Ecology and Function of the Transmissible Locus of Stress Tolerance in Escherichia coli and Plant-Associated Enterobacteriaceae

When the going gets tough, the tough get going-Novel bacterial AAA+ disaggregases provide extreme heat resistance

Heat stress can lead to protein misfolding and aggregation, potentially causing cell death due to the loss of essential proteins. Bacteria, being particularly exposed to environmental stress, are equipped with disaggregases that rescue these aggregated proteins. The bacterial Hsp70 chaperone DnaK and the ATPase associated with diverse cellular activities protein ClpB form the canonical disaggregase in bacteria. While this combination operates effectively during physiological heat stress, it is ineffective against massive aggregation caused by temperature-based sterilization protocols used in the food industry and clinics. This leaves bacteria unprotected against these thermal processes. However, bacteria that can withstand extreme, man-made stress conditions have emerged. These bacteria possess novel ATPase associated with diverse cellular activities disaggregases, ClpG and ClpL, which are key players in extreme heat resistance. These disaggregases, present in selected Gram-negative or Gram-positive bacteria, respectively, function superiorly by exhibiting increased thermal stability and enhanced threading power compared to DnaK/ClpB. This enables ClpG and ClpL to operate at extreme temperatures and process large and tight protein aggregates, thereby contributing to heat resistance. The genes for ClpG and ClpL are often encoded on mobile genomic islands or conjugative plasmids, allowing for their rapid spread among bacteria via horizontal gene transfer. This threatens the efficiency of sterilization protocols. In this review, we describe the various bacterial disaggregases identified to date, characterizing their commonalities and the specific features that enable these novel disaggregases to provide stress protection against extreme stress conditions.

Influence of the Antibiotic Oxytetracycline on the Morphometric Characteristics and Endophytic Bacterial Community of Lettuce (Lactuca sativa L.)

Antibiotics enter the soil with compost prepared from livestock manures and other sources. There is concern that they may influence plant growth and cause antibiotic resistance in soil and plant endospheric microbiomes. In the present work, lettuce plants were cultivated in soil and hydroponics spiked with oxytetracycline (0, 15, and 300 mg × kg-1 and 0, 15, and 50 mg × L-1, respectively) during a 28-day greenhouse experiment. It was revealed that the antibiotic reduced the chlorophyll content, the biomass, and the length of the roots and stems by 1.4-4.7, 1.8-39, 2.5-3.2, and 1.8-6.3 times in soil and in hydroponics. The copy numbers of the tet(A) and tet(X) genes were revealed to be 4.51 × 103-1.58 × 105 and 8.36 × 106-1.07 × 108 copies × g-1, respectively, suggesting the potential migration of these genes from soil/hydroponics to plant roots and leaves. According to a non-metric multidimensional scaling (NMDS) analysis of the 16S rRNA amplicon sequencing data, endospheric bacterial communities were similar in leaves and roots independent of the growing substrate and antibiotic concentration. While soil bacterial communities were unaffected by the presence of antibiotics, hydroponic communities exhibited dependency, likely attributable to the absence of the mitigating effect of soil particle absorption.

Association of resistance to quaternary ammonium compounds and organic acids with genetic markers and their relationship to Escherichia coli serogroup

Sanitizer resistance is being extensively investigated due to the potential for bacterial survival and cross-resistance with other antimicrobials. Similarly, organic acids are being used due to their microbial inactivation potential as well as being generally recognized as safe (GRAS). However, little is known about associations of genetic and phenotypic factors in Escherichia coli related to resistance to sanitizers and organic acids as well as differences between "Top 7" serogroups. Therefore, we investigated 746 E. coli isolates for resistance to lactic acid and two commercial sanitizers based on quaternary ammonium and peracetic acid. Furthermore, we correlated resistance to several genetic markers and investigated 44 isolates using Whole Genome Sequencing. Results indicate that factors related to motility, biofilm formation, and Locus of Heat Resistance played a role in resistance to sanitizers and lactic acid. In addition, Top 7 serogroups significantly differed in sanitizer and acid resistance, with O157 being the most consistently resistant to all treatments. Finally, mutations in rpoA, rpoC, and rpoS genes were observed, in addition to presence of a Gad gene with alpha-toxin formation in all O121 and O145 isolates, which may be related to increased resistance of these serogroups to the acids used in the present study.

Heat-resistant and biofilm-forming Escherichia coli in pasteurized milk from Brazil

Escherichia coli harboring a transmissible locus of stress tolerance (tLST) and the ability to form biofilms represent a serious risk in dairy production. Thus, we aimed to evaluate the microbiological quality of pasteurized milk from two dairy producers in Mato Grosso, Brazil, with a focus on determining the possible presence of E. coli with heat resistance (60 °C/6 min), biofilm-forming potential phenotypes and genotypes, and antimicrobial susceptibility. For this, fifty pasteurized milk samples from producers named A and B were obtained for 5 weeks to investigate the presence of Enterobacteriaceae members, coliforms, and E. coli. For heat resistance, E. coli isolates were exposed to a water bath at 60 °C for 0 and 6 min. In antibiogram analysis, eight antibiotics belonging to six antimicrobial classes were analyzed. The potential to form biofilms was quantified at 570 nm, and curli expression by Congo Red was analyzed. To determine the genotypic profile, we performed PCR for the tLST and rpoS genes, and pulsed-field gel electrophoresis (PFGE) was used to investigate the clonal profile of the isolates. Thus, producer A presented unsatisfactory microbiological conditions regarding Enterobacteriaceae and coliforms for weeks 4 and 5, while all samples analyzed for producer B were contaminated at above-the-limit levels established by national and international legislation. These unsatisfactory conditions enabled us to isolate 31 E. coli from both producers (7 isolates from producer A and 24 isolates from producer B). In this way, 6 E. coli isolates (5 from producer A and 1 from producer B) were highly heat resistant. However, although only 6 E. coli showed a highly heat-resistant profile, 97% (30/31) of all E. coli were tLST-positive. In contrast, all isolates were sensitive to all antimicrobials tested. In addition, moderate or weak biofilm potential was verified in 51.6% (16/31), and the expression of curli and presence of rpoS was not always related to this biofilm potential. Therefore, the results emphasize the spreading of heat-resistant E. coli with tLST in both producers and indicate the biofilm as a possible source of contamination during milk pasteurization. However, the possibility of E. coli producing biofilm and surviving pasteurization temperatures cannot be ruled out, and this should be investigated.

Distribution of Extremely Heat-Resistant Escherichia coli in the Beef Production and Processing Continuum

Understanding the dynamics of stress-resistant Escherichia coli (E. coli) across the meat production and processing continuum is important for tracking sources of such microbes and devising effective modes of control. The Locus of Heat Resistance (LHR) is a ∼14-19 Kb genetic element imparting extreme heat resistance (XHR) in Enterobacteriaceae. It has been hypothesized that thermal and antimicrobial interventions applied during meat processing may select for LHR⁺E. coli. Thus, our goal was to study the prevalence and molecular biology of LHR⁺E. coli among lots of beef cattle (n = 3) from production through processing. Two hundred thirty-two generic E. coli isolated from the same animals through seven stages of the beef processing continuum (cattle in feedyards to packaged strip loins) were examined. LHR⁺E. coli were rare (0.6%; 1 of 180) among the early stages of the beef continuum (feces and hides at feedlot, feces and hides at harvest, and preevisceration carcasses), whereas the prevalence of LHR⁺E. coli on final carcasses and strip loins was remarkably higher. Half (14 of 28) of the final carcass E. coli possessed the LHR, while 79.2% (19 of 24) of the strip loin E. coli did. Eighty-five percent (29 of 34) of the LHR⁺E. coli presented with the XHR phenotype. The selection or enrichment of LHR⁺E. coli from harvest steps to the final products appeared unlikely as the LHR⁺E. coli isolates were effectively controlled by antimicrobial interventions typically used during beef processing. Further, whole-genome sequencing of the isolates suggested LHR⁺E. coli are persisting in the chilled processing environment and that horizontal LHR transfer among E. coli isolates may take place.

Whole-Genome Sequencing Analyses of Heat-Resistant Escherichia coli Isolated from Brazilian Beef

Four Escherichia coli isolates with moderate or high heat resistance were sequenced. Through sequencing, truncated transmissible locus of stress tolerance (tLST) variants tLST1 and tLSTa were identified in the three isolates. The most identified tLST genes (clpK and hsp) are responsible for the homeostasis module.

Genetic Characteristics of the Transmissible Locus of Stress Tolerance (tLST) and tLST Harboring Escherichia coli as Revealed by Large-Scale Genomic Analysis

The transmissible locus of stress tolerance (tLST) confers resistance to multiple stresses in E. coli. Utilizing 18,959 E. coli genomes available in the NCBI database, we investigated the prevalence, phylogenetic distribution, and configuration patterns of tLST, and correlations between tLST, and virulence and antimicrobial resistance (AMR) genes in E. coli. Four tLST variants were found in 2.7% of E. coli, with the most prevalent (77.1%) variant being tLST1 followed by tLST2 (8.3%), tLST3b (8.3%) and tLST3a (6.3%). The majority (93%) of those tLST were in E. coli belonging to phylogroup A in which the prevalence was 10.4%. tLST was also found in phylogroup B1 (0.5%) and C (0.5%) but not found in B2 or D-G. An additional 1% of the 18,959 E. coli genomes harbored tLST fragments to various extent. Phylogenetic analysis revealed both intra- and interspecies transmission of both chromosomal and plasmid-borne tLST, with E. coli showing a preference of chromosomal over plasmid-borne tLST. The presence of tLST and virulence genes in E. coli was overall negatively correlated, but tLST was found in all genomes of a subgroup of enterotoxigenic E. coli (ST2332). Of note, no Shiga toxin-producing E. coli (n = 3,492) harbored tLST. The prevalence of tLST and AMR genes showed different temporal trends over the period 1985 to 2019. However, a substantial fraction of tLST positive E. coli harbor AMR genes, posing a threat to public health. In conclusion, this study improves our understanding of the genetic characteristics of tLST and E. coli harboring tLST. IMPORTANCE This study, through a large-scale genomic analysis, demonstrated that the genomic island tLST related to multiple stress resistance (such as extreme heat resistance and oxidative stress tolerance) in E. coli is differentially present in subgroups of E. coli and is strongly associated with certain phylogenetic background of the host strain. The study also shows the transmission mechanisms of tLST in E. coli and other bacterial species. The overall negative association of tLST, and virulence genes and antimicrobial (AMR) genes suggest the selective pressures for the acquisition and transmission of these traits likely differ. Even so, the high prevalence of tLST in the enterotoxigenic E. coli clone ST2332 and co-occurrence of tLST and AMR genes in E. coli are concerning. Thus, the findings better our understanding of tLST evolution and provide information for risk assessment of tLST harboring bacteria.

Coated Zinc Oxide Improves Growth Performance of Weaned Piglets via Gut Microbiota

Weaned piglets stayed in transitional stages of internal organ development and external environment change. The dual stresses commonly caused intestinal disorders followed by damaged growth performance and severe diarrhea. High dose of zinc oxide could improve production efficiency and alleviate disease status whereas caused serious environmental pollution. This research investigated if coated ZnO (C_ZnO) in low dose could replace the traditional dose of ZnO to improve the growth performance, intestinal function, and gut microbiota structures in the weaned piglets. A total of 126 cross-bred piglets (7.0 ± 0.5 kg body weight) were randomly allocated into three groups and fed a basal diet or a basal diet supplemented with ZnO (2,000 mg Zn/kg) or C_ZnO (500 mg Zn/kg), respectively. The test lasted for 6 weeks. C_ZnO improved average daily gain (ADG) and feed efficiency, alleviated diarrhea, decreased the lactulose/mannitol ratio (L/M) in the urine, increased the ileal villus height, and upregulated the expression of Occludin in the ileal tissue and the effect was even better than a high concentration of ZnO. Importantly, C_ZnO also regulated the intestinal flora, enriching Streptococcus and Lactobacillus and removing Bacillus and intestinal disease-associated pathogens, including Clostridium_sensu_stricto_1 and Cronobacter in the ileal lumen. Although, colonic microbiota remained relatively stable, the marked rise of Blautia, a potential probiotic related to body health, could still be found. In addition, C_ZnO also led to a significant increase of acetate and propionate in both foregut and hindgut. Collectively, a low concentration of C_ZnO could effectively promote growth performance and reduce diarrhea through improving small intestinal morphology and permeability, enhancing the barrier function, adjusting the structure of gut microbiota, and raising the concentration of short-chain fatty acids (SCFAs) in the weaned piglets.