Escherichia coli O157:H7: animal reservoir and sources of human infection

High frequency of multidrug-resistant Escherichia coli from cattle in the Cerrado and Pantanal biomes of Brazil

The indiscriminate use of antimicrobials has led to the emergence of resistant bacteria, especially pathogenic strains of Escherichia coli, which are associated with diseases in animals and humans. The aim of the present study was to characterize E. coli isolates in calves with regards to the presence of virulence genes and investigate the resistance of the isolates to different antimicrobials. Between 2021 and 2023, 456 fecal samples were collected from calves in the Pantanal and Cerrado biomes of the state of Mato Grosso do Sul, Brazil. All samples were subjected to microbiological analysis and disc diffusion antibiogram testing. The polymerase chain reaction method was used to detect virulence genes. Bacterial growth was found in 451 of the 456 samples and biochemically identified as Escherichia coli. All 451 isolates (100 %) exhibited some phenotypic resistance to antimicrobials and 67.62 % exhibited multidrug resistance. The frequency of multidrug-resistant isolates in the Cerrado biome was significantly higher than that in the Pantanal biome (p = 0.0001). In the Cerrado, the most common pathotype was Shiga toxin-producing Escherichia coli (STEC) (28 %), followed by toxigenic Escherichia coli (ETEC) (11 %), enterohemorrhagic Escherichia coli (EHEC) (8 %) and enteropathogenic Escherichia coli (EPEC) (2 %). In most cases, the concomitant occurrence of pathotypes was more common, the most frequent of which were ETEC + STEC (33 %), ETEC + EHEC (15 %) and ETEC + EPEC (3 %). The STEC pathotype (30 %) was also found more frequently in the Pantanal, followed by EHEC (12 %), ETEC (9 %) and EPEC (6 %). The STEC pathotype had a significantly higher frequency of multidrug resistance (p = 0.0486) compared to the other pathotypes identified. The frequency of resistance was lower in strains from the Pantanal biome compared to those from the Cerrado biome. Although some factors are discussed in this paper, it is necessary to clarify the reasons for this difference and the possible impacts of these findings on both animal and human health in the region.

Selective bacteriophages reduce the emergence of resistant bacteria in bacteriophage-antibiotic combination therapy

Escherichia coli O157:H7 is a globally important foodborne pathogen with implications for food safety. Antibiotic treatment for O157 may potentially contribute to the exacerbation of hemolytic uremic syndrome, and the increasing prevalence of antibiotic-resistant strains necessitates the development of new treatment strategies. In this study, the bactericidal effects and resistance development of antibiotic and bacteriophage monotherapy were compared with those of combination therapy against O157. Experiments involving continuous exposure of O157 to phages and antibiotics, along with genetic deletion studies, revealed that the deletion of glpT and uhpT significantly increased resistance to fosfomycin. Furthermore, we found that OmpC functions as a receptor for the PP01 phage, which infects O157, and FhuA functions as a receptor for the newly isolated SP15 phage, targeting O157. In the glpT and uhpT deletion mutants, additional deletion in ompC, the receptor for the PP01 phage, increased resistance to fosfomycin. These findings suggest that specific phages may contribute to antibiotic resistance by selecting the emergence of gene mutations responsible for both phage and antibiotic resistance. While combination therapy with phages and antibiotics holds promise for the treatment of bacterial infections, careful consideration of phage selection is necessary.IMPORTANCEThe combination treatment of fosfomycin and bacteriophages against Escherichia coli O157 demonstrated superior bactericidal efficacy compared to monotherapy, effectively suppressing the emergence of resistance. However, mutations selected by phage PP01 led to enhanced resistance not only to the phage but also to fosfomycin. These findings underscore the importance of exercising caution in selecting phages for combination therapy, as resistance selected by specific phages may increase the risk of developing antibiotic resistance.

Escherichia coli isolates from vegetable farms in Addis Ababa, Ethiopia: Antimicrobial susceptibility profile and associated resistance genetic markers

The use of animal manure to fertilize soil is an emerging concern contributing to the transfer of antimicrobial-resistant pathogens to vegetables. Hence, assessing antimicrobial susceptibility profile of Escherichia coli in vegetable farms is essential to design appropriate interventions against antimicrobial resistance (AMR) in the food chain. This study assessed antimicrobial resistance profile and associated genetic markers among E. coli isolated from vegetable farms fertilized with animal manure in Addis Ababa, Ethiopia. A total of 1044 samples were collected using convenience sampling: soil (n = 271), manure (n = 375), and vegetables (n = 398) from 81 vegetable farms in Addis Ababa, Ethiopia. Antimicrobial susceptibility test was conducted for 100 E. coli isolates and antimicrobial resistance genes (ARGs) were tested by polymerase chain reaction (PCR). Of the 1044 collected samples, 25.3% were positive for E. coli, with significantly higher prevalence in the manure sample and samples collected from Akaki Kality sub-city (p < .05). The highest resistance rate was recorded for tetracycline (72%), followed by streptomycin (63%), and sulfamethoxazole +trimethoprim (56%). Multidrug resistance was detected in 61% of the E. coli isolates. The aac(3)-IV (76.9%), bla TEM (65.4%), aadA (60.3%), tet(A) (58.3%), and sulI (51.7%) were the commonly detected resistance genes. The current study showed a high burden of antimicrobial resistance among E. coli isolated from manure-amended vegetable farms, with potential of playing a significant role in the dissemination of antimicrobial resistance in the food chain. Efforts should be made to reduce the burden of resistant organisms and ARGs through prudent use of antimicrobials in livestock and application of appropriate composting techniques before using manure as fertilizer.

Two synonymous single-nucleotide polymorphisms promoting fluoroquinolone resistance of Escherichia coli in the environment

Single-nucleotide polymorphism (SNP) is one of the core mechanisms that respond to antibiotic resistance of Escherichia coli (E. coli), which is a major issue in environmental pollution. A specific type of SNPs, synonymous SNPs, have been generally considered as the "silent" SNPs since they do not change the encoded amino acid. However, the impact of synonymous SNPs on mRNA splicing, nucleo-cytoplasmic export, stability, and translation was gradually discovered in the last decades. Figuring out the mechanism of synonymous SNPs in regulating antibiotic resistance is critical to improve antimicrobial therapy strategies in clinics and biological treatment strategies of antibiotic-resistant E. coli-polluted materials. With our newly designed antibiotic resistant SNPs prediction algorithm, Multilocus Sequence Type based Identification for Phenotype-single nucleotide polymorphism Analysis (MIPHA), and in vivo validation, we identified 2 important synonymous SNPs 522 G>A and 972 C>T, located at hisD gene, which was previously predicted as a fluoroquinolone resistance-related gene without a detailed mechanism in the E. coli samples with environmental backgrounds. We first discovered that hisD causes gyrA mutation via the upregulation of sbmC and its downstream gene umuD. Moreover, those 2 synonymous SNPs of hisD cause its own translational slowdown and further reduce the expression levels of sbmC and its downstream gene umuD, making the fluoroquinolone resistance determining region of gyrA remains unmutated, ultimately causing the bacteria to lose their ability to resist drugs. This study provided valuable insight into the role of synonymous SNPs in mediating antibiotic resistance of bacteria and a new perspective for the treatment of environmental pollution caused by drug-resistant bacteria.

Molecular detection and antibiogram of Shiga toxin-producing Escherichia coli (STEC) from raw milk in and around Bahir Dar town dairy farms, Ethiopia

Illnesses associated with consuming infected milk and milk products are a widespread problem in low and middle-income countries. Shiga toxin-producing Escherichia coli (STEC) is a bacterium commonly found in raw milk and causes foodborne diseases ranging from mild diarrhea to severe hemorrhagic colitis and hemolytic uremic syndrome. This study aimed to investigate the virulence gene and antimicrobial resistance profiles of Shiga toxin-producing E. coli strains isolated from raw milk in dairy farms in and around Bahir Dar town. Raw milk samples (n = 128) collected from December 2021 to July 2022 were cultured, and E. coli strains were isolated using standard methods. Shiga toxin-producing E. coli strains were identified genotypically by the presence of the virulence markers using a single-plex polymerase chain reaction. The antibiotic susceptibility testing of Shiga toxin-producing E. coli isolates was done by the agar disk diffusion method. In total, 32 E. coli isolates were recovered from milk samples from lactating animals. PCR screening of these isolates resulted in 19 (59.3%) positives for Shiga toxin-producing E. coli. The stx2 gene was detected in 53% of cases, followed by stx1 (31%) and eae (16%. The STEC isolates were highly sensitive to ciprofloxacin (94.7%) and kanamycin (89.5%), while exhibiting significant resistance to amoxicillin (89.5%) and streptomycin (73.7%). The present study points out the occurrence of virulent and antibiotic-resistant Shiga toxin-producing E. coli strains in raw milk that could pose a potential risk to public health. Further analysis by whole genome sequencing is necessary for an in-depth assessment and understanding of their virulence and resistance factors. Moreover, large-scale studies are needed to identify the prevalence and potential risk factors and to prevent the spread of antibiotic-resistant STEC strains in the milk production chain.

Three different routes of EHEC O157:H7 infection were used to establish EHEC broiler model

In order to study the prevention and control EHEC disease measures in poultry, the infection process and development of this disease and the pathological changes of various organs were to be observed. In this study, chickens were infected with different doses of enterohemorrhagic Escherichia coli (EHEC) O157:H7 using different routes of administration to establish EHEC broiler model. A total of 195 14-day-old broilers were randomly divided into 13 groups: including control group, Enema-drip groups (1010, 1011, 1012, 1013 CFUs E. coli O157:H7), gavage groups (P.O) (1011, 1012, 1013, 1014 CFUs E. coli O157:H7), and intraperitoneal injection group (I.P.) (108, 109, 1010, 1011 CFUs E. coli O157:H7). Escherichia coli (E. coli) was given using enema-drip, gavage or intraperitoneal infection. Then the feed intake, weight changes, stool and clinical symptoms of the chicks were recorded during the experiment. 7 d after E. coli infection, blood was collected from the jugular vein and serological tests were carried out. The liver, spleen, and colon of the chicks were extracted to get the organ index, bacteria load, and their histopathological changes. After infection with E. coli, some chicks feces were green or red watery stool, sometimes accompanied by foam, and the material to weight ratio of broilers in I.P. group increased significantly (P < 0.05), the 108 CFUs group were 1.3 times as large as control group. Three modeling methods can result in abnormal serum lipid metabolism and liver function indexes (increase of AST, TBA, T-Bil and TC level; decrease of ALB, TG, and TP level). Infection of chicks with O157:H7 by all 3 methods resulted in its detection in the liver, spleen, and colon. Three modeling methods significantly decreased liver index, and inflammatory cell infiltration and hyperemia were observed in liver. The spleen index in E. coli broilers by gavage and enema-drip was significantly decreased, splenic hyperemia and periarteriolar hyalinosis were observed. The spleen was enlarged with purplish-black spheroids in I.P. group broilers, and the spleen histological changes was more serious. The colon villi of broilers in gavage and enema-drip groups were thinner, more prone to rupture, intestinal lamina propria hyperemia, and inflammatory cell infiltration. Moreover, the number of goblet cells in the mucosal epithelium increased. E. coli O157:H7 can induce liver, spleen and intestinal damage and reduce growth performance of chicks. By comparing these 3 methods, we found that chicks infected with O157:H7 by gavage had more severe liver and intestinal damage, the enema-drip method caused most serious intestinal damage, and I.P. method significantly damaged the liver and spleen of chickens.

Epidemiology of multidrug-resistant zoonotic E. coli from beef processing and retail points in Delta State, Nigeria: Public health implications

Some sorbitol non-fermenting E. coli (SN-F E. coli) and all E. coli O157 are zoonotic. Contamination of beef with zoonotic E. coli at the processing or retail point is a significant public health problem. Despite the public health importance of these organisms, there is no published data on the prevalence and antimicrobial resistance (AMR) of zoonotic E. coli from Delta State, Nigeria. Consequently, this study determined the prevalence and AMR of SN-F E. coli and E. coli O157 isolates from meat contact surfaces at the processing and retail points in the study area. The isolation, biochemical and serological characterisations and AMR status of the isolates were performed following standard microbiological methods. Overall prevalence of SN-F E. coli and E. coli O157 were 13.8% (56/406) and 1.5% (6/406), respectively. Majority of the 56 SN-F E. coli (64.3%, 36/56) and all the six E. coli O157 (10.7%, 6/56) detected in this study were found at the meat processing points. Most of the SN-F E. coli were isolated at the slaughterhouse floor (31%), meat hooks (17.2%) and meat sellers' knives (17.2%). The SN-F E. coli exhibited greater AMR to ampicillin (67.9%), gentamycin (64.3%) and tetracycline (50%) than other antimicrobial agents tested. No isolate was resistant to aztreonam. All six E. coli O157 isolates were resistant to enrofloxacin. Overall, 23 AMR patterns, comprised 14 from meat processing points and nine from meat retailing points, were observed from the 56 antimicrobial-resistant SN-F E. coli isolates. All the six E. coli O157 and 73.2% (41/56) of the SN-F E. coli isolates were multidrug-resistant. An overall mean multiple antimicrobial resistance index of 0.6 was recorded. Multidrug-resistant zoonotic E. coli were detected at meat processing and retail points in Delta State, Nigeria. The findings warrant the adoption of One Health control approach, "farm to fork" principle of food safety and prudent use of antimicrobial agents in animal agriculture. These may help to limit beef contamination with multidrug-resistant zoonotic E. coli at the processing and retailing points, for public health safety.

Escherichia coli and their potential transmission of carbapenem and colistin-resistant genes in camels

BACKGROUND

Camels harbouring multidrug-resistant Gram-negative bacteria are capable of transmitting various microorganisms to humans. This study aimed to determine the distribution of anti-microbial resistance among Escherichia coli (E. coli) isolated from the feces of apparently healthy camels in Egyptian abattoirs. Additionally, we sought to characterize Shiga toxin-producing E. coli (STEC) strains, assess their virulence potential, and investigate the possibility of camels spreading carbapenem- and colistin-resistant E. coli.

METHODS

121 fecal swaps were collected from camels in different abattoirs in Egypt. Isolation and identification of E. coli were performed using conventional culture techniques and biochemical identification. All isolates obtained from the examined samples underwent genotyping through polymerase chain reaction (PCR) of the Shiga toxin-encoding genes (Stx1 and Stx2), the carbapenemase-encoding genes (blaKPC, blaOXA-48, blaNDM, and blaVIM), and the mcr genes for mcr-1 to mcr-5.

RESULT

Bacteriological examination revealed 75 E. coli isolates. PCR results revealed that one strain (1.3%) tested positive for Stx1, and five (6.6%) were positive for Stx2. Among the total 75 strains of E. coli, the overall prevalence of carbapenemase-producing E. coli was 27, with 7 carrying blaOXA48, 14 carrying blaNDM, and 6 carrying blaVIM. Notably, no strains were positive for blaKPC but a high prevalence rate of mcr genes were detected. mcr-1, mcr-2, mcr-3, and mcr-4 genes were detected among 3, 2, 21, and 3 strains, respectively.

CONCLUSION

The results indicate that camels in Egypt may be a primary source of anti-microbial resistance (AMR) E. coli, which could potentially be transmitted directly to humans or through the food chain.

Genome sequence of Shiga toxin-producing Escherichia coli jumbo bacteriophage vB_EcoM_JNE01

Bacteriophage vB_EcoM_JNE01 was isolated from chicken farm sewage using Escherichia coli O157:H7 as the host bacteria. The total length of the vB_EcoM_JNE01 genome is 355,583 bp, with 584 open reading frames and 36% G+C content. It shares an 80% nucleotide identity with 59% query coverage with the bacteriophage PBECO4 (NC_027364).

Animal and environmental risk factors for sporadic Shiga toxin-producing Escherichia coli (STEC) infection in England: a case control study for O157, O26 and other STEC serotypes

Most Shiga toxin-producing E. coli (STEC) infections are sporadic. Routine enhanced surveillance questionnaires of confirmed STEC cases in England contained promising data to conduct a case-control study to identify non-food exposures linked to the risk of becoming infected with different STEC serotypes, including O157, O26 and all others; this study pulled eligible cases from the recorded enhanced surveillance data. Controls were recruited from the general population and answered a comparable postal questionnaire. Logistic regression was performed to identify risk factors associated with STEC infection for O157, O26 and other serotype cases. In adjusted models, travel outside of the U.K. and childcare occupations raised the risk of infection for all serotypes. Day trips within the UK, exposure to dogs and contact with soil were linked to lower infection risk. Resident region within England was often linked to decreased risk. Summer season was linked to O157 and O26, but not other STEC. Swimming in the sea was linked to increased risk of infection by O157, but not other types of STEC. Correlations between exposures and infection were similar when the analysis was repeated excluding participants with a history of foreign travel. As the first case-control study in England to include sporadic non-O157 STEC, the varying risk factors between O157 and non-O157 cases suggest there are potentially unique reservoirs for different serotypes.

Comparative evaluation of antimicrobial activity of human granulysin, bovine and porcine NK-lysins against Shiga toxin-producing Escherichia coli O157:H7

Shiga toxin-producing Escherichia coli (STEC) O157:H7 (O157) is a foodborne pathogen causing human disease ranging from hemorrhagic colitis and hemolytic uremic syndrome to kidney failure, while remaining harmless to cattle, its primary reservoir. The severity of the human disease associated mainly with Shiga toxin production and a global emergence of antibiotic resistant STEC highlights the need for effective non-antibiotic, pre-harvest strategies to reduce O157 in cattle, the principal source of human infection. Towards this goal three synthetic antimicrobial peptides (AMPs): human granulysin (hGRNL), bovine NK-lysin (bNK2A), and porcine NK-lysin (pNKL), were tested in vitro against O157 isolates. As expected, circular dichroism spectroscopy findings were consistent with a predominantly α-helical conformation for all three AMPs in an environment mimicking bacterial outer surface or liposaccharides. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations of hGRNL (200 μM), bNK2A (12.5 μM against strain 86-24 and 25 μM against EDL933), and pNKL (6.25 μM) were determined using the Clinical and Laboratory Standards Institute broth microdilution method in Müeller-Hinton broth (cation-adjusted). The bNK2A and pNKL AMPs did not induce Shiga toxin expression in O157 at MIC, as there was a significant decrease or no change in toxin expression following 4- or 20 h incubation with the AMPs; bNK2A p <0.0001 (4 h) and p = 0.4831 (20 h); pNKL p <0.0001 (4 h) and p = 0.0001 (20 h). Propidium iodide uptake assay revealed faster O157 membrane damage or killing kinetics with bNK2A and pNKL compared to hGRNL. Nonetheless, transmission electron microscopy demonstrated that all three AMPs mediated damage to O157 membranes. In contrast, the three AMPs showed minimal cytotoxicity (<2%) against cattle red blood cells at tested concentrations (0.39-50 μM). Overall, our results demonstrate the potential for bNK2A and pNKL to be further developed into novel non-antibiotic agents to reduce O157 shedding in cattle.

Molecular Characterization of Cryptosporidium spp., Giardia duodenalis, Enterocytozoon bieneusi and Escherichia coli in Dairy Goat Kids with Diarrhea in Partial Regions of Shaanxi Province, China

Cryptosporidium spp., Giardia duodenalis, Enterocytozoon bieneusi and Escherichia coli are important diarrheal pathogens threatening the health of humans and various animals. Goats, especially pre-weaned goat kids, that carry these pathogens are important reservoirs related to human infection. In the present study, PCR-based sequencing techniques were applied to characterize Cryptosporidium spp., G. duodenalis, E. bieneusi and E. coli in 202 fecal samples of diarrheal kids for Guanzhong dairy goats from five locations in Shaanxi Province. The positive rates of Cryptosporidium spp., G. duodenalis, E. bieneusi and E. coli were 37.6% (76/202), 16.3% (33/202), 55.4% (112/202) and 78.7% (159/202) in these goat kids, respectively. Co-infection of two to four pathogens was found in 114 of 202 fecal samples. Significant differences (p < 0.001) in the positive rates of Cryptosporidium spp. and G. duodenalis were found among locations and age groups. Furthermore, two Cryptosporidium species (C. parvum and C. xiaoi), two G. duodenalis assemblages (E and A), nine E. bieneusi genotypes (CHG3, CHG1, BEB6, CHG5, CHG2, SX1, CHG28, COS-II and CD6) and two E. coli pathotypes (EPEC and EHEC) were identified. As for Cryptosporidium, two (IIdA19G1 and IIdA19G2) and two (XXIIIa and XXIIIg) subtypes were recognized in samples positive for C. parvum and C. xiaoi, respectively. A phylogenetic analysis based on the ITS locus of E. bieneusi indicated that all nine genotypes of E. bieneusi identified in this study belonged to the group 2. Four virulence factors (ehxA, eae, stx2 and stx1) of EPEC and EHEC were found in E. coli strains. Collectively, this study explored the colonization frequency of Cryptosporidium spp., G. duodenalis, E. bieneusi and E. coli in diarrheal kids of Guanzhong dairy goats in Shaanxi Province and expanded our understanding of the genetic composition and zoonotic potential of these pathogens in goats.

Highly catalytic and stable Au@AuPt nanoparticles for visual and quantitative detection of E. coli O157:H7

A visual and quantitative ELISA-like method for Escherichia coli O157:H7 is developed based on highly catalytic and stable Au@AuPt nanoparticles. The proposed enhanced ELISA method can visually detect 100 CFU mL-1 O157:H7 with high specificity and without the need for strict low-temperature reagent storage, thereby increasing the utility. Moreover, it is applicable to spiked tap water and milk tea samples without additional treatments.

Prevalence of Shiga Toxin-Producing Escherichia coli O157 in Wild Scottish Deer with High Human Pathogenic Potential

Shiga toxin-producing E. coli (STEC) infections associated with wildlife are increasing globally, highlighting many 'spillover' species as important reservoirs for these zoonotic pathogens. A human outbreak of STEC serogroup O157 in 2015 in Scotland, associated with the consumption of venison meat products, highlighted several knowledge gaps, including the prevalence of STEC O157 in Scottish wild deer and the potential risk to humans from wild deer isolates. In this study, we undertook a nationwide survey of wild deer in Scotland and determined that the prevalence of STEC O157 in wild deer is low 0.28% (95% confidence interval = 0.06-0.80). Despite the low prevalence of STEC O157 in Scottish wild deer, identified isolates were present in deer faeces at high levels (>104 colony forming units/g faeces) and had high human pathogenic potential based on whole genome sequencing and virulence gene profiling. A retrospective epidemiological investigation also identified one wild deer isolate from this study as a possible source of a Scottish human outbreak in 2017. These results emphasise the importance of food hygiene practices during the processing of wild deer carcasses for human consumption.

Isolation and pathogenicity evaluation of Escherichia coli O157:H7 from common carp, Cyprinus carpio

Escherichia coli O157:H7 is the primary serotype of enterohaemorrhagic E. coli (EHEC), which can cause diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome. It is considered as a major health concern due to it being a zoonotic disease that is transmitted through food. In this study, a pathogenic bacterium was isolated from infected carp, which identified as E. coli O157:H7 named X21 through genetic sequencing, phylogenetic analysis, physiological and biochemical tests. In the experiment, crucian carp was used as a model to study the pathogenicity of the isolate, the pathological histological observations and cytokines expression of fish tissues were determined after bacterial challenge. The results showed that severe pathological damage observed in the liver, spleen, headkidney of fish infected with isolate X21. Besides, we found that accumulation of IgT+ B cells in the lamina propria of intestine, and up-regulation of SUCH-r, IL-1β, IL-10, IL-11, MyD88, and TNF-α gene in various tissues. After challenged, the survivability of crucian carp infected with isolate X21 stands at a mere 14.27%. To our knowledge, this is the first report that E. coli O157:H7 infected the freshwater fish C. carpio, which indicates that this bacterium is a potential threat to public health and freshwater fish aquaculture.

Epidemiological Characterization of Isolates of Salmonella enterica and Shiga Toxin-Producing Escherichia coli from Backyard Production System Animals in the Valparaíso and Metropolitana Regions

Backyard production systems (BPS) are distributed worldwide, rearing animals recognized as reservoirs of Salmonella enterica and Shiga toxin-producing Escherichia coli (STEC), both zoonotic pathogens. The aim of this study was to characterize isolates of both pathogens obtained from animals raised in BPS from two central Chile regions. The presence of pathogens was determined by bacterial culture and confirmatory PCR for each sampled BPS, calculating positivity rates. Multivariate logistic regression was used to determine risk factors. Additionally, phenotypic antimicrobial resistance was determined. A positivity rate of 2.88% for S. enterica and 14.39% for STEC was determined for the complete study region (Valparaíso and Metropolitana regions). Risk factor analysis suggests that the presence of ruminants (OR = 1.03; 95% CI = 1.002-1.075) increases the risk of STEC-positive BPS, and the presence of ruminants (OR = 1.05; 95% CI = 1.002-1.075) and the animal handlers being exclusively women (OR = 3.54; 95% CI = 1.029-12.193) increase the risk for S. enterica/STEC positivity. Eighty percent of S. enterica isolates were multidrug resistant, and all STEC were resistant to Cephalexin. This study evidences the circulation of multidrug-resistant zoonotic bacterial strains in animals kept in BPS and the presence of factors that modify the risk of BPS positivity for both pathogens.

Effectiveness of Bacteriophages against Biofilm-Forming Shiga-Toxigenic Escherichia coli In Vitro and on Food-Contact Surfaces

(1) Background: Formation of biofilms on food-contact surfaces by Shiga-toxigenic Escherichia coli (STEC) can pose a significant challenge to the food industry, making conventional control methods insufficient. Targeted use of bacteriophages to disrupt these biofilms could reduce this problem. Previously isolated and characterized bacteriophages (n = 52) were evaluated against STEC biofilms in vitro and on food-contact surfaces. (2) Methods: Phage treatments (9 logs PFU/mL) in phosphate-buffered saline were used individually or as cocktails. Biofilms of STEC (O157, O26, O45, O103, O111, O121, and O145) were formed in 96-well micro-titer plates (7 logs CFU/mL; 24 h) or on stainless steel (SS) and high-density polyethylene (HDPE) coupons (9 logs CFU/cm²; 7 h), followed by phage treatment. Biofilm disruption was measured in vitro at 0, 3, and 6 h as a change in optical density (A₅₉₅). Coupons were treated with STEC serotype-specific phage-cocktails or a 21-phage cocktail (3 phages/serotype) for 0, 3, 6, and 16 h, and surviving STEC populations were enumerated. (3) Results: Of the 52 phages, 77% showed STEC biofilm disruption in vitro. Serotype-specific phage treatments reduced pathogen population within the biofilms by 1.9-4.1 and 2.3-5.6 logs CFU/cm², while the 21-phage cocktail reduced it by 4.0 and 4.8 logs CFU/cm² on SS and HDPE, respectively. (4) Conclusions: Bacteriophages can be used to reduce STEC and their biofilms.

Survival of Inoculated Vibrio spp., Shigatoxigenic Escherichia coli, Listeria monocytogenes, and Salmonella spp. on Seaweed (Sugar Kelp) During Storage

Bacteria including Vibrio spp. persist in coastal waters and can contaminate edible seaweeds. Pathogens such as Listeria monocytogenes, shigatoxigenic Escherichia coli (STEC), and Salmonella have been associated with and present serious health risks in minimally processed vegetables including seaweeds. This study evaluated the survival of four pathogens inoculated onto two product forms of sugar kelp subjected to different storage temperatures. The inoculation comprised of a cocktail of two Listeria monocytogenes and STEC strains, two Salmonella serovars, and two Vibrio species. STEC and Vibrio were grown and applied in salt-containing media to simulate preharvest contamination, whereas L. monocytogenes and Salmonella inocula were prepared to simulate postharvest contamination. Samples were stored at 4°C and 10°C for 7 days, and 22°C for 8 h. Microbiological analyses were performed periodically (1, 4, 8, 24 h, etc.) to evaluate the effects of storage temperature on pathogen survival. Pathogen populations decreased under all storage conditions, but survival was greatest for all species at 22°C, with STEC exhibiting significantly less reduction (1.8 log CFU/g) than Salmonella, L. monocytogenes, and Vibrio (3.1, 2.7, and 2.7 log CFU/g, respectively) after storage. The largest population reduction (5.3 log CFU/g) was observed in Vibrio stored at 4°C for 7 days. Regardless of storage temperature, all pathogens remained detectable at the end of the study duration. Results emphasize the need for strict adherence to temperature control for kelp as temperature abuse may support pathogen survival, especially STEC, during storage, and the need for prevention of postharvest contamination, particularly with Salmonella.

Fecal Contamination in the Wastewater Irrigation System and its Health Threat to Wastewater-Based Farming Households in Addis Ababa, Ethiopia

Due to rapidly growing demand, the production of vegetables is increasing along the Akaki Rivers. The objective of this study was to examine the degree of fecal contamination and levels of fecal contamination and dissemination throughout the wastewater irrigation system. Irrigation water, irrigated soil, and leafy vegetables were collected twice during 2 vegetable growing seasons, at the maturity period of the growing season, from 19 sampling points along the 2 Akaki Rivers. Composite samples were taken from all sampling points and E.coli was enumerated. The mean E.coli load in wastewater and non-wastewater sources were 1.1⁶±5.5³ CFU/100 ml and 2.23²±1.29² CFU/100 ml respectively. All counts of E. coli in the wastewater exceeded the WHO's standards indicating that the irrigation water quality was unacceptable. In the wastewater-irrigated and non-wastewater-irrigated soil, the mean E.coli were 3.6² ±1.58² CFU/g and 1.32²±87.1 CFU/g respectively. Meanwhile, the mean E.coli counts on the lettuce and Swiss chard were 78 ± 2 CFU/g and 44 ±3CFU/g respectively. The E.coli count on the leafy vegetables was found to be associated with the E.coli in the wastewater and soil. The production of leafy vegetables using wastewater with unacceptably high levels of E.coli and high occupational exposure introduces high levels of risk to the farming communities and to the consumers. Leafy, low-growing raw edible vegetables need careful treatment during food production and harvesting procedures or activities.

Maternal and/or post-weaning supplementation with Bacillus altitudinis spores modulates the microbial composition of colostrum, digesta and faeces in pigs

This study examined the effects of maternal and/or post-weaning Bacillus altitudinis supplementation on the microbiota in sow colostrum and faeces, and offspring digesta and faeces. Sows (n = 12/group) were assigned to: (1) standard diet (CON), or (2) CON supplemented with probiotic B. altitudinis spores (PRO) from day (d)100 of gestation to weaning (d26 of lactation). At weaning, offspring were assigned to CON or PRO for 28d, resulting in: (1) CON/CON, (2) CON/PRO, (3) PRO/CON, and (4) PRO/PRO, after which all received CON. Samples were collected from sows and selected offspring (n = 10/group) for 16S rRNA gene sequencing. Rothia was more abundant in PRO sow colostrum. Sow faeces were not impacted but differences were identified in offspring faeces and digesta. Most were in the ileal digesta between PRO/CON and CON/CON on d8 post-weaning; i.e. Bacteroidota, Alloprevotella, Prevotella, Prevotellaceae, Turicibacter, Catenibacterium and Blautia were more abundant in PRO/CON, with Firmicutes and Blautia more abundant in PRO/PRO compared with CON/CON. Lactobacillus was more abundant in PRO/CON faeces on d118 post-weaning. This increased abundance of polysaccharide-fermenters (Prevotella, Alloprevotella, Prevotellaceae), butyrate-producers (Blautia) and Lactobacillus likely contributed to previously reported improvements in growth performance. Overall, maternal, rather than post-weaning, probiotic supplementation had the greatest impact on intestinal microbiota.

Bacterial and viral rodent-borne infections on poultry farms. An attempt at a systematic review

Introduction

Rodents are quite common at livestock production sites. Their adaptability, high reproductive capacity and omnivorousness make them apt to become a source of disease transmission to humans and animals. Rodents can serve as mechanical vectors or active shedders of many bacteria and viruses, and their transmission can occur through direct contact, or indirectly through contaminated food and water or by the arthropods which parasitise infected rodents. This review paper summarises how rodents spread infectious diseases in poultry production.

Material and Methods

The aim of this review was to use PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) principles to meta-analyse the available data on this topic. Three databases – PubMed, Web of Science and Scopus – and grey literature were searched for papers published from inception to July 2022 using the established keywords.

Results

An initial search identified 2,999 articles that met the criteria established by the keywords. This number remained after removing 597 articles that were repeated in some databases. The articles were searched for any mention of specific bacterial and viral pathogens.

Conclusion

The importance of rodents in the spread of bacterial diseases in poultry has been established, and the vast majority of such diseases involved Salmonella, Campylobacter, Escherichia coli, Staphylococcus (MRSA), Pasteurella, Erysipelothrix or Yersinia infections. Rodents also play a role in the transmission of viruses such as avian influenza virus, avian paramyxovirus 1, avian gammacoronavirus or infectious bursal disease virus, but knowledge of these pathogens is very limited and requires further research to expand it.

Changes in bacterial diversity, co-occurrence pattern, and potential pathogens following digestate fertilization: Extending pathogen management to field for anaerobic digestion of livestock manure

Digestate can spread pathogens into agroecosystem, posing serious threats to public health. However, the effect of digestate fertilization on digestate- or soil-borne pathogens has not been fully explored. Herein, two settings of microcosm experiment were performed with arable soil and digestate collected at two sites (Beilangzhong or Shunyi) to dissect the succession of the total and potential pathogenic bacterial communities following digestate fertilization. Each experimental setting consisted of three treatments, including digestate aerobically incubated in sterilized soil, and soil amended with sterilized or non-sterilized digestate. Digestate-borne potential pathogenic bacteria were enriched after the aerobic incubation, with Streptococcus sobrinus in the Beilangzhong setting, and Escherichia coli and Enterococcus faecium in the Shunyi setting. Potential soil-borne pathogenic bacteria, such as Acinetobacter lowffii and Pseudomonas fluorescens, were stimulated by the sterilized digestate in the Shunyi setting. Interestingly, S. sobrinus, E. coli, and Ent. faecium did not increase when digestate was amended into the non-sterilized soil, suggesting that soil microorganisms can inhibit the resurgence of these digestate-borne pathogens. A large-scale survey further revealed that organic fertilization exerted a site-dependent effect on different species of potential pathogen, but it did not enrich the total relative abundance of potential pathogenic bacteria in soils. Collectively, these results highlight that pathogen management of anaerobic digestion of livestock manure needs to be extended from anaerobic reactor to field.

Boundaries That Prevent or May Lead Animals to be Reservoirs of Escherichia coli O104:H4

Escherichia coli O104:H4, a hybrid serotype carrying virulence factors from enteroaggregative (EAEC) and Shiga toxin-producing (STEC) pathotypes, is the reported cause of a multicountry outbreak in 2011. Evaluation of potential routes of human contamination revealed that this strain is a foodborne pathogen. In contrast to STEC strains, whose main reservoir is cattle, serotype O104:H4 has not been commonly isolated from animals or related environments, suggesting an inability to naturally colonize the gut in hosts other than humans. However, contrary to this view, this strain has been shown to colonize the intestines of experimental animals in infectious studies. In this minireview, we provide a systematic summary of reports highlighting potential evolutionary changes that could facilitate the colonization of new reservoirs by these bacteria.

Disease Occurrence in- and the Transferal of Zoonotic Agents by North American Feedlot Cattle

North America is a large producer of beef and contains approximately 12% of the world's cattle inventory. Feedlots are an integral part of modern cattle production in North America, producing a high-quality, wholesome protein food for humans. Cattle, during their final stage, are fed readily digestible high-energy density rations in feedlots. Cattle in feedlots are susceptible to certain zoonotic diseases that impact cattle health, growth performance, and carcass characteristics, as well as human health. Diseases are often transferred amongst pen-mates, but they can also originate from the environment and be spread by vectors or fomites. Pathogen carriage in the gastrointestinal tract of cattle often leads to direct or indirect contamination of foods and the feedlot environment. This leads to the recirculation of these pathogens that have fecal-oral transmission within a feedlot cattle population for an extended time. Salmonella, Shiga toxin-producing Escherichia coli, and Campylobacter are commonly associated with animal-derived foods and can be transferred to humans through several routes such as contact with infected cattle and the consumption of contaminated meat. Brucellosis, anthrax, and leptospirosis, significant but neglected zoonotic diseases with debilitating impacts on human and animal health, are also discussed.

Occurrence of Escherichia Coli O157:H7 in lactating cows and dairy farm environment and the antimicrobial susceptibility pattern at Adami Tulu Jido Kombolcha District, Ethiopia

BACKGROUND

Food-borne pathogens are the foremost causes of food-borne human illness in the world. Escherichia coli O157:H7 (E. coli O157:H7) is one of the major food-borne pathogenic bacteria around the world. Though evidence is lacking; especially in developing countries like Ethiopia, the potential health impact of E. coli O157:H7 can be high where food production, handling and consumption is often taking place under unhygienic conditions. In Ethiopia, studies reported E. coli and E. coli O157: H7 from food of animal origin, mainly meat and milk, and also animal surfaces and feces. The objective of the present study was to investigate the occurrence of E. coli O157:H7 in raw milk and the dairy production farm environment and further assess the antimicrobial resistance pattern of the bacterium.

METHODS

Samples of milk from individual lactating cows' and dairy farm environmental samples (feces, water and manure) were collected at Adami Tulu Jido Kombolcha district (ATJKD) and analyzed for the presence of E. coli O157:H7. Standard microbiological techniques including culture, biochemical testing and serological test were performed to isolate and identify the bacterium. The bacterial isolates were evaluated for antimicrobial susceptibility patterns using disk diffusion method. A questionnaire was used to collect possible factors affecting E. coli O157:H7 occurrence.

RESULTS

The overall prevalence of E. coli O157:H7 was 4.7% (19/408) (95% CI: 2.6; 6.7). Out of 19 E. coli O157:H7 isolates, 4/50, 7/154, 2/50, and 6/154 were from water, milk, manure, and feces samples, respectively. From potential risk factors considered in this study area, floor type, cleaning of pens, milking location and hand washing during the time of milking were significantly associated with the occurrence of E. coli O157:H7. The antimicrobial susceptibility pattern indicated varying degrees of resistance. All of the isolates were found to be resistant ampicillin, cephalothin, and rifampin, and 100% susceptibility was observed against the drugs: chloramphenicol, ciprofloxacin, gentamicin, nalidixic acid, kanamycin, and tetracycline. Concerning streptomycin, 63.15% of the isolates were susceptible and 36.8% showed intermediate susceptibility.

CONCLUSIONS

The occurrence of multi-drug resistance E. coli O157:H7 observed both in lactating cows and in dairy farm environments can sustain a continuous transmission of the bacteria. The occurrence of multidrug-resistant E. coli o157:H7could hamper the control and prevention efforts.

Disentangling the microbial ecological factors impacting honey bee susceptibility to Paenibacillus larvae infection

Paenibacillus larvae is a spore-forming bacterial entomopathogen and causal agent of the important honey bee larval disease, American foulbrood (AFB). Active infections by vegetative P. larvae are often deadly, highly transmissible, and incurable for colonies but, when dormant, the spore form of this pathogen can persist asymptomatically for years. Despite intensive investigation over the past century, this process has remained enigmatic. Here, we provide an up-to-date synthesis on the often overlooked microbiota factors involved in the spore-to-vegetative growth transition (corresponding with the onset of AFB disease symptoms) and offer a novel outlook on AFB pathogenesis by focusing on the 'collaborative' and 'competitive' interactions between P. larvae and other honey bee-adapted microorganisms. Furthermore, we discuss the health trade-offs associated with chronic antibiotic exposure and propose new avenues for the sustainable control of AFB via probiotic and microbiota management strategies.

Impact of Lactobacillus-originated metabolites on enterohemorrhagic E. coli in rumen fluid

Rumen is one of the richest microbial ecosystems naturally harboring many zoonotic pathogens. Controlling the colonization of cattle originated zoonotic pathogens in rumen, particularly enterohemorrhagic Escherichia coli (EHEC), is critical in reducing foodborne enteric diseases in humans. In this study, we aimed to inhibit the growth of EHEC in a simulated rumen system with collected rumen fluids (RFs) using live probiotics, synbiotics, and their metabolites. EHEC inoculated RF was treated with live wild type Lactobacillus casei (LCwt), LCwt with 0.5% peanut flour (LCwt+PF), an engineered LC capable of overexpressing linoleate isomerase (LCCLA), and their metabolites collected in cell-free culture supernatants (CFCSwt, CFCSwt+PF, and CFCSCLA) at various time points. A growth stimulatory effect toward Lactobacillus spp. was exerted by all CFCS, while the EHEC was suppressed. Among other treatments only LCwt+PF reduced EHEC by 2.68 logs after 72 h. This observation was also supported by metataxonomic analysis. A reduction in Bacteroidetes and Proteobacteria while increase in Firmicutes was observed at 48 h by the presence of CFCSs as compared to the control. Our observation implies probiotic-originated metabolites modulate rumen microbiota positively which can be deployed to control the transmission of cattle-borne pathogens specifically EHEC.

First isolation of verocytotoxin-producing Escherichia coli O157:H7 from sports animals in Southern Thailand

Background and Aim:

Escherichia coli O157:H7 is enterohemorrhagic E. coli, which produces verocytotoxin or Shiga toxin. It is a well-known cause of severe diseases in humans worldwide. Cattle and other ruminants are the main reservoirs of this organism. Sports animals, such as fighting bulls, riding horses, and fighting cocks, are economic animals in Southern Thailand. This study aimed to identify E. coli O157:H7 from the rectal swabs of these sports animals and determine the antimicrobial susceptibility patterns of isolated bacteria.

Materials and Methods:

The rectal swabs were collected from 34 fighting bulls, 32 riding horses, and 31 fighting cocks. The swabs were cultured on MacConkey (MAC) Agar; the suspected colonies were then identified by VITEK^® 2 GN card, and the antimicrobial susceptibility was tested by VITEK^® 2 AST N194 in VITEK^® 2 Compact automation. Escherichia coli O157:H7 was confirmed by culturing on sorbitol MAC agar, the ability to grow at 44°C, and the presence of H7 antigen. In addition, the eaeA (E. coli attaching and effacing), along with stx1 and stx2 (Shiga cytotoxins) genes, were determined using polymerase chain reaction. Finally, the cytotoxicity of Shiga toxin was confirmed using the Vero cytotoxicity test.

Results:

Fifty-five suspected isolates (56.70%), which were collected from 19 fighting bulls (55.88%), 13 riding horses (40.63%), and 23 fighting cocks (71.13%), were identified as E. coli. However, one sample (Bull H9/1) from fighting bulls had an equal confidence level (50%) for E. coli and E. coli O157. The confirmation of this isolate demonstrated that it was sorbitol non-fermenter, could assimilate L-lactate, was unable to grow well at 44°C, and reacted with anti-serum to H7 antigen. In addition, it was positive with stx2 and eaeA genes, and the toxin affected Vero cells by a dose-dependent response. The antimicrobial susceptibility test revealed that five out of 55 (9.09%) E. coli isolates were resistant to antimicrobial agents. All five isolates (21.74%) were collected from fighting cocks. Escherichia coli Cock H4/3 was only one of the five isolates resistant to three antimicrobial agents (ciprofloxacin, moxifloxacin, and trimethoprim/sulfamethoxazole). Fortunately, it was not multidrug-resistant bacteria.

Conclusion:

This is the first report on detection of E. coli O157:H7 in fighting bulls and antibiotic-resistant characteristic of E. coli in fighting cocks in Southern Thailand. This research is beneficial in preventing the dissemination of E. coli O157:H7 or antimicrobial agent-resistant E. coli in sports animals and humans.

Insights into microbial contamination in multi-type manure-amended soils: The profile of human bacterial pathogens, virulence factor genes and antibiotic resistance genes

Concerns regarding biological risk in environment have garnered increasing attention. Manure has been believed to be a significant source of antibiotic resistance genes (ARGs) in agricultural soil. Nevertheless, the profile of microbial contamination including ARGs, virulence factor genes (VFGs) and human bacterial pathogens (HBPs) in different manure-amended soils remain largely unknown. Here, we conducted the systematic metagenome-based study to explore changes in resistome, VFGs and HBPs in soils treated by frequently-used manures. The results revealed that many manure-borne ARGs, VFGs, and HBPs could be spreaded into soils, and their diversity and abundance were significantly different among chemical fertilizer, pig manure, chicken manure, cow dung and silkworm excrement application. A total of 157 potential HBPs accounting about 1.33% of total bacteria were detected. The main ARGs transferred from manures to soil conferred resistance to vancomycin and macrolide-lincosamide-streptogramin. The series analysis revealed positive co-occurrence patterns of ARGs-HBPs, VFGs-HBPs and ARGs-VFGs. Microbial contamination were more serious in pig manure and silkworm excrement sample than in the other samples, implying the usage of these two manures increased the risk of HBPs and dissemination of ARGs. This study confirmed the prevalence and discrepancy of resistome, VFGs and HBPs in different manure-amended soils.

Genomic analysis of plasmid content in food isolates of E. coli strongly supports its role as a reservoir for the horizontal transfer of virulence and antibiotic resistance genes

The link between E. coli strains contaminating foods and human disease is unclear, with some reports supporting a direct transmission of pathogenic strains via food and others highlighting their role as reservoirs for resistance and virulence genes. Here we take a genomics approach, analyzing a large set of fully-assembled genomic sequences from E. coli available in GenBank. Most of the strains isolated in food are more closely related to each other than to clinical strains, arguing against a frequent direct transmission of pathogenic strains from food to the clinic. We also provide strong evidence of genetic exchanges between food and clinical strains that are facilitated by plasmids. This is based on an overlapped representation of virulence and resistance genes in plasmids isolated from these two sources. We identify clusters of phylogenetically-related plasmids that are largely responsible for the observed overlap and see evidence of specialization, with some food plasmid clusters preferentially transferring virulence factors over resistance genes. Consistent with these observations, food plasmids have a high mobilization potential based on their plasmid taxonomic unit classification and on an analysis of mobilization gene content. We report antibiotic resistance genes of high clinical relevance and their specific incompatibility group associations. Finally, we also report a striking enrichment for adhesins in food plasmids and their association with specific IncF replicon subtypes. The identification of food plasmids with specific markers (Inc and PTU combinations) as mediators of horizontal transfer between food and clinical strains opens new research avenues and should assist with the design of surveillance strategies.

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.

Enteric Escherichia coli O157:H7 in Cattle, and the Use of Mice as a Model to Elucidate Key Aspects of the Host-Pathogen-Microbiota Interaction: A Review

Enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7 is responsible for foodborne disease outbreaks, typically associated with the consumption of undercooked foods contaminated with cattle manure containing the bacterium. At present, effective mitigations do not exist. Many of the factors regulating enteric colonization by E. coli O157:H7 in cattle, and how cattle respond to the bacterium are unknown. In this regard, intestinal colonization locations, shedding patterns, interactions with the enteric microbiota, and host immune responses to infection are current knowledge gaps. As disturbances to host homeostasis are believed to play an important role in the enteric survival of the bacterium, it is important to consider the potential importance of stress during cattle production. Husbandry logistics, cost, and the high genetic, physiological, and microbial heterogeneity in cattle has greatly hampered the ability of researchers to elucidate key aspects of the host-pathogen-microbiota interaction. Although mice have not been extensively used as a cattle model, the utilization of murine models has the potential to identify mechanisms to facilitate hypothesis formulation and efficacy testing in cattle. Murine models have been effectively used to mechanistically examine colonization of the intestine, host responses to infection, and to interactively ascertain how host physiological status (e.g., due to physiological stress) and the enteric microbiota influences colonization and disease. In addition to reviewing the relevant literature on intestinal colonization and pathogenesis, including existing knowledge gaps, the review provides information on how murine models can be used to elucidate mechanisms toward the development of rationale-based mitigations for E. coli O157:H7 in cattle.

Persistence of E. coli O157:H7 in urban recreational waters from Spring and Autumn: a comparison analysis

People might get infected by pathogens found in urban recreational waters during water-contact activities, such as swimming, boating, bathing, and yachting. However, the persistence of pathogenic bacteria in those waters was not well documented. In this study, persistence of E. coli O157:H7 (EcO157) in 48 water samples (24 Spring samples and 24 Autumn samples) from the 3 urban recreational waters was investigated. Multivariate statistical analysis was performed to correlate survival data with water physicochemical properties and bacterial communities. Our data showed that EcO157 survived longer in Spring samples than in Autumn samples regardless of the lakes. Results revealed that recreational water physicochemical properties and bacterial community in Spring samples were different from those in Autumn samples. Mantel and Partial Mantel tests, as well as co-occurrence network analysis illustrated that EC salinity, TOC, and bacterial community were correlated with survival time (ttd) (p < 0.05). Variation partition analysis (VPA) indicated that bacterial community, EC, TOC, and TN explained about 64.81% of overall ttd variation in Spring samples, and bacterial community, EC, pH, and TP accounted for about 56.59% of overall ttd variation in Autumn samples. Structural equation model (SEM) illustrated that EC indirectly positively affected ttd through bacterial community. The correlation between bacterial community and ttd was negative in Spring samples and positive in Autumn samples. TN appeared a direct positive effect on ttd in Spring samples. TP displayed a direct negative effect on ttd in Autumn samples. Our results concluded that there was seasonal variation in environmental factors that directly or indirectly affected the survival of EcO157 in urban recreational waters.

Antimicrobial drug resistance against Escherichia coli and its harmful effect on animal health

Multidrug resistance among pathogenic bacteria is imperilling the worth of antibiotic infection, which has become an emerging problem, which previously transformed the veterinary sciences. Since its discovery, many antibiotics have been effective in treating bacterial infections in animals. Escherichia coli, a bacterium, is one of the reservoirs of antibiotic resistance genes in a community. The current use of antibiotics and demographic factors usually increase multidrug resistance. Genetically, the continuous adoption of environmental changes by E. coli allows it to acquire many multidrug resistance. During the host's life, antimicrobial resistance rarely poses a threat to the E. coli strain and pressure, similar to that of a flexible animal lower intestine. In this review, we describe the E. coli antibiotic drug–resistance mechanism driving transmission, the causes of transmission and the harmful effects on animal health.

Persistent Circulation of Enterohemorrhagic Escherichia coli (EHEC) O157:H7 in Cattle Farms: Characterization of Enterohemorrhagic Escherichia coli O157:H7 Strains and Fecal Microbial Communities of Bovine Shedders and Non-shedders

Cattle are carriers, without clinical manifestations, of enterohemorrhagic Escherichia coli (EHEC) O157:H7 responsible for life-threatening infections in humans. A better identification of factors playing a role in maintaining persistence of such strains in cattle is required to develop more effective control measures. Hence, we conducted a study to identify farms with a persistent circulation of EHEC O157:H7. The EHEC O157:H7 herd status of 13 farms, which had previously provided bovine EHEC O157:H7 carriers at slaughter was investigated. Two farms were still housing positive young bulls, and this was true over a 1-year period. Only one fecal sample could be considered from a supershedder, and 60% of the carriers shed concentrations below 10 MPN/g. Moreover, EHEC O157:H7 represented minor subpopulations of E. coli. PFGE analysis of the EHEC O157:H7 strains showed that persistent circulation was due either to the persistence of a few predominant strains or to the repeated exposure of cattle to various strains. Finally, we compared fecal microbial communities of shedders (S) (n = 24) and non-shedders (NS) (n = 28), including 43 young bulls and nine cows, from one farm. Regarding alpha diversity, no significant difference between S vs. NS young bulls (n = 43) was observed. At the genus level, we identified 10 amplicon sequence variant (ASV) indicators of the S or NS groups. The bacterial indicators of S belonged to the family XIII UCG-001, Slackia, and Campylobacter genera, and Ruminococcaceae NK4A21A, Lachnospiraceae-UGC-010, and Lachnospiraceae-GCA-900066575 groups. The NS group indicator ASVs were affiliated to Pirellulaceae-1088-a5 gut group, Anaerovibrio, Victivallis, and Sellimonas genera. In conclusion, the characteristics enhancing the persistence of some predominant strains observed here should be explored further, and studies focused on mechanisms of competition among E. coli strains are also needed.

Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche

Background

Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a pathogen known to reside in cattle feedlots. This retrospective study examined 181 STEC O157:H7 strains collected over 23 years from a closed-system feedlot. All strains were subjected to short-read sequencing, with a subset of 36 also subjected to long-read sequencing.

Results

Over 96% of the strains fell into four phylogenetically distinct clades. Clade membership was associated with multiple factors including stx composition and the alleles of a well-characterized polymorphism (tir 255 T > A). Small plasmids (2.7 to 40 kb) were found to be primarily clade specific. Within each clade, chromosomal rearrangements were observed along with a core phageome and clade specific phages. Across both core and mobile elements of the genome, multiple SNP alleles were in complete linkage disequilibrium across all strains within specific clades. Clade evolutionary rates varied between 0.9 and 2.8 SNP/genome/year with two tir A allele clades having the lowest evolutionary rates. Investigation into possible causes of the differing rates was not conclusive but revealed a synonymous based mutation in the DNA polymerase III of the fastest evolving clade. Phylogenetic trees generated through our bioinformatic pipeline versus the NCBI’s pathogen detection project were similar, with the two tir A allele clades matching individual NCBI SNP clusters, and the two tir T allele clades assigned to multiple closely-related SNP clusters.

Conclusions

In one ecological niche, a diverse STEC O157:H7 population exhibited different rates of evolution that associated with SNP alleles in linkage disequilibrium in the core genome and mobile elements, including tir 255 T > A.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08497-6.

The Survival of Salmonella Senftenberg, Escherichia coli O157:H7, Listeria monocytogenes, Enterococcus faecalis and Clostridium sporogenes in Sandy and Clay Loam Textured Soils When Applied in Bovine Slurry or Unpasteurised Digestate and the Run-Off Rate for a Test Bacterium, Listeria innocua, When Applied to Grass in Slurry and Digestate

This study investigated the survival of Salmonella Senftenberg, Escherichia coli O157:H7, Listeria monocytogenes, Enterococcus faecalis and Clostridium sporogenes in sandy and clay loam textured soils when applied in bovine slurry or unpasteurised digestate, using laboratory based inoculation studies. The run-off rate for a test bacterium, Listeria innocua, when applied to grass in slurry and digestate, was also examined using field studies. Bovine slurry and digestate were inoculated with the target bacteria to a final concentration of 106 log10 cfu/g or spores/g, thoroughly mixed into soil samples and incubated at 4°C or 14°C. Samples were removed periodically and the surviving cells enumerated using AOAC or equivalent methods. The loss of viability/culturability phase followed first order kinetics and T90 values ranged from 11.9 to 166.7 d at 4°C and from 6.0 to 156 d at 14°C. With the exception of E. coli O157:H7 and E. faecalis in sandy loam textured soil at 14°C (T90 values were significantly (P &lt; 0.05) higher in slurry) the type of soil texture or application material (slurry or digestate) did not affect survival rates. In the field study, 12 grass covered micro-plots were prepared. L. innocua was applied in digestate and bovine slurry and rainfall was simulated at a target rate of ~11 mm per plot per h−1. Rainfall simulation (30 min) took place after 24, 48 h, 14 d and 30 d. Run-off samples were tested for the L. innocua strain using Brilliance Listeria agar supplemented with streptomycin sulphate (1,000 μg/ml) at 37°C for 48 h, as were soil samples after 30, 58, 86 and 112 d. Significantly (P &lt; 0.05) lower counts were obtained in the run-off from digestate after 1, 2 and 30 d as compared to slurry. It was concluded that the type of organic fertiliser does not affect the bacterial survival rates in sandy and clay soils, with the exception of E. coli O157:H7 and E. faecalis in sandy loam textured soil at 14°C. Furthermore, bacteria may be retained better in the soil-digestate matrices during rainfall although additional research is required to further validate and provide the scientific basis for this observation.

Metabolic responses of indigenous bacteria in chicken faeces and maggots to multiple antibiotics via heavy water labeled single-cell Raman spectroscopy

The use of maggots derived from chicken faeces as fish diets might serve as a vehicle for the widespread of multiple antibiotic resistant bacteria (ARB) in the environment. Heavy water labeled single-cell Raman spectroscopy (D₂O-Raman) was applied to detect the metabolic responses of indigenous bacteria in chicken faeces and maggots to different concentrations of combined colistin, kanamycin, and vancomycin. By incubating the samples with D₂O and antibiotics, metabolically active bacterial cells to antibiotics were distinguished from those inactive by the exhibition of C-D Raman band. Using the C-D band as a universal metabolic biomarker, 96% and 100% of cells in chicken faeces and maggots were revealed to be metabolically active to 1 × minimum inhibition concentration (MIC) of the afore-mentioned antibiotics. A noticeable decrease in the percentage of active cells from 96% to 76% in faeces and 100% to 93% in maggots was observed at 5 × MIC of antibiotics. However, these ratios were still far above that obtained from the same faeces (1.84%) and maggots (0.51%) samples using a cultivation method, indicating the wide presence of nongrowing but metabolically active bacterial cells under antibiotic treatment. Conclusively, the culture-independent D₂O-Raman approach detected and quantified a large portion of metabolically active indigenous bacteria to multiple antibiotics in their native environments, illustrating the great potential risks of these active cells to spread antibiotic resistance via food chain.

Microbial Activity during Composting and Plant Growth Impact: A Review

Replacing harmful chemical pesticides with compost extracts is steadily gaining attention, offering an effective way for plant growth enhancement and disease management. Food waste has been a major issue globally due to its negative effects on the environment and human health. The methane and other harmful organisms released from the untreated waste have been identified as causes of this issue. Soil bacteria impart a very important role in biogeochemical cycles. The interactions between plants and bacteria in the rhizosphere are some of the factors that determine the health and fertility of the soil. Free-living soil bacteria are known to promote plant growth through colonizing the plant root. PGPR (Plant Growth Promoting Rhizobacteria) inoculants in compost are being commercialized as they help in the improvement of crop growth yield and provide safeguard and resistance to crops from disease. Our focus is to understand the mechanism of this natural, wet waste recycling process and implementation of a sustainable operative adaptation with microbial association to ameliorate the waste recycling system.

Ruminant-Related Risk Factors are Associated with Shiga Toxin-Producing Escherichia coli Infection in Children in Southern Ghana

Livestock can provide benefits to low-income households, yet may expose children to zoonotic enteropathogens that cause illness and negative long-term health outcomes. The aim of this cross-sectional study was to determine whether livestock-related risk factors, including animal ownership, exposure to animal feces, and consumption of animal-source foods, were associated with bacterial zoonotic enteropathogen infections in children 6-59 months old in Greater Accra, Ghana. Stool samples from 259 children and 156 household chickens were analyzed for atypical enteropathogenic Escherichia coli (aEPEC), Campylobacter jejuni/coli (C. jejuni/coli), Salmonella, and Shiga toxin-producing Escherichia coli (STEC) using quantitative polymerase chain reaction (qPCR). aEPEC, C. jejuni/coli, STEC, and Salmonella were detected in 45.6%, 11.6%, 4.3%, and 0.8% of children's stool samples, respectively. In adjusted logistic regression models, household ownership of goats or sheep was associated with STEC detection in children (odds ratio [95% confidence interval]: 4.30 [1.32, 14.08]), as were positive detection of STEC in chicken feces (7.85 [2.54, 24.30]) and frequent consumption of fresh cow's milk (3.03 [1.75, 5.24]). No livestock-related risk factors were associated with aEPEC or C. jejuni/coli infection in children. Our findings suggest that ruminant ownership in southern Ghana may expose children to STEC through household fecal contamination and foodborne routes. The lack of association between livestock risk factors and the more commonly detected pathogens, aEPEC and C. jejuni/coli, warrants further research, particularly to help explain how animal-keeping and sanitation practices affect transmission of fecal pathogens that were highly prevalent in chicken feces.

Innovative Treatments Enhancing the Functionality of Gut Microbiota to Improve Quality and Microbiological Safety of Foods of Animal Origin

The gastrointestinal tract, or gut, microbiota is a microbial community containing a variety of microorganisms colonizing throughout the gut that plays a crucial role in animal health, growth performance, and welfare. The gut microbiota is closely associated with the quality and microbiological safety of foods and food products originating from animals. The gut microbiota of the host can be modulated and enhanced in ways that improve the quality and safety of foods of animal origin. Probiotics—also known as direct-fed microbials—competitive exclusion cultures, prebiotics, and synbiotics have been utilized to achieve this goal. Reducing foodborne pathogen colonization in the gut prior to slaughter and enhancing the chemical, nutritional, or sensory characteristics of foods (e.g., meat, milk, and eggs) are two of many positive outcomes derived from the use of these competitive enhancement–based treatments in food-producing animals.

Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The potential role of fertilizer-derived exogenous bacteria on soil bacterial community assemblage and network formation

Manure fertilization contributes to crop production and sustainable agriculture by introducing large amounts of nutrients and exogenous microbes into soil. However, the contribution of exogenous microbes in shaping soil bacterial community and network structure after fertilization are still controversial. In this study, bacterial communities and network structure that received unsterilized (R + C) or sterilized (R + SC) manure fertilizers, as well as no fertilizer control (R), were characterized using high throughput sequencing. Results showed that the relative abundance of fertilizer-derived OTUs decreased from 10.4% to 4.6% after 90 days incubation, while the Bray-Curtis distance between the control and fertilization group (R + C and R + SC) gradually increased with the culture time. It can be supposed that manure fertilization altered soil bacterial communities by interfering the growth of indigenous bacteria rather than the colonization of fertilizer-derived bacteria. Network analysis showed that a subset of the fertilizer-derived OTUs identified as Xanthomonadales order and Promicromonospora, Constrictibacter genera acted as connectors between modules. They enhanced the interactions not only between soil-derived OTUs and fertilizer-derived OTUs, but also within indigenous bacteria, supported that the introduction of fertilizer-derived exogenous bacteria contributes large to soil bacterial network association. Moreover, fertilizer-derived OTUs presented to be positively correlated with soil pH, while majority soil-derived OTUs presented to be negatively correlated with various physicochemical variables (pH, DOC, NO₃^-, and LAP). Our study highlighted the critical role of fertilizer-derived bacteria in regulating indigenous soil microbial community and network formation after fertilization.

Prevalence of Shiga Toxin-Producing Escherichia coli and Salmonella in Native Pecan Orchards as Influenced by Waiting Periods between Grazing and Harvest

ABSTRACT

Animals (grazing, working, or intrusion) in produce production areas may present a potential contamination source of foodborne pathogens on produce. Cattle grazing on native pecan production orchards, a common practice in the southern United States, provides an opportunity to study the impact of grazing practice and waiting periods on contamination rates of foodborne pathogens of tree nuts. Therefore, the objective of this study was to determine the prevalence of Salmonella and Shiga toxin-producing Escherichia coli (STEC) in native pecan production orchards as influenced by waiting periods between grazing cattle and pecan harvest. Soil (10 g), cattle feces (10 g), and in-shell pecans (25 g) were sampled from five cattle-grazed orchards in areas with cattle removed 2 or 4 months before harvest and not removed. Five nongrazing orchards were sampled at harvest for comparison. Detection and isolation of the pathogens were performed by enrichment, selective isolation, and multiplex PCR. Statistical analyses were performed using contingency tables with Pearson's chi-square test. The prevalence of STEC (36%) and Salmonella (29%) in cattle-grazed orchards was significantly higher than in nongrazed orchards (13 and 7%, respectively). STEC prevalence in cattle-grazed orchards was higher (38%) in areas with cattle at harvest than in fenced areas where cattle were removed 2 (29%) and 4 (27%) months before harvest. Salmonella prevalence was similar in areas without fencing (31%) and areas with cattle removed at 2 (22%) and 4 (30%) months before harvest. However, there were no significant differences (P > 0.05) in contamination rates between waiting periods for either pathogen, suggesting a limited impact of waiting periods on reducing the risk of contamination.

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