in the oral cavity of the newborn babies in all cases. Maternal and neonatal isolates shared similar characteristics.

CONCLUSIONS

Cumulative antibiogram is useful in case of empiric treatment needed in diverse emergencies, such as transmission of resistant bacteria to oral cavity of newborn babies.

Isolation, characterization, and antimicrobial susceptibility pattern of Escherichia coli O157:H7 from foods of bovine origin in Mekelle, Tigray, Ethiopia

Escherichia coli O157:H7 is an emerging and major zoonotic foodborne pathogen. It has an increasing concern about the spread of antimicrobial-resistant strains. This study aimed to isolate and characterize Shiga toxin-producing E. coli O157:H7 from raw milk, yogurt, and meat of bovine origin and determine their antimicrobial susceptibility pattern. A cross-sectional study was conducted from December 2014 to June 2015, and a total of 284 milk and meat samples were collected from different sources in Mekelle. The collected samples were analyzed for the presence of E. coli and Shiga toxin-producing E. coli O157:H7 and the determination of their antimicrobial susceptibility pattern following the standard bacteriological and molecular techniques and procedures and antimicrobial sensitivity test. Out of the total 284 samples, 70 (24.6%) were bacteriologically positive for E. coli and 14.3% were found to be Shiga toxin-producing E. coli O157:H7. Of note, 100% of E. coli isolates carried the pal gene and 41.7% eaeA gene (EHEC). Of these EHEC isolates, 40% and 60% were positive for stx1 and stx2, respectively. E. coli isolates showed the highest level of susceptibility to gentamycin (91.7%) but the highest level of resistance to amoxicillin (95.8%). Of the tested isolates, 18 (75%) of E. coli showed multidrug-resistant. This study revealed the occurrence of Shiga toxin-producing E. coli O157:H7 in foods of bovine origin in the study area. In conclusion, a nationwide phenotypic and molecular characterization, in-depth typing, and drug-resistant gene identification of E. coli O157:H7 should be undertaken.

Bacterial Stress Responses as Potential Targets in Overcoming Antibiotic Resistance

Bacteria can be adapted to adverse and detrimental conditions that induce general and specific responses to DNA damage as well as acid, heat, cold, starvation, oxidative, envelope, and osmotic stresses. The stress-triggered regulatory systems are involved in bacterial survival processes, such as adaptation, physiological changes, virulence potential, and antibiotic resistance. Antibiotic susceptibility to several antibiotics is reduced due to the activation of stress responses in cellular physiology by the stimulation of resistance mechanisms, the promotion of a resistant lifestyle (biofilm or persistence), and/or the induction of resistance mutations. Hence, the activation of bacterial stress responses poses a serious threat to the efficacy and clinical success of antibiotic therapy. Bacterial stress responses can be potential targets for therapeutic alternatives to antibiotics. An understanding of the regulation of stress response in association with antibiotic resistance provides useful information for the discovery of novel antimicrobial adjuvants and the development of effective therapeutic strategies to control antibiotic resistance in bacteria. Therefore, this review discusses bacterial stress responses linked to antibiotic resistance in Gram-negative bacteria and also provides information on novel therapies targeting bacterial stress responses that have been identified as potential candidates for the effective control of Gram-negative antibiotic-resistant bacteria.

Plasmonic Au@Ag@mSiO2 Nanorattles for In Situ Imaging of Bacterial Metabolism by Surface-Enhanced Raman Scattering Spectroscopy

It is well known that microbial populations and their interactions are largely influenced by their secreted metabolites. Noninvasive and spatiotemporal monitoring and imaging of such extracellular metabolic byproducts can be correlated with biological phenotypes of interest and provide new insights into the structure and development of microbial communities. Herein, we report a surface-enhanced Raman scattering (SERS) hybrid substrate consisting of plasmonic Au@Ag@mSiO₂ nanorattles for optophysiological monitoring of extracellular metabolism in microbial populations. A key element of the SERS substrate is the mesoporous silica shell encapsulating single plasmonic nanoparticles, which furnishes colloidal stability and molecular sieving capabilities to the engineered nanostructures, thereby realizing robust, sensitive, and reliable measurements. The reported SERS-based approach may be used as a powerful tool for deciphering the role of extracellular metabolites and physicochemical factors in microbial community dynamics and interactions.