Antibiotic resistance among Escherichia coli and Salmonella isolated from dairy cattle feces in Texas

Virulome analysis of Escherichia coli ST117 from bovine sources identifies similarities and differences with strains isolated from other food animals

Escherichia coli ST117 is a pandemic extraintestinal pathogenic E. coli (ExPEC) causing significant morbidity globally. Poultry are a known reservoir of this pathogen, but the characteristics of ST117 strains from other animal sources have not been adequately investigated. Here we characterize the genomes of 36 ST117 strains recovered primarily from preweaned dairy calves, but also from older postweaned calves and lactating cows, in the context of other bovine-associated strains and strains from poultry, swine, and humans. Results of this study demonstrate that bovine-associated ST117 genomes encode virulence factors (VFs) known to be involved in extraintestinal infections, but also occasionally encode the Shiga toxin, a virulence factor (VF) involved in severe gastrointestinal infections and more frequently identified in E. coli from ruminants than other animals. Bovine-associated ST117 genomes were also more likely to encode afa-VIII (adhesins), pap (P-fimbriae), cdt (cytolethal distending toxin), and stx (Shiga toxins) than were poultry and swine-associated genomes. All of the ST117 genomes were grouped into seven virulence clusters, with bovine-associated genomes grouping into Clusters 1, 2, 4, 5, but not 3, 6, or 7. Major differences in the presence of virulence factors between clusters were observed as well. Antimicrobial resistance genes were detected in 112 of 122 (91%) bovine-associated genomes, with 103 of these being multidrug-resistant (MDR). Inclusion of genomes that differed from ST117 by one multi-locus sequence type (MLST) allele identified 31 STs, four of these among the bovine-associated genomes. These non-ST117 genomes clustered with the ST117 genomes suggesting that they may cause similar disease as ST117. Results of this study identify cattle as a reservoir of ST117 strains, some of which are highly similar to those isolated from other food animals and some of which have unique bovine-specific characteristics.

Enteropathogenic Escherichia coli is a predominant pathotype in healthy pigs in Hubei Province of China

AIM

This study aims to investigate the prevalence of intestinal pathogenic Escherichia coli (InPEC) in healthy pig-related samples and evaluate the potential virulence of the InPEC strains.

METHODS AND RESULTS

A multiplex PCR method was established to identify different pathotypes of InPEC. A total of 800 rectal swab samples and 296 pork samples were collected from pig farms and slaughterhouses in Hubei province, China. From these samples, a total of 21 InPEC strains were isolated, including 19 enteropathogenic E. coli (EPEC) and 2 shiga toxin-producing E. coli (STEC) strains. By whole-genome sequencing and in silico typing, it was shown that the sequence types and serotypes were diverse among the strains. Antimicrobial susceptibility assays showed that 90.48% of the strains were multi-drug resistant. The virulence of the strains was first evaluated using the Galleria mellonella larvae model, which showed that most of the strains possessed medium to high pathogenicity. A moderately virulent EPEC isolate was further selected to characterize its pathogenicity using a mouse model, which suggested that it could cause significant diarrhea. Bioluminescence imaging (BLI) was then used to investigate the colonization dynamics of this EPEC isolate, which showed that the EPEC strain could colonize the mouse cecum for up to 5 days.

Antibiotic resistance mechanism and diagnosis of common foodborne pathogens based on genotypic and phenotypic biomarkers

The emergence of antibiotic-resistant bacteria due to the overuse or inappropriate use of antibiotics has become a significant public health concern. The agri-food chain, which serves as a vital link between the environment, food, and human, contributes to the large-scale dissemination of antibiotic resistance, posing a concern to both food safety and human health. Identification and evaluation of antibiotic resistance of foodborne bacteria is a crucial priority to avoid antibiotic abuse and ensure food safety. However, the conventional approach for detecting antibiotic resistance heavily relies on culture-based methods, which are laborious and time-consuming. Therefore, there is an urgent need to develop accurate and rapid tools for diagnosing antibiotic resistance in foodborne pathogens. This review aims to provide an overview of the mechanisms of antibiotic resistance at both phenotypic and genetic levels, with a focus on identifying potential biomarkers for diagnosing antibiotic resistance in foodborne pathogens. Furthermore, an overview of advances in the strategies based on the potential biomarkers (antibiotic resistance genes, antibiotic resistance-associated mutations, antibiotic resistance phenotypes) for antibiotic resistance analysis of foodborne pathogens is systematically exhibited. This work aims to provide guidance for the advancement of efficient and accurate diagnostic techniques for antibiotic resistance analysis in the food industry.

P, Molina CA, Castillejo P. Beta-Lactam Antibiotic Resistance Genes in the Microbiome of the Public Transport System of Quito, Ecuador

Multidrug-resistant bacteria present resistance mechanisms against β-lactam antibiotics, such as Extended-Spectrum Beta-lactamases (ESBL) and Metallo-β-lactamases enzymes (MBLs) which are operon encoded in Gram-negative species. Likewise, Gram-positive bacteria have evolved other mechanisms through mec genes, which encode modified penicillin-binding proteins (PBP2). This study aimed to determine the presence and spread of β-lactam antibiotic resistance genes and the microbiome circulating in Quito's Public Transport (QTP). A total of 29 station turnstiles were swabbed to extract the surface environmental DNA. PCRs were performed to detect the presence of 13 antibiotic resistance genes and to identify and to amplify 16S rDNA for barcoding, followed by clone analysis, Sanger sequencing, and BLAST search. ESBL genes bla_TEM-1 and bla_CTX-M-1 and MBL genes bla_OXA-181 and mecA were detected along QPT stations, blaTEM being the most widely spread. Two subvariants were found for bla_TEM-1, bla_CTX-M-1, and bla_OXA-181. Almost half of the circulating bacteria found at QPT stations were common human microbiota species, including those classified by the WHO as pathogens of critical and high-priority surveillance. β-lactam antibiotic resistance genes are prevalent throughout QPT. This is the first report of bla_OXA-181 in environmental samples in Ecuador. Moreover, we detected a new putative variant of this gene. Some commensal coagulase-negative bacteria may have a role as mecA resistance reservoirs.

Tocopherol-assisted magnetic Ag-Fe3O4-TiO2 nanocomposite for photocatalytic bacterial-inactivation with elucidation of mechanism and its hazardous level assessment with zebrafish model

In recent years, many endeavours have been prompted with photocatalytic nanomaterials by the need to eradicate pathogenic microorganisms from water bodies. Herein, a tocopherol-assisted Ag-Fe₃O₄-TiO₂ nanocomposite (TAFTN) was synthesized for photocatalytic bacterial inactivation. The prepared TAFTN became active under sunlight due to its narrowed bandgap, inactivating the bacterial contaminants via photo-induced ROS stress. The ROS radicals destroy bacteria by creating oxidative stress, which damages the cell membrane and cellular components such as nucleic acids and proteins. For the first time, the nano-LC-MS/MS-based quantitative proteomics reveals that the disrupted proteins are involved in a variety of cellular functions; the most of these are involved in the metabolic pathway, eventually leading to bacterial death during TAFTN-photocatalysis under sunlight. Furthermore, the toxicity analysis confirmed that the inactivated bacteria seemed to have no detrimental impact on zebrafish model, showing that the disinfected water via TAFTN-photocatalysis is enormously safe. Furthermore, the TAFTN-photocatalysis successfully killed the bacterial cells in natural seawater, indicating the consistent photocatalytic efficacy when recycled repeatedly. The results of this work demonstrate that the produced nanocomposite might be a powerful recyclable and sunlight-active photocatalyst for environmental water treatment.

Antimicrobial resistance genes of Escherichia coli, a bacterium of "One Health" importance in South Africa: Systematic review and meta-analysis

This is a systematic review and meta-analysis that evaluated the prevalence of Escherichia coli antibiotic-resistant genes (ARGs) in animals, humans, and the environment in South Africa. This study followed Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines to search and use literature published between 1 January 2000 to 12 December 2021, on the prevalence of South African E. coli isolates' ARGs. Articles were downloaded from African Journals Online, PubMed, ScienceDirect, Scopus, and Google Scholar search engines. A random effects meta-analysis was used to estimate the antibiotic-resistant genes of E. coli in animals, humans, and the environment. Out of 10764 published articles, only 23 studies met the inclusion criteria. The obtained results indicated that the pooled prevalence estimates (PPE) of E. coli ARGs was 36.3%, 34.4%, 32.9%, and 28.8% for bla_TEM-M-1 , ampC, tetA, and bla _TEM, respectively. Eight ARGs (bla_CTX-M , bla_CTX-M-1 , bla_TEM , tetA, tetB, sul1, sulII, and aadA) were detected in humans, animals and the environmental samples. Human E. coli isolate samples harboured 38% of the ARGs. Analyzed data from this study highlights the occurrence of ARGs in E. coli isolates from animals, humans, and environmental samples in South Africa. Therefore, there is a necessity to develop a comprehensive "One Health" strategy to assess antibiotics use in order to understand the causes and dynamics of antibiotic resistance development, as such information will enable the formulation of intervention strategies to stop the spread of ARGs in the future.

To decipher the phytochemical agent and mechanism for Urginea indica mediated green synthesis of Ag nanoparticles and investigation of its antibacterial activity against Methicillin-resistant Staphylococcus aureus

Globally, Methicillin-Resistant Staphylococcus aureus bacteraemia is one of the commonest bloodstream infections associated with clinical complications and high mortality. Thence, devising effective and targeted biogenic silver based strategies are in great demand. However, limited insights regarding the biosynthesis methodologies impedes the possible scale up and commercial potentials. We, hereby demonstrate the biosynthesis of Ag nanoparticles using the phytochemical agent extracted and purified from bulb extract of Urginea indica. The chemical structure of the phytochemical agent is investigated by various chromatographic and spectroscopic techniques and was found closely relatable to N-ethylacetamide. Ag nanoparticles synthesis by this agent was found to have a strong Surface Plasmon band at 402 nm. X-ray diffraction and transmission electron microscopy further validated the formation of Ag nanoparticles with face-centred cubic structure with a size range of 20-30 nm. The biogenic metal nanoparticles have shown potential antibacterial activity against S. aureus and MRSA (within a range of 10-50 μg/mL). The nanoparticles have also shown promising anti-biofim activity against the above mentioned strains. The nanoparticles were expected to induce ROS mediated bactericidal mechamism. Cell viability and in-vitro infection studies advocate noticeable biocompatibility and future clinical potential of the developed nanoparticles against Staphylococcus infections.

Phylogenetic analysis and antibiotic resistance of Escherichia coli isolated from wild and domestic animals at an agricultural land interface area of Salaphra wildlife sanctuary, Thailand

Background and Aim

Domestic and wild animals are important reservoirs for antibiotic-resistant bacteria. This study aimed to isolate Escherichia coli from feces of domestic and wild animals at an agricultural land interface area of Salaphra Wildlife Sanctuary, Thailand, and study the phylogenic characteristics and antibiotic resistance in these isolates.

Materials and Methods

In this cross-sectional, descriptive study, we randomly collected ground feces from free-ranging wild animals (deer and elephants) and domestic animals (cattle and goats). All fecal samples were inoculated onto MacConkey agar plates, and lactose-fermenting colonies were identified as E. coli. Antibiotic susceptibility of the E. coli isolates was determined using the disc diffusion method. Polymerase chain reaction assays were used to detect antibiotic resistance and virulence genes.

Results

We obtained 362 E. coli isolates from the collected fecal samples. The E. coli isolates were categorized into four phylogenetic groups according to the virulence genes (chuA, vjaA, and TspE4C2). Phylogenetic Group D was predominant in the deer (41.67%) and elephants (63.29%), whereas phylogenetic Group B1 was predominant in the cattle (62.31%), and phylogenetic Groups A (36.36%) and B2 (33.33%) were predominant in the goats. Antibiotic susceptibility testing revealed that most antibiotic-resistant E. coli were isolated from domestic goats (96.96%). Among the 362 E. coli isolates, 38 (10.5%) were resistant to at least one antibiotic, 21 (5.8%) were resistant to two antibiotics, and 6 (1.66%) were resistant to three or more antibiotics. Ampicillin (AMP) was the most common antibiotic (48.48%) to which the E. coli were resistant, followed by tetracycline (TET) (45.45%) and trimethoprim-sulfamethoxazole (3.03%). One isolate from an elephant was resistant to five antibiotics: AMP, amoxicillin, sulfisoxazole, TET, and ciprofloxacin. Determination of antibiotic resistance genes confirmed that E. coli isolates carried antibiotic resistance genes associated with phenotypic resistance to antibiotics. Most antibiotic-resistant E. coli belonged to phylogenic Groups A and B1, and most non-resistant E. coli belonged to phylogenic Groups B2 and D.

Conclusion

Monitoring E. coli isolates from wild and domestic animals showed that all four phylogenic groups of E. coli have developed antibiotic resistance and are potential sources of multidrug resistance. High levels of antibiotic resistance have been linked to domestic animals. Our results support strengthening surveillance to monitor the emergence and effects of antibiotic-resistant microorganisms in animals.

Antimicrobial Susceptibility and Molecular Characterization of Escherichia coli Recovered from Milk and Related Samples

There is a rising concern about illnesses resulting from milk consumption due to contamination by pathogenic microorganisms including Escherichia coli. This study examined the occurrence and antimicrobial susceptibility of E. coli isolated from cow milk and related samples. Furthermore, partial sequencing was done to ascertain the genetic relatedness and possible cross contamination among the samples. In all, 250 samples, that is, 50 each of raw milk, cow teat, milkers’ hands, milking utensils, and fecal matter of cows, were cultured for the identification of E. coli. E. coli was detected in 101/250 samples (40.4%). Milk and fecal samples recorded the highest percentages of 68.0% and 66.0%, respectively. Forty-two (42) E. coli strains examined for antimicrobial resistance showed an overall 25.5% resistance, 15.0% intermediate resistance, and 59.5% susceptibility. The isolates had a high level of resistance to teicoplanin (100.0%), but were susceptible to chloramphenicol (95.2%) and azithromycin (92.9%). The Multiple Antibiotic Resistance (MAR) index pattern ranged from 0.1 to 0.5, and 40.5% exhibited multiple drug resistance. The E. coli strains formed 11 haplotypes, and a phylogenic tree analysis showed relatedness among the isolates in other African countries. This observation is an indication of cross contamination among the milk and its related samples.

Salmonella Carriage in Peripheral Lymph Nodes and Feces of Cattle at Slaughter Is Affected by Cattle Type, Region, and Season

Salmonella is a significant food safety concern in commercial beef production, and some contamination is thought to occur by inclusion of Salmonella-infected peripheral lymph nodes (LN) in ground beef and through fecal contamination. Surveillance in processing plants assists packers in risk management of Salmonella by understanding seasonal trends and risks associated with different cattle types. Approximately 25 fecal samples and 20 LN were collected from animals representing each of five cattle types (cull beef cattle, cull dairy cows, conventional feedlot cattle, all-natural feedlot cattle raised without pharmaceuticals, and grass-finished cattle) and each of five climate regions (mixed-temperatures and dry, mixed-temperatures and humid, hot and humid, hot and dry, cold) during each of three seasons (summer, fall, winter) to better characterize Salmonella inputs into a commercial cattle processing facility. In total, 1,840 fecal samples and 1,550 LN samples were collected. Fecal samples and LN were cultured for Salmonella, and select isolates were serogrouped and screened for antimicrobial resistance. Conventional feedlot cattle had the highest LN Salmonella concentrations (1.17 log10 CFU/g LN) in this data set, while cull dairy cows had the highest fecal Salmonella concentrations (1.96 log10 CFU/g feces). Conventional feedlot cattle and cull dairy cows had the greatest Salmonella prevalence in both LN (32 and 18%, respectively) and feces (37 and 49%, respectively), while all-natural feedlot cattle had the lowest prevalence in the LN (3%) and feces (7%). As expected, Salmonella prevalence and concentration was lowest for all cattle types during winter compared to warmer seasons. When examined by climate region, a greater Salmonella prevalence in both feces and LN was observed in climate region 4 (hot-dry), than the other regions. Only 21 of 50 Salmonella isolates examined for antimicrobial susceptibility were identified as multidrug resistant (MDR); cull dairy cows were responsible for 48% of MDR isolates, cull beef cattle were responsible for 38%, and conventional feedlot, grass-fed, and all-natural feedlot cattle were each responsible for 4.8%. These results indicate that different production schemes, season, and climate region may influence which cattle are most likely to introduce Salmonella to the abattoir, allowing for greater risk awareness during the slaughter process.

Antimicrobial Resistance in Escherichia coli Isolates from Healthy Food Animals in South Korea, 2010-2020

Antimicrobial-resistant bacteria in food animals pose a major public health threat worldwide. In this study, we aimed to assess the antimicrobial resistance profiles and resistance trends of commensal Escherichia coli isolated from the feces of healthy cattle, pigs, and chickens in South Korea during 2010 and 2020. A total of 7237 E. coli isolates (2733 cattle, 2542 pig, and 1962 chicken isolates) were tested for susceptibility towards 12 antimicrobials. About 48%, 90%, and 97% of cattle, pig, and chicken isolates, respectively, were resistant to one or more antimicrobial agents. Cattle isolates presented low resistance (<15%) to most of the tested antimicrobials. In contrast, chicken and pig isolates demonstrated a relatively high (>45%) resistance rate to ampicillin, chloramphenicol, streptomycin, and tetracycline. We observed high ciprofloxacin and nalidixic acid resistance rates in chicken (76.1% and 88.6%, respectively), isolates in pig (12.7% and 26.7%, respectively) and cattle (2.7% and 8.2%, respectively) isolates. Notably, a very small proportion of isolates (<5%) from cattle, chickens, and pigs demonstrated resistance to amoxicillin/clavulanic acid, cefoxitin, and colistin. We identified ceftiofur resistance in a small proportion of chicken (8.8%), pig (3.7%), and cattle (0.7%) isolates. We noted an increasing but fluctuating trend of ampicillin, amoxicillin/clavulanic acid, ceftiofur, cefoxitin, chloramphenicol, ciprofloxacin, and streptomycin resistance in pig isolates. Similarly, the ampicillin, ceftiofur, and chloramphenicol resistance rates were increased but fluctuated through time in chicken isolates. Overall, 56% of the isolates showed multidrug-resistant (MDR). The proportion of MDR isolates was low in cattle (17.1%); however, this proportion was high in chickens (87.1%) and pigs (73.7%). Most of the resistance patterns included streptomycin and tetracycline in pigs and cattle, and ciprofloxacin and nalidixic acid in chickens. In conclusion, this study showed high resistance of commensal E. coli isolated from major food animals in Korea to commonly used antimicrobials including critically important antimicrobials. These bacteria could not only be a resistance reservoir but also could have potential to spread this resistance through gene transfer to pathogenic bacteria. Thus, the high prevalence of antimicrobial resistance in food animals highlights the urgent need for measures to restrict and ensure the prudent use of antimicrobials in Korea.

Antibiotic-Resistant Escherichia coli and Salmonella from the Feces of Food Animals in the East Province of Rwanda

In Rwanda, information on antibiotic resistance in food animals is scarce. This study was conducted to detect and phenotypically characterize antibiotic-resistant Escherichia coli and Salmonella in feces of cattle, goats, pigs, and poultry in the East province of Rwanda. We isolated non-type-specific (NTS) E. coli and Salmonella using plain culture media. In addition, we used MacConkey agar media supplemented with cefotaxime at 1.0 μg/mL and ciprofloxacin at 0.5 μg/mL to increase the probability of detecting E. coli with low susceptibility to third-generation cephalosporins and quinolones, respectively. Antibiotic susceptibility testing was performed using the disk diffusion test. Among 540 NTS E. coli isolates, resistance to tetracycline was the most frequently observed (35.6%), followed by resistance to ampicillin (19.6%) and streptomycin (16.5%). Percentages of NTS E. coli resistant to all three antibiotics and percentages of multidrug-resistant strains were higher in isolates from poultry. All isolated Salmonella were susceptible to all antibiotics. The sample-level prevalence for resistance to third-generation cephalosporins was estimated at 35.6% with all third-generation cephalosporin-resistant E. coli, expressing an extended-spectrum beta-lactamase phenotype. The sample-level prevalence for quinolone resistance was estimated at 48.3%. These results provided a baseline for future research and the development of integrated surveillance initiatives.