Mechanisms of acid resistance in enterohemorrhagic Escherichia coli

Increased antimicrobial resistance of acid-adapted pathogenic Escherichia coli, and transcriptomic analysis of polymyxin-resistant strain

This study investigated the acid adaptation and antimicrobial resistance of seven pathogenic Escherichia coli strains and one commensal strain under nutrient-rich acidic conditions. After acid adaptation, three pathogenic E. coli survived during 100 h incubation in tryptic soy broth at pH 3.25. Acid-adapted (AA) strains showed increased resistance to antimicrobials including ampicillin, ciprofloxacin and especially polymyxins (colistin and polymyxin B), the last resort antimicrobial for multidrug-resistant Gram-negative bacteria. Enterotoxigenic E. coli strain (NCCP 13717) showed significantly increased resistance to acids and polymyxins. Transcriptome analysis of the AA NCCP 13717 revealed upregulation of genes related to the acid fitness island and the arn operon, which reduces lipopolysaccharide binding affinity at the polymyxin site of action. Genes such as eptA, tolC, and ompCF were also upregulated to alter the structure of the cell membrane, reducing the outer membrane permeability compared to the control, which is likely to be another mechanism for polymyxin resistance. This study highlights the emergence of antimicrobial resistance in AA pathogenic E. coli strains, particularly polymyxin resistance, and the mechanisms behind the increased antimicrobial resistance, providing important insights for the development of risk management strategies to effectively control the antimicrobial resistant foodborne pathogens.

Molecular mechanism of proteolytic cleavage-dependent activation of CadC-mediated response to acid in E. coli

Colonizing in the gastrointestinal tract, Escherichia coli confronts diverse acidic challenges and evolves intricate acid resistance strategies for its survival. The lysine-mediated decarboxylation (Cad) system, featuring lysine decarboxylase CadA, lysine/cadaverine antiporter CadB, and transcriptional activator CadC, plays a crucial role in E. coli's adaptation to moderate acidic stress. While the activation of the one-component system CadC and subsequent upregulation of cadBA operon in response to acid and lysine presence have been proposed, the molecular mechanisms governing the transition of CadC from an inactive to an active state remain elusive. Under neutral conditions, CadC is inhibited by forming a complex with lysine-specific permease LysP, stabilized in this inactive state by a disulfide bond. Our study unveils that, in an acidic environment, the disulfide bond in CadC is reduced by the disulfide bond isomerase DsbC, exposing R184 to periplasmic proteases, namely DegQ and DegP. Cleavage at R184 by DegQ and DegP generates an active N-terminal DNA-binding domain of CadC, which binds to the cadBA promoter, resulting in the upregulated transcription of the cadA and cadB genes. Upon activation, CadA decarboxylates lysine, producing cadaverine, subsequently transported extracellularly by CadB. We propose that accumulating cadaverine gradually binds to the CadC pH-sensing domain, preventing cleavage and activation of CadC as a feedback mechanism. The identification of DegP, DegQ, and DsbC completes a comprehensive roadmap for the activation and regulation of the Cad system in response to moderate acidic stress in E. coli.

Comparative experiment to select water quality parameters for modelling the survival of Escherichia coli in lakes

Numerical health risk assessment models have been developed to describe faecal contamination of water using Escherichia coli as an indicator bacterium. Although many previously established numerical models for E. coli in aquatic environments have only considered the effects of one or two water quality parameters such as temperature and sunlight, it is difficult to simulate E. coli survival with only one or two parameters because the aquatic environment is a complex system. This study conducted a series of comparative experiments to select water quality parameters that should be preferentially considered in a numerical model for E. coli survival in lakes. The parameters considered were temperature, pH, dissolved oxygen (DO), total dissolved solids (TDS), suspended solids (SS), coexisting microbes, and light intensity. In the laboratory experiments, the survival of E. coli was observed by controlling two of these seven parameters, and the effects of these parameters on the rate of E. coli population change were statistically compared. Consequently, light intensity affected the survival of E. coli most significantly, followed by the presence of coexisting microbes, temperature, pH, and TDS. However, DO and SS had smaller effects on survival than other parameters. High-impact interactions on E. coli survival were observed between temperature and TDS and temperature and coexisting microbes. These results suggest that existing numerical models for simulating E. coli survival in lakes should be modified to consider the independent and interactive effects of multiple parameters such as sunlight, coexisting microbes, temperature, pH, and TDS.

Resistance or tolerance? Highlighting the need for precise terminology in the field of disinfection

The terms 'resistance' and 'tolerance' are well defined in the context of antibiotic research. However, in the field of disinfection, these terms are often used synonymously, which creates ambiguity and can lead to misunderstandings and misconceptions. In addition, this inconsistency in terminology makes it difficult to assess the risk of a disinfectant resistance. This general review aims to discuss existing definitions of the terms 'adaptation', 'susceptibility', 'tolerance', 'persistence' and 'resistance' in the light of disinfectants. The most ambiguity is found between tolerance and resistance. Whereas the former describes the not necessarily heritable survival of transient exposure to usually lethal concentrations, resistance is the strictly heritable ability to survive otherwise lethal concentrations of an antimicrobial agent, regardless of exposure time. A simple transfer of experience from antibiotic research is not recommended when assessing the risk of resistance to disinfectants, as there are important differences between antibiotics and disinfectants, although both are antimicrobials: (i) disinfectants are usually applied at concentrations that exceed the minimum inhibitory concentration by orders of magnitude, (ii) the exposure times of disinfectants are in the range of seconds, minutes, or a few hours, (iii) the mode of action of disinfectants is less specific, and (iv) disinfectants often contain more than one active agent with additive or synergistic effects. It is important to recognize that disinfectants, like other antimicrobial agents such as antibiotics, have a dualistic nature and should be used correctly and with caution.

A current insight into Salmonella's inducible acid resistance

Salmonella is a diverse and ubiquitous group of bacteria and a major zoonotic pathogen implicated in several foodborne disease outbreaks worldwide. With more than 2500 distinct serotypes, this pathogen has evolved to survive in a wide spectrum of environments and across multiple hosts. The primary and most common source of transmission is through contaminated food or water. Although the main sources have been primarily linked to animal-related food products, outbreaks due to the consumption of contaminated plant-related food products have increased in the last few years. The perceived ability of Salmonella to trigger defensive mechanisms following pre-exposure to sublethal acid conditions, namely acid adaptation, has renewed a decade-long attention. The impact of acid adaptation on the subsequent resistance against lethal factors of the same or multiple stresses has been underscored by multiple studies. Α plethora of studies have been published, aiming to outline the factors that- alone or in combination- can impact this phenomenon and to unravel the complex networking mechanisms underlying its induction. This review aims to provide a current and updated insight into the factors and mechanisms that rule this phenomenon.

Significant Factors for Modelling Survival of Escherichia coli in Lake Sediments

Currently available numerical models that describe the fecal contamination of aquatic environments using Escherichia coli as an indicator bacterium did not consider its survival in sediments. We conducted a series of comparative experiments to reveal the independent and interactive effects of sediment factors, including temperature, pH, water-extractable total dissolved solids (TDSs), coexisting microbes, and sampling sites, in lake environments on E. coli survival. In experiments, E. coli survival was observed by controlling any two factors at a time. Consequently, the decrease in pH and presence of coexisting microbes enhanced E. coli die-off, whereas the addition of water-extractable TDSs promoted its growth. To select factors to be considered for modelling E. coli survival in sediments, the independent effects of each factor and the interaction effect of the two factors were statistically compared based on their effect sizes (η2). As a result, pH (η2 = 59.5-89.0%) affected E. coli survival most significantly, followed by coexisting microbes (1.7-48.4%). Among the interactions affecting E. coli survival, including pH or coexisting microbes-which had larger independent effects-relatively larger statistically significant interactions were observed between pH and coexisting microbes (31.1%), coexisting microbes and water-extractable TDSs (85.4%), and coexisting microbes and temperature (26.4%).

Enzymatic properties of ornithine decarboxylase from Clostridium aceticum DSM1496

Clostridium aceticum DSM1496 is an acid-resistant strain in which ornithine decarboxylase (ODC) plays a crucial role in acid resistance. In this study, we expressed ODC derived from C. aceticum DSM1496 in Escherichia coli BL21 (DE3) and thoroughly examined its enzymatic properties. The enzyme has a molecular weight of 55.27 kDa and uses pyridoxal-5'-phosphate (PLP) as a coenzyme with a Km = 0.31 mM. ODC exhibits optimal activity at pH 7.5, and it maintains high stability even at pH 4.5. The peak reaction temperature for ODC is 30°C. Besides, it can be influenced by certain metal ions such as Mn2+. Although l-ornithine serves as the preferred substrate for ODC, the enzyme also decarboxylates l-arginine and l-lysine simultaneously. The results indicate that ODC derived from C. aceticum DSM1496 exhibits the ability to produce putrescine, cadaverine, and agmatine through decarboxylation. These polyamines have the potential to neutralize acid in an acidic environment, facilitating the growth of microorganisms. These significant findings provide a strong basis for further investigation into the acid-resistant mechanisms contributed by ODC.

Physiology of γ-aminobutyric acid production by Akkermansia muciniphila

Gut bacteria hold the potential to produce a broad range of metabolites that can modulate human functions, including molecules with neuroactive potential. One such molecule is γ-aminobutyric acid (GABA), the main inhibitory neurotransmitter of the central nervous system in animals. Metagenomic analyses suggest that the genomes of many gut bacteria encode glutamate decarboxylase (GAD), the enzyme that catalyzes GABA production. The genome of Akkermansia muciniphila, a mucin specialist and potential next-generation probiotic from the human gut, is predicted to encode GAD, suggesting a contributing role in GABA production in the human gut. In this study, A. muciniphila was grown in batch cultures with and without pH control. In both experiments, A. muciniphila was found to produce GABA as a response to acid (pH <5.5), although only when GABA precursors, either glutamate or glutamine, were present in the medium. Proteomic analysis comparing A. muciniphila grown with and without precursors at pH 4 did not show a difference in GAD expression, suggesting that it is expressed regardless of the presence of GABA precursors. To further investigate the function of A. muciniphila GAD, we heterologously expressed the gad gene (encoded by locus tag Amuc_0372) with a His tag in Escherichia coli and purified the GAD protein. Enzyme assays showed GAD activity in a pH range between 4 and 6, with the highest specific activity at pH 5 of 144 ± 16 µM GABA/min/mg. Overall, our results demonstrate the ability of A. muciniphila to produce GABA as an acid response and unravel the conditions under which GABA production in A. muciniphila occurs.IMPORTANCEAkkermansia muciniphila is considered to be a beneficial bacterium from the human gut, but the exact mechanisms by which A. muciniphila influences its host are not yet fully understood. To this end, it is important to identify which metabolites are produced and consumed by A. muciniphila that may contribute to a healthy gut. In the present study, we demonstrate the ability of A. muciniphila to produce γ-aminobutyric acid (GABA) when grown in an acidic environment, which often occurs in the gut. GABA is the major inhibitory neurotransmitter in the central nervous system and is present in the human gut. For this reason, it is considered an important bacterial metabolite. Our finding that A. muciniphila produces GABA in acidic environments adds to the growing body of understanding of its relationship with host health and provides an explanation on how it can survive acid stress in the human gut.

Modelling the Survival of Acid-Adapted and Nonadapted Escherichia coli O157:H7 in Burkina: A Western African Traditional Fermented Milk Product

Burkina, a traditional fermented dairy product, is consumed in most parts of West Africa, including Ghana. Studies on the microflora of Burkina have indicated the presence of Escherichia coli and other pathogenic organisms. Thus, predicting the survival of E. coli in the product will inform the best manufacturing and handling practices. This study investigated the combined effect of storage temperature and time on the survival of acid-adapted and acid-non-adapted E. coli O157:H7 in Burkina. Samples were pasteurised and inoculated with acid-adapted or acid-non-adapted E. coli O157:H7. They were stored at 5, 15, and 30°C for 0, 2, 4, 6, 8, 10, 12, 14, 18, and 48 h, and the bacteria colonies were enumerated. Growth rate (survival versus time) models were developed using MATLAB software. Observed data were fitted to the Baranyi model using the DMFit curve fitting software. The E. coli O157:H7 strain appeared inherently tolerant to acid, with storage time having the most significant effect on the response parameter, survival (log CFU/mL). A negative correlation was observed for the primary models (survival versus time), which accounted for 79-97% of the relationship (p < 0.05). Although E. coli survived, its growth was inhibited over time regardless of acid adaptation.

First Report and Characterization of the mcr-1 Positive Multidrug-Resistant Escherichia coli Strain Isolated from Pigs in Croatia

The emergence and rapid spread of the plasmid-mediated colistin-resistant mcr-1 gene introduced a serious threat to public health. In 2021, a multi-drug resistant, mcr-1 positive Escherichia coli EC1945 strain, was isolated from pig caecal content in Croatia. Antimicrobial susceptibility testing and whole genome sequencing were performed. Bioinformatics tools were used to determine the presence of resistance genes, plasmid Inc groups, serotype, sequence type, virulence factors, and plasmid reconstruction. The isolated strain showed phenotypic and genotypic resistance to nine antimicrobial classes. It was resistant to colistin, gentamicin, ampicillin, cefepime, cefotaxime, ceftazidime, sulfamethoxazole, chloramphenicol, nalidixic acid, and ciprofloxacin. Antimicrobial resistance genes included mcr-1, blaTEM-1B, blaCTX-M-1, aac(3)-IId, aph(3')-Ia, aadA5, sul2, catA1, gyrA (S83L, D87N), and parC (A56T, S80I). The mcr-1 gene was located within the conjugative IncX4 plasmid. IncI1, IncFIB, and IncFII plasmids were also detected. The isolate also harbored 14 virulence genes and was classified as ST744 and O101:H10. ST744 is a member of the ST10 group which includes commensal, extraintestinal pathogenic E. coli isolates that play a crucial role as a reservoir of genes. Further efforts are needed to identify mcr-1-carrying E. coli isolates in Croatia, especially in food-producing animals to identify such gene reservoirs.

Acid tolerance of enterohemorrhagic Escherichia coli O157:H7 strain ATCC 43894 and its relationship with a large virulence plasmid pO157

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a zoonotic pathogen that causes a severe intestinal infection including hemolytic uremic syndrome in humans. Various factors contribute to its pathogenesis, including a large virulence plasmid pO157. This F-like 92-kb plasmid is isolated in virtually all clinical EHEC isolates, and is considered a hallmark of EHEC virulence. A previous report stated that removal of pO157 from EHEC ATCC 43894 induced overexpression of GadAB that are essential in glutamate-dependent acid resistance (GDAR) system, yet the mechanism remains elusive. Based on this observation, we surmised that pO157 is involved in the regulation of GDAR system. We comparatively analyzed 43894 and its pO157-cured (ΔpO157) mutant 277 for i) their acid resistance, ii) changes in the transcriptional profiles and iii) expression of GDAR associated genes/proteins. Survivability of 43894 upon exposure to acidic conditions was significantly lower than the ΔpO157 mutant. In addition, RNA-sequencing revealed that genes involved in GDAR were significantly down-regulated in 43894 when compared to the ΔpO157 mutant. Exogenous expression of GadE in 43894 led to expression of GadAB, suggesting possible intervention of pO157 in GDAR regulation. Despite these findings, reintroduction of pO157 into 277 did not reverted Gad overexpression. Likewise, removing pO157 from 43894 using the plasmid incompatibility method did not induce Gad overexpression as shown in 277. Taken together, the results suggest that variation in acid resistance among EHEC isolates exists, and the large virulence plasmid pO157 has no effect on weak acid resistance phenotype displayed in 43894.

Influence of antibiotic-resistance and exudate on peroxyacetic acid tolerance in O157 and non-O157 Shiga toxin producing E. coli

Shiga toxin producing Escherichia coli (STEC) continues to cause foodborne outbreaks associated with beef and beef products despite consistent use of antimicrobial interventions. In this study, the influence of antibiotic resistance (ABR) in E. coli O157:H7 H1730, O157:H7 43,895, O121:H19 and O26:H11 on tolerance to peroxyacetic acid (PAA) was evaluated. Further, bactericidal concentrations of PAA in the presence of nutrient rich media (Tryptic Soy Broth, TSB and beef exudates) and nutrient deficient media (Sterile Deionized Water, SDW and Phosphate Buffered Saline, PBS) were evaluated for all bacterial strains. Antibiotic resistance to ampicillin (amp C), or ampicillin and streptomycin (amp P strep C) was generated in each bacterial strain through incremental exposure to the antibiotics or by plasmid transformation (n = 12 total strains). The mean bactericidal concentrations of PAA were higher (p ≤ 0.05) in nutrient rich media (205.55 ± 31.11 in beef exudate and 195.83 ± 25.00 ppm in TSB) than in nutrient deficient media (57.91 ± 11.97 ppm in SDW and 56.66 ± 9.56 ppm in PBS). Strain O157: H7 ampP strepC was the most tolerant to PAA (p ≤ 0.05). At 200 ppm in nutrient rich media and 60 ppm in nutrient deficient media, all bacterial strains declined in population to below the limit of detection. Analysis of the beef exudates indicated the presence of diverse amino acids that have been associated with acid tolerance. The results from this study indicate that beef exudates could contribute to acid tolerance and suggest that some STEC bacterial strains with certain ABR profiles might be more tolerant to PAA.

The prophage-encoded transcriptional regulator AppY has pleiotropic effects on E. coli physiology

Bacterial genome diversity is influenced by prophages, which are viral genomes integrated into the bacterial chromosome. Most prophage genes are silent but those that are expressed can provide unexpected properties to their host. Using as a model E. coli K-12 that carries 9 defective prophages in its genome, we aimed at highlighting the impact of genes encoded by prophages on host physiology. We focused our work on AppY, a transcriptional regulator encoded on the DLP12 prophage. By performing RNA-Seq experiments, we showed that AppY production modulates the expression of more than 200 genes. Among them, 11 were identified by ChIP-Seq as direct AppY targets. AppY directly and positively regulates several genes involved in the acid stress response including the master regulator gene gadE but also nhaR and gadY, two genes important for biofilm formation. Moreover, AppY indirectly and negatively impacts bacterial motility by favoring the degradation of FlhDC, the master regulator of the flagella biosynthesis. As a consequence of these regulatory effects, AppY increases acid stress resistance and biofilm formation while also causing a strong defect in motility. Our research shed light on the importance to consider the genetic interactions occurring between prophages and bacteria to fully understand bacterial physiology. It also highlights how a prophage-encoded transcriptional regulator integrates in a complex manner into the host regulatory network and how it benefits its host, allowing it to cope with changing environmental conditions.

Mutating both relA and spoT of enteropathogenic Escherichia coli E2348/69 attenuates its virulence and induces interleukin 6 in vivo

Here, we report for the first time that disrupting both relA and spoT genes in enteropathogenic Escherichia coli E2348/69 can attenuate its virulence and significantly induce interleukin 6 (IL-6) in vivo. Our experimental analyses demonstrated that an E2348/69 ΔrelAΔspoT double mutant strain derepressed the expression of type IV bundle forming pilus (BFP) and repressed the expression of glutamate decarboxylase (GAD) and locus of enterocyte effacement (LEE). Whole genome-scale transcriptomic analysis revealed that 1,564 EPEC genes were differentially expressed in the ΔrelAΔspoT double mutant strain (cut-off > two-fold). Such depletion of relA and spoT attenuated the virulence of E2348/69 in a Caenorhabditis elegans infection model. Surprisingly, IL-6 was highly induced in porcine macrophages infected with the ΔrelAΔspoT double mutant strain compared to those with its wildtype strain. Coinciding with these in vitro results, in vivo murine peritoneal challenge assays showed high increase of IL-6 and improved bacterial clearance in response to infection by the ΔrelAΔspoT double mutant strain. Taken together, our data suggest that relA and spoT play an essential role in regulating biological processes during EPEC pathogenesis and that their depletion can affect host immune responses by inducing IL-6.

Serine Deamination Is a New Acid Tolerance Mechanism Observed in Uropathogenic Escherichia coli

Escherichia coli associates with humans early in life and can occupy several body niches either as a commensal in the gut and vagina, or as a pathogen in the urinary tract. As such, E. coli has an arsenal of acid response mechanisms that allow it to withstand the different levels of acid stress encountered within and outside the host. Here, we report the discovery of an additional acid response mechanism that involves the deamination of l-serine to pyruvate by the conserved l-serine deaminases SdaA and SdaB. l-serine is the first amino acid to be imported in E. coli during growth in laboratory media. However, there remains a lack in knowledge as to how l-serine is utilized. Using a uropathogenic strain of E. coli, UTI89, we show that in acidified media, l-serine is brought into the cell via the SdaC transporter. We further demonstrate that deletion of the l-serine deaminases SdaA and SdaB renders E. coli susceptible to acid stress, similar to other acid stress deletion mutants. The pyruvate produced by l-serine deamination activates the pyruvate sensor BtsS, which in concert with the noncognate response regulator YpdB upregulates the putative transporter YhjX. Based on these observations, we propose that l-serine deamination constitutes another acid response mechanism in E. coli. IMPORTANCE The observation that l-serine uptake occurs as E. coli cultures grow is well established, yet the benefit E. coli garners from this uptake remains unclear. Here, we report a novel acid tolerance mechanism where l-serine is deaminated to pyruvate and ammonia, promoting survival of E. coli under acidic conditions. This study is important as it provides evidence of the use of l-serine as an acid response strategy, not previously reported for E. coli.

Detection and genetic analysis of Escherichia coli from Tonle Sap Lake and its tributaries in Cambodia: Spatial distribution, seasonal variation, pathogenicity, and antimicrobial resistance

As an indicator of fecal contamination, Escherichia coli was monitored in Tonle Sap Lake, Cambodia, and its tributaries during low- and high-water seasons, focusing on the impacts on floating villagers inhabiting boathouses. E. coli concentrations in the floating villages (3.6 × 10³ and 5.7 × 10³ CFU/100 mL during the low- and high-water seasons, respectively) were significantly higher than those in other lake sites (4.0 × 10¹ and 7.0 × 10⁰ CFU/100 mL during the low- and high-water seasons, respectively) and rivers (3.3 × 10² and 8.9 × 10² CFU/100 mL during the low- and high-water seasons, respectively), most likely because fecal materials from the boathouses were discharged without treatment. At most of the lake sampling sites remote from the boathouses, the E. coli concentration was lower during the high-water season than that during the low-water season, due to dilution by lake water. E. coli colonies detected during monitoring were isolated for pathotyping, antimicrobial susceptibility testing, beta-lactamase gene detection, and multilocus sequencing typing (MLST). Of the 659 E. coli isolates, 101 (15.3%) were diarrheagenic E. coli (DEC). The prevalence of DEC (52.2%) in the floating villages during the low-water season was higher than that during the high-water season (4.2%) and that in other sites during both seasons (10.6-21.3%). The DEC isolates from the floating villages during the low-water season showed high antimicrobial resistance, including ampicillin (83.4%) and ciprofloxacin (83.4%), and frequently possessed a beta-lactamase gene (bla_TEM) (83.4%). MLST analysis indicated that the predominant sequence type (ST) of DEC isolates from the floating villages possibly originated from humans, whereas more diverse STs were detected in isolates from other sites. We revealed the wide presence of diarrheagenic and antimicrobial-resistant E. coli in Tonle Sap Lake and identified a considerable infection risk in floating villages, especially during the low-water season.

Bacterial battle against acidity

The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.

Lactic Acid Resistance and Population Structure of Escherichia coli from Meat Processing Environment

To explore the effect of beef processing on Escherichia coli populations in relation to lactic acid resistance, this study investigated the links among acid response, phylogenetic structure, genome diversity, and genotypes associated with acid resistance of meat plant E. coli. Generic E. coli isolates (n = 700) were from carcasses, fabrication equipment, and beef products. Acid treatment was carried out in Luria-Bertani broth containing 5.5% lactic acid (pH 2.9). Log reductions of E. coli ranged from <0.5 to >5 log CFU/mL (median: 1.37 log). No difference in lactic acid resistance was observed between E. coli populations recovered before and after a processing step or antimicrobial interventions. E. coli from the preintervention carcasses were slightly more resistant than E. coli isolated from equipment, differing by <0.5 log unit. Acid-resistant E. coli (log reduction <1, n = 45) had a higher prevalence of genes related to energy metabolism (ydj, xap, ato) and oxidative stress (fec, ymjC) than the less resistant E. coli (log reduction >1, n = 133). The ydj and ato operons were abundant in E. coli from preintervention carcasses. In contrast, fec genes were abundant in E. coli from equipment surfaces. The preintervention E. coli contained phylogroups A and B1 in relatively equal proportions. Phylogroup B1 predominated (95%) in the population from equipment. Of note, E. coli collected after sanitation shared either the antigens of O8 or H21. Additionally, genome diversity decreased after chilling and equipment sanitation. Overall, beef processing did not select for E. coli resistant to lactic acid but shaped the population structure. IMPORTANCE Antimicrobial interventions have significantly reduced the microbial loads on carcasses/meat products; however, the wide use of chemical and physical biocides has raised concerns over their potential for selecting resistant populations in the beef processing environment. Phenotyping of acid resistance and whole-genome analysis described in this study demonstrated beef processing practices led to differences in acid resistance, genotype, and population structure between carcass- and equipment-associated E. coli but did not select for the acid-resistant population. Results indicate that genes coding for the metabolism of long-chain sugar acids (ydj) and short-chain fatty acids (ato) were more prevalent in carcass-associated than equipment-associated E. coli. These results suggest E. coli from carcasses and equipment surfaces have been exposed to different selective pressures. The findings improve our understanding of the microbial ecology of E. coli in food processing environments and in general.

Regulation Mechanisms of Virulence Genes in Enterohemorrhagic Escherichia coli

Enterohemorrhagic Escherichia coli (EHEC) is one of the most common E. coli pathotypes reported to cause several outbreaks of foodborne illnesses. EHEC is a zoonotic pathogen, and ruminants, especially cattle, are considered important reservoirs for the most common EHEC serotype, E. coli O157:H7. Humans are infected indirectly through the consumption of food (milk, meat, leafy vegetables, and fruits) and water contaminated by animal feces or direct contact with carrier animals or humans. E. coli O157:H7 is one of the most frequently reported causes of foodborne illnesses in developed countries. It employs two essential virulence mechanisms to trigger damage to the host. These are the development of attaching and effacing (AE) phenotypes on the intestinal mucosa of the host and the production of Shiga toxin (Stx) that causes hemorrhagic colitis and hemolytic uremic syndrome. The AE phenotype is controlled by the pathogenicity island, the locus of enterocyte effacement (LEE). The induction of both AE and Stx is under strict and highly complex regulatory mechanisms. Thus, a good understanding of these mechanisms, major proteins expressed, and environmental cues involved in the regulation of the expression of the virulence genes is vital to finding a method to control the colonization of reservoir hosts, especially cattle, and disease development in humans. This review is a concise account of the current state of knowledge of virulence gene regulation in the LEE-positive EHEC.

Comparison of enrichment methods for isolating Enterohemorrhagic Escherichia coli in kimchi

This study was conducted to compare the efficiency of four enrichment methods of Enterohemorrhagic Escherichia coli by using the 16S rRNA amplicon sequencing and a predictive model. Four different methods (US FDA, ISO, Japan Food Hygiene Association and Korea Ministry of Food and Drug Safety) were used to enrich EHEC in kimchi inoculated with cocktails of EHEC strains (NCCP 13720, NCCP 13721, and NCCP 14134). The maximum growth rate (μ_max) and lag phase duration (LPD) were compared using the Baranyi model, and 16S rRNA targeted sequencing was performed with samples at the end of the exponential phase. As a result, the μ_max and LPD values of Baranyi model developed for the four enriched media ranged from 0.82 to 0.92 and from 2.35 to 2.68, respectively, suggesting that the growth of EHEC was similar in all four enrichment media. As for the relative abundance of the bacterial composition at the family level, Enterobacteriaceae was identified as the major component (>50%) in all four enriched media. The relative abundance of Enterobacteriaceae was highest (>90%) in the two enriched media with 20 mg/L novobiocin, demonstrating that significant growth of non-targeted bacteria takes place in enrichment broths utilizing <20 mg/L novobiocin or different antibiotics. In conclusion, this study suggests that all four enrichment broth are suitable for growing EHEC in kimchi and the use and concentration of antibiotics such as novobiocin in enrichment media may have a critical role in species diversity.

Strategies for anti-oxidative stress and anti-acid stress in bioleaching of LiCoO2 using an acidophilic microbial consortium

High metal ion concentrations and low pH cause severely inhibit the activity of an acidophilic microbial consortium (AMC) in bioleaching. This work investigated the effects of exogenous spermine on biofilm formation and the bioleaching efficiency of LiCoO₂ by AMC in 9K medium. After the addition of 1 mM spermine, the activities of glutathione peroxidase and catalase increased, while the amount of H₂O₂, intracellular reactive oxygen species (ROS) and malondialdehyde in AMC decreased. These results indicated that the ability of AMC biofilm to resist oxidative stress introduced by 3.5 g/L Li⁺ and 30.1 g/L Co²⁺ was improved by spermine. The activity of glutamate decarboxylase was promoted to restore the intracellular pH buffering ability of AMC. Electrochemical measurements showed that the oxidation rate of pyrite was increased by exogenous spermine. As a result, high bioleaching efficiencies of 97.1% for Li⁺ and 96.1% for Co²⁺ from a 5.0% (w v^-1) lithium cobalt oxide powder slurry were achieved. This work demonstrated that Tafel polarization can be used to monitor the AMC biofilm's ability of uptaking electrons from pyrite during bioleaching. The corrosion current density increased with 1 mM spermine, indicating enhanced electron uptake by the biofilm from pyrite.

TorR/TorS Two-Component system resists extreme acid environment by regulating the key response factor RpoS in Escherichia coli

Response to acid stress is critical for Escherichia coli to successfully complete its life-cycle. Acid resistance is an indispensable mechanism that allows neutralophilic bacteria, such as E. coli, to survive in the gastrointestinal tract. Escherichia coli acid tolerance has been extensively studied over the past decades, and most studies have focused on mechanisms of gene regulation. Bacterial two-component signal transduction systems sense and respond to external environmental changes through regulating genes expression. However, there has been little research on the mechanism of the TorR/TorS system in acid resistance, and how TorR/TorS regulate the expression ofacid-resistantgenes is still unclear. We found that TorR/TorS deletion in E. coli cells led to a growth defect in extreme acid conditions,andthis defectmightdepend on the nutritional conditionsand growth phase.TorS/TorR sensed an extremely acidic environment, and this TorR phosphorylation process might not be entirely dependent on TorS.RNA-seqand RT-qPCR results suggested that TorR regulated expressions of gadB, gadC, hdeA, gadE, mdtE, mdtF, gadX, and slp acid-resistant genes. Compared with wild-type cells, the stress response factor RpoSlevels and itsexpressions were significantly decreased in Δ torR cellsstimulated by extreme acid. And under these circumstances, the expression of iraM was significantly reduced to 0.6-fold inΔ torR cells. Electrophoreticmobility shift assay showed that TorR-His₆ could interact with the rpoS promoter sequence in vitro. β-galactosidase activity assayresultsapprovedthat TorR might bind the rpoS promoter region in vivo. After the mutation of the TorR-box in the rpoS promoter region, these interactions were no longer observed. Taken together, we propose thatTorS and potential Hanks model Ser/Thr kinase received an external acid stress signal and then phosphorylated TorR, which guided the expressions of a variety of acid resistance genes. Moreover,TorRcoped with extreme acid environmentsthroughRpoS, levels of which might be maintained byIraM. Finally,TorR may confer E. coli with the abilityto resist gastric acid, allowing the bacterium to reach the surface of the terminal ileum and large intestine mucosal epithelial cells through the gastric acid barrier, andestablishcolonization and pathogenicity.

Exometabolomic Analysis of Susceptible and Multi-Drug Resistant Pseudomonas aeruginosa

Multidrug resistant (MDR) Pseudomonas aeruginosa strains have recently become one of the major public health concerns worldwide leading to difficulties in selecting appropriate antibiotic treatment. Thus, it is important to elucidate the characteristics of MDR isolates. Herein, we aimed to determine the unique exometabolome profile of P. aeruginosa clinical isolates in monocultures that comprise high resistance to multiple antibiotics, and compare the differential metabolite profiles obtained from susceptible isolates by using GC/MS. Our results showed that partial least square-discriminant analysis (PLS-DA) score plot clearly discriminated the MDR and susceptible isolates indicating the altered exometabolite profiles, and highlighted the significantly enriched levels of trehalose and glutamic acid in MDR isolates. Expression of trehalose synthase (treS) was also 1.5 fold higher in MDR isolates, relatively to susceptible isolates. Overall, our study provides insights into the distinct footprints of MDR P. aeruginosa isolates in mono-culture.

Regulation of Escherichia coli fim gene transcription by GadE and other acid tolerance gene products

Uropathogenic Escherichia coli (UPEC) cause millions of urinary tract infections each year in the United States. Type 1 pili are important for adherence of UPEC to uroepithelial cells in the human and murine urinary tracts where osmolality and pH vary. Previous work has shown that an acidic pH adversely affects the expression of type 1 pili. To determine if acid tolerance gene products may be regulating E. coli fim gene expression, a bank of K-12 strain acid tolerance gene mutants were screened using fimA-lux, fimB-lux, and fimE-lux fusions on single copy number plasmids. We have determined that a mutation in gadE increased transcription of all three fim genes, suggesting that GadE may be acting as a repressor in a low pH environment. Complementation of the gadE mutation restored fim gene transcription to wild-type levels. Moreover, mutations in gadX, gadW, crp, and cya also affected transcription of the three fim genes. To verify the role GadE plays in type 1 pilus expression, the NU149 gadE UPEC strain was tested. The gadE mutant had higher fimE gene transcript levels, a higher frequency of Phase-OFF positioning of fimS, and hemagglutination titres that were lower in strain NU149 gadE cultured in low pH medium as compared to the wild-type bacteria. The data demonstrate that UPEC fim genes are regulated directly or indirectly by the GadE protein and this could have some future bearing on the ability to prevent urinary tract infections by acidifying the urine and shutting off fim gene expression.

Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation

Escherichia coli is a Gram-negative bacterium that colonises the human intestine and virulent strains can cause severe diarrhoeal and extraintestinal diseases. The protein SslE is secreted by a range of pathogenic and commensal E. coli strains. It can degrade mucins in the intestine, promotes biofilm maturation and it is a major determinant of infection in virulent strains, although how it carries out these functions is not well understood. Here, we examine SslE from the commensal E. coli Waksman and BL21 (DE3) strains and the enterotoxigenic H10407 and enteropathogenic E2348/69 strains. We reveal that SslE has a unique and dynamic structure in solution and in response to acidification within mature biofilms it can form a unique aggregate with amyloid-like properties. Furthermore, we show that both SslE monomers and aggregates bind DNA in vitro and co-localise with extracellular DNA (eDNA) in mature biofilms, and SslE aggregates may also associate with cellulose under certain conditions. Our results suggest that interactions between SslE and eDNA are important for biofilm maturation in many E. coli strains and SslE may also be a factor that drives biofilm formation in other SslE-secreting bacteria.

Genomewide transcriptional response of Escherichia coli O157:H7 to norepinephrine

Background

Chemical signaling between a mammalian host and intestinal microbes is health and maintenance of ‘healthy’ intestinal microbiota. Escherichia coli O157:H7 can hijack host- and microbiota-produced chemical signals for survival in a harsh and nutritionally competitive gastrointestinal environment and for intestinal colonization. Norepinephrine (NE) produced by sympathetic neurons of the enteric nervous system has been shown in vitro to induce expression of genes controlling E. coli O157:H7 swimming motility, acid resistance, and adherence to epithelial cells. A previous study used a microarray approach to identify differentially expressed genes in E. coli O157:H7 strain EDL933 in response to NE. To elucidate a comprehensive transcriptional response to NE, we performed RNA-Seq on rRNA-depleted RNA of E. coli O157:H7 strain NADC 6564, an isolate of a foodborne E. coli O157:H7 strain 86–24. The reads generated by RNA-Seq were mapped to NADC 6564 genome using HiSat2. The mapped reads were quantified by htseq-count against the genome of strain NADC 6564. The differentially expressed genes were identified by analyzing quantified reads by DESeq2.

Results

Of the 585 differentially expressed genes (≥ 2.0-fold; p < 0.05), many encoded pathways promoting ability of E. coli O157:H7 strain NADC 6564 to colonize intestines of carrier animals and to produce disease in an incidental human host through increased adherence to epithelial cells and production of Shiga toxins. In addition, NE exposure also induced the expression of genes encoding pathways conferring prolonged survival at extreme acidity, controlling influx/efflux of specific nutrients/metabolites, and modulating tolerance to various stressors. A correlation was also observed between the EvgS/EvgA signal transduction system and the ability of bacterial cells to survive exposure to high acidity for several hours. Many genes involved in nitrogen, sulfur, and amino acid uptake were upregulated while genes linked to iron (Fe³⁺) acquisition and transport were downregulated.

Conclusion

The availability of physiological levels of NE in gastrointestinal tract could serve as an important cue for E. coli O157:H7 to engineer its virulence, stress, and metabolic pathways for colonization in reservoir animals, such as cattle, causing illness in humans, and surviving outside of a host.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08167-z.

Gamma-aminobutyric acid fermentation in MRS-based medium by the fructophilic Lactiplantibacillus plantarum Y7

Among the key metabolites produced by probiotic lactic acid bacteria (LAB), the use of gamma-aminobutyric acid (GABA), which alleviates hypertension, depression, and sleepiness in humans, is gaining popularity. Thus, GABA-producing LAB are sought after. GABA-producing LAB were preliminarily screened in acidified-MRS broth and quantified via GABase assays. The one-factor-at-a-time strategy was applied to determine the optimal conditions for GABA production. GABA production in reconstituted skim milk medium (RSM) and antibiotic susceptibility testing were performed to evaluate the potential of the strain as a yogurt starter. L. plantarum Y7 produced 4,856.86 ± 82.47 μg/mL of GABA at optimal culture conditions. Co-cultivation of Y7 and commercial Lactobacillus bulgaricus affected the amount of GABA production (6.85 ± 0.20 μg/mL) in RSM. Y7 was susceptible to ampicillin, erythromycin, and tetracycline. Therefore, L. plantarum Y7 represents a promising strain for GABA production in the food industry.

Pathophysiology of enteropathogenic Escherichia coli during a host infection

Enteropathogenic Escherichia coli (EPEC) is a major cause of infantile diarrhea in developing countries. However, sporadic outbreaks caused by this microorganism in developed countries are frequently reported recently. As an important zoonotic pathogen, EPEC is being monitored annually in several countries. Hallmark of EPEC infection is formation of attaching and effacing (A/E) lesions on the small intestine. To establish A/E lesions during a gastrointestinal tract (GIT) infeciton, EPEC must thrive in diverse GIT environments. A variety of stress responses by EPEC have been reported. These responses play significant roles in helping E. coli pass through GIT environments and establishing E. coli infection. Stringent response is one of those responses. It is mediated by guanosine tetraphosphate. Interestingly, previous studies have demonstrated that stringent response is a universal virulence regulatory mechanism present in many bacterial pathogens including EPEC. However, biological signficance of a bacterial stringent response in both EPEC and its interaction with the host during a GIT infection is unclear. It needs to be elucidated to broaden our insight to EPEC pathogenesis. In this review, diverse responses, including stringent response, of EPEC during a GIT infection are discussed to provide a new insight into EPEC pathophysiology in the GIT.

Experimentally observed Campylobacter jejuni survival kinetics in chicken meat products during model gastric digestion tended to be lower than model predictions

Campylobacter jejuni-related foodborne diseases are mainly attributed to the consumption of undercooked chicken meat and cross-contaminated produce. This study aimed to develop a survival kinetics model, based on the Weibull model, for predicting foodborne C. jejuni survival during gastric digestion in a model stomach. We previously confirmed that C. jejuni can survive temperatures up to 62 °C; therefore, certain types of grilled chicken skewers (yakitori) were examined for C. jejuni survival during simulated gastric digestion. C. jejuni survival on a chicken thigh following grilling was examined to confirm the foods for digestion experiments. Further, C. jejuni survival during model digestion was investigated through simultaneous digestion of raw chicken and cross-contaminated iceberg lettuce. The model stomach pH increased from 1.5 to 6.0 immediately after yakitori ingestion and did not decrease below 4.0 within 3 h of digestion. Gastric digestion did not significantly contribute to C. jejuni inactivation (<1.5 log reduction after 3 h digestion). Our model could predict C. jejuni survival kinetics in simulated gastric fluid under varying pH during model digestion. This approach can be used to predict C. jejuni survival rates following digestion to improve food safety and reduce Campylobacter-related disease outbreaks.

Transcriptional analysis reveals specific niche factors and response to environmental stresses of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents

Background

Enterohemorrhagic Escherichia coli (EHEC) are responsible for severe diseases in humans, and the ruminant digestive tract is considered as their main reservoir. Their excretion in bovine feces leads to the contamination of foods and the environment. Thus, providing knowledge of processes used by EHEC to survive and/or develop all along the bovine gut represents a major step for strategies implementation.

Results

We compared the transcriptome of the reference EHEC strain EDL933 incubated in vitro in triplicate samples in sterile bovine rumen, small intestine and rectum contents with that of the strain grown in an artificial medium using RNA-sequencing (RNA-seq), focusing on genes involved in stress response, adhesion systems including the LEE, iron uptake, motility and chemotaxis. We also compared expression of these genes in one digestive content relative to the others. In addition, we quantified short chain fatty acids and metal ions present in the three digestive contents. RNA-seq data first highlighted response of EHEC EDL933 to unfavorable physiochemical conditions encountered during its transit through the bovine gut lumen. Seventy-eight genes involved in stress responses including drug export, oxidative stress and acid resistance/pH adaptation were over-expressed in all the digestive contents compared with artificial medium. However, differences in stress fitness gene expression were observed depending on the digestive segment, suggesting that these differences were due to distinct physiochemical conditions in the bovine digestive contents. EHEC activated genes encoding three toxin/antitoxin systems in rumen content and many gene clusters involved in motility and chemotaxis in rectum contents. Genes involved in iron uptake and utilization were mostly down-regulated in all digestive contents compared with artificial medium, but feo genes were over-expressed in rumen and small intestine compared with rectum. The five LEE operons were more expressed in rectum than in rumen content, and LEE1 was also more expressed in rectum than in small intestine content.

Conclusion

Our results highlight various strategies that EHEC may implement to survive in the gastrointestinal environment of cattle. These data could also help defining new targets to limit EHEC O157:H7 carriage and shedding by cattle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02343-7.

Preharvest Management and Postharvest Intervention Strategies to Reduce Escherichia coli Contamination in Goat Meat: A Review

Simple Summary

Goat farms and processing facilities worldwide are primarily small-scale, limited resource operations. Cost-effectiveness and practicality are critical factors to be considered before adopting any pre- and/or post-harvest strategies for pathogen reduction in goat meat. Preharvest management methods in goats that can reduce Escherichia coli in meat include minimizing animal stress, selecting diets and feed deprivation times that can reduce fecal shedding of bacteria, and adding tannin-rich feed supplements. In addition, use of appropriate postharvest nonthermal intervention technologies that can reduce microbial loads in carcasses and meat can extend the shelf-life and marketability of goat meat products. Reducing stress prior to slaughter and using nonthermal intervention methods can result in better meat quality and economic returns for producers.

Abstract

Goat meat is the main source of animal protein in developing countries, particularly in Asia and Africa. Goat meat consumption has also increased in the US in the recent years due to the growing ethnic population. The digestive tract of goat is a natural habitat for Escherichia coli organisms. While researchers have long focused on postharvest intervention strategies to control E. coli outbreaks, recent works have also included preharvest methodologies. In goats, these include minimizing animal stress, manipulating diet a few weeks prior to processing, feeding diets high in tannins, controlling feed deprivation times while preparing for processing, and spray washing goats prior to slaughter. Postharvest intervention methods studied in small ruminant meats have included spray washing using water, organic acids, ozonated water, and electrolyzed water, and the use of ultraviolet (UV) light, pulsed UV-light, sonication, low-voltage electricity, organic oils, and hurdle technologies. These intervention methods show a strong antimicrobial activity and are considered environmentally friendly. However, cost-effectiveness, ease of application, and possible negative effects on meat quality characteristics must be carefully considered before adopting any intervention strategy for a given meat processing operation. As discussed in this review paper, novel pre- and post-harvest intervention methods show significant potential for future applications in goat farms and processing plants.

The challenges and prospects of Escherichia coli as an organic acid production host under acid stress

OBJECTIVE

Organic acids have a wide range of applications and have attracted the attention of many industries, and their large-scale applications have led fermentation production to low-cost development. Among them, the microbial fermentation method, especially using Escherichia coli as the production host, has the advantages of fast growth and low energy consumption, and has gradually shown better advantages and prospects in organic acid fermentation production.

IMPORTANCE

However, when the opportunity comes, the acidified environment caused by the acid products accumulated during the fermentation process also challenges E. coli. The acid sensitivity of E. coli is a core problem that needs to be solved urgently. The addition of neutralizers in traditional operations led to the emergence of osmotic stress inadvertently, the addition of strong acid substances to recover products in the salt state not only increases production costs, but the discharged sewage is also harmful to the environment.

ELABORATION

This article summarizes the current status of the application of E. coli in the production of organic acids, and based on the impact of acid stress on the physiological state of cells and the impact of industrial production profits, put forward some new conjectures that can make up for the deficiencies in existing research and application.

IMPLICATION

At this point, the diversified transformation of E. coli has become a chassis microbe that is more suitable for industrial fermentation, enhancing industrial application value.

KEY POINTS

• E. coli is a potential host for high value-added organic acids production. • Classify the damage mechanism and coping strategies of E. coli when stimulated by acid molecules. • Multi-dimensional expansion tools are needed to create acid-resistant E. coli chassis.

Comparative phenotypic characterization of hybrid Shiga toxin-producing / uropathogenic Escherichia coli, canonical uropathogenic and Shiga toxin-producing Escherichia coli

Hybrid Shiga toxin (Stx)-producing Escherichia coli (STEC) and uropathogenic E. coli (UPEC) strains are phylogenetically positioned between STEC and UPEC and can cause both diarrhea and urinary tract infections (UTIs). However, their virulence properties and adaptation to different host milieu in comparison to canonical UPEC and STEC strains are unknown. We determined phenotypes of the STEC/UPEC hybrid with respect to virulence including acid resistance, motility, biofilm formation, siderophore production, and adherence to human colonic Caco-2 and bladder T24 cells and compared to phenotypes of commensal strain MG1655, UPEC strain 536, and STEC strains B2F1 and Sakai. Moreover, we assessed the adaptation of the hybrid to artificial urine medium (AUM) and simulated colonic environment medium (SCEM). Overall acid resistance at pH 2.5 was high except in strains B2F1 and hybrid 05-00787 which showed reduced and extremely low acid resistance, respectively. Motility was reduced in hybrid 05-00787 and 09-05501 but strong in the remaining hybrids. While some hybrids showed high biofilm formation in LB, overall biofilm formation in SCEM and AUM were low and non-existent, respectively. All strains tested showed siderophore activity at equilibrium. All strains except MG1655 adhered to Caco-2 cells with the hybrid having similar adherence when compared to 536 but exhibited 2 and 3 times lower adherence when compared to B2F1 and Sakai, respectively. All Stx-producing strains adhered stronger to T24 cells than strains 536 and MG1655. Overall growth in LB, SCEM and AUM was consistent within the hybrid strains, except hybrid 05-00787 which showed significantly different growth patterns. Our data suggest that the hybrid is adapted to both, the intestinal and extraintestinal milieu. Expression of phenotypes typical of intestinal and extraintestinal pathogens thereby supports its potential to cause diarrhea and UTI.

Soil salinity, pH, and indigenous bacterial community interactively influence the survival of E. coli O157:H7 revealed by multivariate statistics

Complexities of biotic-abiotic interactions in soils result in the lack of integrated understanding of environmental variables that restrict the survival of shiga toxin-producing E. coli O157:H7. Herein, we reanalyzed previously published data and highlighted the influence of soil abiotic factors on E. coli O157:H7 survivability and elucidated how these factors took effect indirectly through affecting indigenous bacterial community. Interaction network analysis indicated salinity and pH decreased the relative abundances of some bacterial taxa (e.g., Acidobacteria_Gp4, Acidobacteria_Gp6, and Deltaproteobacteria) which were positively correlated with the survival of E. coli O157:H7 in soils, and vice versa (e.g., Gammaproteobacteria and Flavobacteria) (P < 0.05). An array of multivariate statistical approaches including partial Mantel test, variation partition analysis (VPA), and structural equation model (SEM) further confirmed that biotic and abiotic factors interactively shaped the survival profile of E. coli O157:H7. This study revealed that some bacterial taxa were correlated with survival of E. coli O157:H7 directly, and salinity and pH could affect E. coli O157:H7 survival through changing these bacterial taxa. These findings suggest that salinity in soil might benefit the control of fecal pathogenic E. coli invasion, while soil acidification caused by anthropogenic influences could potentially increase the persistence of E. coli O157:H7 in agro-ecosystem.

Tyrosine phosphorylation-dependent localization of TmaR that controls activity of a major bacterial sugar regulator by polar sequestration

The poles of Escherichia coli cells are emerging as hubs for major sensory systems, but the polar determinants that allocate their components to the pole are largely unknown. Here, we describe the discovery of a previously unannotated protein, TmaR, which localizes to the E. coli cell pole when phosphorylated on a tyrosine residue. TmaR is shown here to control the subcellular localization and activity of the general PTS protein Enzyme I (EI) by binding and polar sequestration of EI, thus regulating sugar uptake and metabolism. Depletion or overexpression of TmaR results in EI release from the pole or enhanced recruitment to the pole, which leads to increasing or decreasing the rate of sugar consumption, respectively. Notably, phosphorylation of TmaR is required to release EI and enable its activity. Like TmaR, the ability of EI to be recruited to the pole depends on phosphorylation of one of its tyrosines. In addition to hyperactivity in sugar consumption, the absence of TmaR also leads to detrimental effects on the ability of cells to survive in mild acidic conditions. Our results suggest that this survival defect, which is sugar- and EI-dependent, reflects the difficulty of cells lacking TmaR to enter stationary phase. Our study identifies TmaR as the first, to our knowledge, E. coli protein reported to localize in a tyrosine-dependent manner and to control the activity of other proteins by their polar sequestration and release.

Mapping the Transcriptional and Fitness Landscapes of a Pathogenic E. coli Strain: The Effects of Organic Acid Stress under Aerobic and Anaerobic Conditions

Several methods are available to probe cellular responses to external stresses at the whole genome level. RNAseq can be used to measure changes in expression of all genes following exposure to stress, but gives no information about the contribution of these genes to an organism’s ability to survive the stress. The relative contribution of each non-essential gene in the genome to the fitness of the organism under stress can be obtained using methods that use sequencing to estimate the frequencies of members of a dense transposon library grown under different conditions, for example by transposon-directed insertion sequencing (TraDIS). These two methods thus probe different aspects of the underlying biology of the organism. We were interested to determine the extent to which the data from these two methods converge on related genes and pathways. To do this, we looked at a combination of biologically meaningful stresses. The human gut contains different organic short-chain fatty acids (SCFAs) produced by fermentation of carbon compounds, and Escherichia coli is exposed to these in its passage through the gut. Their effect is likely to depend on both the ambient pH and the level of oxygen present. We, therefore, generated RNAseq and TraDIS data on a uropathogenic E. coli strain grown at either pH 7 or pH 5.5 in the presence or absence of three SCFAs (acetic, propionic and butyric), either aerobically or anaerobically. Our analysis identifies both known and novel pathways as being likely to be important under these conditions. There is no simple correlation between gene expression and fitness, but we found a significant overlap in KEGG pathways that are predicted to be enriched following analysis of the data from the two methods, and the majority of these showed a fitness signature that would be predicted from the gene expression data, assuming expression to be adaptive. Genes which are not in the E. coli core genome were found to be particularly likely to show a positive correlation between level of expression and contribution to fitness.

Mechanisms involved in the adaptation of Escherichia coli O157:H7 to the host intestinal microenvironment

Host adaptation of pathogens may increase intra- and interspecies transmission. We showed previously that the passage of a clinically isolated enterohemorrhagic Escherichia coli (EHEC) O157 strain (125/99) through the gastrointestinal tract of mice increases its pathogenicity in the same host. In this work, we aimed to elucidate the underlying mechanism(s) involved in the patho-adaptation of the stool-recovered (125RR) strain. We assessed the global transcription profile by microarray and found almost 100 differentially expressed genes in 125RR strain compared with 125/99 strain. We detected an overexpression of Type Three Secretion System (TTSS) proteins at the mRNA and protein levels and demonstrated increased adhesion to epithelial cell lines for the 125RR strain. Additional key attributes of the 125RR strain were: increased motility on semisolid agar, which correlated with an increased fliC mRNA level; reduced Stx2 production at the mRNA and protein levels; increased survival at pH 2.5, as determined by acid resistance assays. We tested whether the overexpression of the LEE-encoded regulator (ler) in trans in the 125/99 strain could recreate the increased pathogenicity observed in the 125RR strain. As anticipated ler overexpression led to increased expression of TTSS proteins and bacterial adhesion to epithelial cells in vitro but also increased mortality and intestinal colonization in vivo. We conclude that this host-adaptation process required changes in several mechanisms that improved EHEC O157 fitness in the new host. The research highlights some of the bacterial mechanisms required for horizontal transmission of these zoonotic pathogens between their animal and human populations.

Comparative Review of the Responses of Listeria monocytogenes and Escherichia coli to Low pH Stress

Acidity is one of the principal physicochemical factors that influence the behavior of microorganisms in any environment, and their response to it often determines their ability to grow and survive. Preventing the growth and survival of pathogenic bacteria or, conversely, promoting the growth of bacteria that are useful (in biotechnology and food production, for example), might be improved considerably by a deeper understanding of the protective responses that these microorganisms deploy in the face of acid stress. In this review, we survey the molecular mechanisms used by two unrelated bacterial species in their response to low pH stress. We chose to focus on two well-studied bacteria, Escherichia coli (phylum Proteobacteria) and Listeria monocytogenes (phylum Firmicutes), that have both evolved to be able to survive in the mammalian gastrointestinal tract. We review the mechanisms that these species use to maintain a functional intracellular pH as well as the protective mechanisms that they deploy to prevent acid damage to macromolecules in the cells. We discuss the mechanisms used to sense acid in the environment and the regulatory processes that are activated when acid is encountered. We also highlight the specific challenges presented by organic acids. Common themes emerge from this comparison as well as unique strategies that each species uses to cope with acid stress. We highlight some of the important research questions that still need to be addressed in this fascinating field.

Prevalence of Colistin Resistance in Escherichia coli in Eastern Turkey and Genomic Characterization of an mcr-1 Positive Strain from Retail Chicken Meat

Colistin is one of the most effective antibiotics against multidrug resistant Gram-negative bacteria. However, the recent emergence of plasmid-borne mobilized colistin resistance (mcr) genes is considered a serious antimicrobial resistance challenge worldwide. In this study, we report detection of an mcr-1 carrying Escherichia coli isolate (named ATAVET mcr-1 Turkey) from retail raw chicken meat in Turkey. Of the 11 (from 500 total tested) phenotypically colistin-resistant isolates, 1 was shown to carry the mcr-1 gene by PCR. Whole-genome sequencing indicated that mcr-1 was located on a ∼13 kb-long contig that was almost identical to the corresponding part in pZJ1635, an IncI2 plasmid encoding mcr-1 in the same genetic context in another E. coli strain. In addition, ATAVET mcr-1 Turkey harbored bla_CTX-M-8, qnrB19, mdf(A), tet(A), sul2, aph(3″)-Ib, aph(6)-Id, and floR resistance genes. Phylogenetic analysis based on whole genome and multilocus sequence typing indicated that ATAVET mcr-1 Turkey was more closely related to mcr-1 carrying E. coli isolates from food and human clinical samples previously reported from different parts of the world than to those from Turkey. These findings further emphasize the worldwide emergence and spread of mcr meditated colistin resistance in bacteria with zoonotic potential within animals and the food chain.

Integrated gold superparticles into lateral flow immunoassays for the rapid and sensitive detection of Escherichia coli O157:H7 in milk

Escherichia coli O157:H7 is a common harmful foodborne pathogen that can cause severe diseases at low infectious doses. Traditional lateral flow immunoassay (LFIA) for the rapid screening of E. coli O157:H7 in food suffers from low sensitivity due to its dependence on 20- to 40-nm gold nanoparticles (AuNP) with insufficient brightness as labels. To address this issue, we reported for the first time the successful synthesis of gold superparticles (GSP) by encapsulating numerous small AuNP into a polymer nanobead using an evaporation-induced self-assembly method. Results indicated that the resultant GSP exhibited remarkably enhanced absorbance compared with the most widely used 40 nm AuNP in LFIA. In addition, the absorbance of GSP could be easily tuned by varying GSP sizes. Under optimized conditions, we achieved a rapid and sensitive determination of E. coli O157:H7 in milk with a detection limit of 5.95 × 10² cfu/mL when using the GSP with a size of 342 nm as LFIA signal reporters, exhibiting improvement of approximately 32-fold relative to the conventional 40 nm AuNP-LFIA method. We further demonstrated the selectivity, accuracy, reliability, and practicality of the proposed GSP-LFIA strip. In summary, this work offers a new strategy for improving LFIA sensitivity using assembled GSP as markers and demonstrates huge potential in rapidly and sensitively detecting foodborne pathogens.

RNase E-dependent degradation of tnaA mRNA encoding tryptophanase is prerequisite for the induction of acid resistance in Escherichia coli

Acid-resistance systems are essential for pathogenic Escherichia coli to survive in the strongly acidic environment of the human stomach (pH < 2.5). Among these, the glutamic acid decarboxylase (GAD) system is the most effective. However, the precise mechanism of GAD induction is unknown. We previously reported that a tolC mutant lacking the TolC outer membrane channel was defective in GAD induction. Here, we show that indole, a substrate of TolC-dependent efflux pumps and produced by the tryptophanase encoded by the tnaA gene, negatively regulates GAD expression. GAD expression was restored by deleting tnaA in the tolC mutant; in wild-type E. coli, it was suppressed by adding indole to the growth medium. RNA-sequencing revealed that tnaA mRNA levels drastically decreased upon exposure to moderately acidic conditions (pH 5.5). This decrease was suppressed by RNase E deficiency. Collectively, our results demonstrate that the RNase E-dependent degradation of tnaA mRNA is accelerated upon acid exposure, which decreases intracellular indole concentrations and triggers GAD induction.

An acid-tolerance response system protecting exponentially growing Escherichia coli

The ability to grow at moderate acidic conditions (pH 4.0–5.0) is important to Escherichia coli colonization of the host’s intestine. Several regulatory systems are known to control acid resistance in E. coli, enabling the bacteria to survive under acidic conditions without growth. Here, we characterize an acid-tolerance response (ATR) system and its regulatory circuit, required for E. coli exponential growth at pH 4.2. A two-component system CpxRA directly senses acidification through protonation of CpxA periplasmic histidine residues, and upregulates the fabA and fabB genes, leading to increased production of unsaturated fatty acids. Changes in lipid composition decrease membrane fluidity, F₀F₁-ATPase activity, and improve intracellular pH homeostasis. The ATR system is important for E. coli survival in the mouse intestine and for production of higher level of 3-hydroxypropionate during fermentation. Furthermore, this ATR system appears to be conserved in other Gram-negative bacteria.

The ability to grow at acidic pH is crucial for E. coli colonization of the host’s intestine. Here, the authors identify an acid-tolerance response system that is important for E. coli exponential growth at pH 4.2, survival in the mouse intestine, and production of 3-hydroxypropionate during fermentation.

Hydroxylamine Analogue of Agmatine: Magic Bullet for Arginine Decarboxylase

The biogenic polyamines, spermine, spermidine (Spd) and putrescine (Put) are present at micro-millimolar concentrations in eukaryotic and prokaryotic cells (many prokaryotes have no spermine), participating in the regulation of cellular proliferation and differentiation. In mammalian cells Put is formed exclusively from L-ornithine by ornithine decarboxylase (ODC) and many potent ODC inhibitors are known. In bacteria, plants, and fungi Put is synthesized also from agmatine, which is formed from L-arginine by arginine decarboxylase (ADC). Here we demonstrate that the isosteric hydroxylamine analogue of agmatine (AO-Agm) is a new and very potent (IC50 3•10-8 M) inhibitor of E. coli ADC. It was almost two orders of magnitude less potent towards E. coli ODC. AO-Agm decreased polyamine pools and inhibited the growth of DU145 prostate cancer cells only at high concentration (1 mM). Growth inhibitory analysis of the Acremonium chrysogenum demonstrated that the wild type (WT) strain synthesized Put only from L-ornithine, while the cephalosporin C high-yielding strain, in which the polyamine pool is increased, could use both ODC and ADC to produce Put. Thus, AO-Agm is an important addition to the set of existing inhibitors of the enzymes of polyamine biosynthesis, and an important instrument for investigating polyamine biochemistry.

A survey of extended-spectrum beta-lactamase-producing Enterobacteriaceae in urban wetlands in southwestern Nigeria as a step towards generating prevalence maps of antimicrobial resistance

In many countries, emission of insufficiently treated wastewater into water bodies appears to be an important factor in spreading clinically relevant antimicrobial resistant bacteria. In this study, we looked for the presence of Enterobacteriaceae strains with resistance to 3rd generation cephalosporin antibiotics in four urban wetlands in southwestern Nigeria by isolation, whole genome sequencing and qPCR enumeration of marker genes. Genome analysis of multi-drug resistant and potentially pathogenic Escherichia coli isolates (members of the widely distributed ST10 complex) revealed the presence of the extended spectrum beta-lactamase gene blaCTX-M-15 on self-transmissible IncF plasmids. The gene was also present together with a blaTEM-1B gene on self-transmissible IncH plasmids in multi-drug resistant Enterobacter cloacae isolates. A Citrobacter freundii isolate carried blaTEM-1B on an IncR-type plasmid without discernable conjugation apparatus. All strains were isolated from a wetland for which previous qPCR enumeration of marker genes, in particular the ratio of intI1 to 16S rRNA gene copy numbers, had indicated a strong anthropogenic impact. Consistent with the isolation origin, qPCR analysis in this study showed that the blaCTX-M gene was present at an abundance of 1x10-4 relative to bacterial 16S rRNA gene copy numbers. The results indicate that contamination of these urban aquatic ecosystems with clinically relevant antibiotic resistant bacteria is substantial in some areas. Measures should therefore be put in place to mitigate the propagation of clinically relevant antimicrobial resistance within the Nigerian aquatic ecosystems.

Heat Adaptation Improved Cell Viability of Probiotic Enterococcus faecium HL7 upon Various Environmental Stresses

The production of viable functional probiotics presupposes stability of strain features in the final product. In previous studies, Enterococcus faecium HL7 was found to have relatively higher cell viability after freeze-drying and the long-lasting resistance to heat (60 °C) as well as higher antimicrobial activities against some of fish and human pathogens among isolated strains. For heat adaptation, E. faecium HL7 cells were exposed to 52 °C for 15 min. After adaption, slight decreases of unsaturated membrane fatty acid ratios were confirmed through fatty acid analysis. Upon subsequent exposure to various stress conditions such as H₂O₂ (0.01%), ethanol (20%), acid (pH 3), and alkali (pH 12), the survival rate of heat-adapted HL7 was 10³-10⁵-fold higher than that of non-adapted one. These results highlight the potential of preconditioning treatments for maximizing survival of probiotic bacteria during development of probiotic functional foods. The cross-protection afforded by acid against thermal stress may indicate that certain common protective mechanisms are induced by both heat and acid stress. These results can be applied to enhancing the cell viability during live cell formulation of E. faecium HL7 to be used as a potential probiotics in aquaculture.

The role of bacterial cell envelope structures in acid stress resistance in E. coli

Acid resistance (AR) is an indispensable mechanism for the survival of neutralophilic bacteria, such as Escherichia coli (E. coli) strains that survive in the gastrointestinal tract. E. coli acid tolerance has been extensively studied during past decades, with most studies focused on gene regulation and mechanisms. However, the role of cell membrane structure in the context of acid stress resistance has not been discussed in depth. Here, we provide a comprehensive review of the roles and mechanisms of the E. coli cell envelope from different membrane components, such as membrane proteins, fatty acids, chaperones, and proton-consuming systems, and particularly focus on the innovative effects revealed by recent studies. We hope that the information guides us to understand the bacterial survival strategies under acid stress and to further explore the AR regulatory mechanisms to prevent or treat E. coli and other related Gram-negative bacteria infection, or to enhance the AR of engineering E. coli.

Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex

The hexameric MoxR AAA+ ATPase RavA and the decameric lysine decarboxylase LdcI form a 3.3 MDa cage, proposed to assist assembly of specific respiratory complexes in E. coli. Here, we show that inside the LdcI-RavA cage, RavA hexamers adopt an asymmetric spiral conformation in which the nucleotide-free seam is constrained to two opposite orientations. Cryo-EM reconstructions of free RavA reveal two co-existing structural states: an asymmetric spiral, and a flat C2-symmetric closed ring characterised by two nucleotide-free seams. The closed ring RavA state bears close structural similarity to the pseudo two-fold symmetric crystal structure of the AAA+ unfoldase ClpX, suggesting a common ATPase mechanism. Based on these structures, and in light of the current knowledge regarding AAA+ ATPases, we propose different scenarios for the ATP hydrolysis cycle of free RavA and the LdcI-RavA cage-like complex, and extend the comparison to other AAA+ ATPases of clade 7.