Whole Genome Sequencing of Escherichia coli and Enterococcus spp. in wildlife-livestock interface: a pilot study. - Related Documents




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561901.0000Whole Genome Sequencing of Escherichia coli and Enterococcus spp. in wildlife-livestock interface: a pilot study. OBJECTIVES: This pilot study provides a multidisciplinary investigation to monitor livestock-wildlife interface. Ecological data, microbiological investigations, and whole genome sequencing were used to characterize eight bacterial isolates obtained from sympatric domestic and wild ruminants in Maiella National Park (Italy) in terms of genetic patterns of antimicrobial resistance. METHODS: Using selective culturing of fresh fecal samples of monitored and georeferenced populations of Apennine chamois, goats, red deer, and sheep, Escherichia coli, Enterococcus faecium, and Enterococcus faecalis isolates were isolated and subjected to minimum inhibitory concentration determination and whole genome sequencing. RESULTS: The analyzed isolates showed phenotypic and genotypic resistance to tetracycline and critically important antibiotics such as linezolid and carbapenems. Virulence genes related to biofilm regulation and Shiga toxins were also detected. Furthermore, serotypes related to nosocomial infections, harbouring plasmids recognized as important mobile resistance gene transmitters, were identified. CONCLUSIONS: This multidisciplinary pilot study represents a promising initial step to identify the environmental drivers and the transmission routes of antimicrobial resistance and virulence factors, providing new data on bacteria from rare and endangered species such as Apennine chamois.202336764655
571610.9998Genomic analysis of Salmonella isolated from canal water in Bangkok, Thailand. Antimicrobial resistance (AMR) poses an escalating global public health threat. Canals are essential in Thailand, including the capital city, Bangkok, as agricultural and daily water sources. However, the characteristic and antimicrobial-resistance properties of the bacteria in the urban canals have never been elucidated. This study employed whole genome sequencing to characterize 30 genomes of a causal pathogenic bacteria, Salmonella enterica, isolated from Bangkok canal water between 2016 and 2020. The dominant serotype was Salmonella Agona. In total, 35 AMR genes and 30 chromosomal-mediated gene mutations were identified, in which 21 strains carried both acquired genes and mutations associated with fluoroquinolone resistance. Virulence factors associated with invasion, adhesion, and survival during infection were detected in all study strains. 75.9% of the study stains were multidrug-resistant and all the strains harbored the necessary virulence factors associated with salmonellosis. One strain carried 20 resistance genes, including mcr-3.1, mutations in GyrA, ParC, and ParE, and typhoid toxin-associated genes. Fifteen plasmid replicon types were detected, with Col(pHAD28) being the most common type. Comparative analysis of nine S. Agona from Bangkok and 167 from public databases revealed that specific clonal lineages of S. Agona might have been circulating between canal water and food sources in Thailand and globally. These findings provide insight into potential pathogens in the aquatic ecosystem and support the inclusion of environmental samples into comprehensive AMR surveillance initiatives as part of a One Health approach. This approach aids in comprehending the rise and dissemination of AMR and devising sustainable intervention strategies.IMPORTANCEBangkok is the capital city of Thailand and home to a large canal network that serves the city in various ways. The presence of pathogenic and antimicrobial-resistant Salmonella is alarming and poses a significant public health risk. The present study is the first characterization of the genomic of Salmonella strains from Bangkok canal water. Twenty-two of 29 strains (75.9%) were multidrug-resistant Salmonella and all the strains carried essential virulence factors for pathogenesis. Various plasmid types were identified in these strains, potentially facilitating the horizontal transfer of AMR genes. Additional investigations indicated a potential circulation of S. Agona between canal water and food sources in Thailand. The current study underscores the role of environmental water in an urban city as a reservoir of pathogens and these data obtained can serve as a basis for public health risk assessment and help shape intervention strategies to combat AMR challenges in Thailand.202438563788
573820.9998Unveiling the Genomic Landscape of Understudied Salmonella enterica Serovars from Poultry and Human: Implications for Food Safety. Despite the bacteria of the genus Salmonella are pathogens of zoonotic importance, the factors associated with some serovars genetic diversity remain unclear. We investigated genotypic profiles of antimicrobial resistance, plasmid replicons, and virulence factors in 301 S. enterica genomes from human and animal sources, supplemented by ten sequenced genomes from fecal samples of laying hens in Brazil. Many antimicrobial resistance genes have been detected across various Salmonella serovars; with a limited number of unique resistance genes predicted in poultry isolates compared to human isolates. Specifically, among the 52 antimicrobial resistance genes identified, 48% were shared between poultry and human isolates, while 21.1% were exclusive to poultry isolates and 30.7% were exclusive to human isolates. Chromosomal mutations in the gyrA and parC genes were also predicted. To the best of our knowledge, this is the first work to report S. Braenderup carrying the SPI-10. SGI-1 was detected in a few isolates of S. Schwarzengrund from poultry and the CS54 island was solely noticed in genomes referring to the serovars S. Saintpaul and S. Braenderup. Among the serovars analyzed, S. Saintpaul showed the lowest plasmid diversity. A total of 161 (161/271) virulence genes were common to all serovars, the remaining genes were exclusively identified within specific serovars, revealing a distinct distribution pattern within the S. enterica population. Overall, our study brings to light the genetic potential of Salmonella serovars frequently neglected in poultry production, which threatens public health, particularly due to multidrug-resistant profiles against active principles used to treat human infections.202540327155
552530.9998A comprehensive survey of Aeromonas sp. and Vibrio sp. in seabirds from southeastern Brazil: outcomes for public health. AIMS: To perform a microbiological survey regarding the presence, prevalence and characterization of Aeromonas sp. and Vibrio sp. in debilitated wrecked marine birds recovered from the centre-north coast of the state of Rio de Janeiro, Brazil. METHODS AND RESULTS: Swabs obtained from 116 alive and debilitated wrecked marine birds, comprising 19 species, from the study area were evaluated by biochemical methods. Antimicrobial susceptibility tests and pathogenicity gene screening were performed for bacterial strains of public health importance. Vibrio sp. and Aeromonas sp. were identified, as well as certain pathogenic genes and resistance to selected antimicrobials. CONCLUSIONS: This study demonstrates that the identified bacteria, mainly Vibrio sp., are fairly prevalent and widespread among several species of seabirds and highlights the importance of migratory birds in bacterial dispersion. In addition, it demonstrates the importance of the bacterial strains regarding their pathogenic potential. Therefore, seabirds can act as bacterial reservoirs, and their monitoring is of the utmost importance in a public health context. SIGNIFICANCE AND IMPACT OF THE STUDY: The study comprehensively evaluates the importance of seabirds as bacteria of public health importance reservoirs, since birds comprising several pathogenic bacterial species were evaluated.201829356247
551440.9998Resistance and virulence gene analysis and molecular typing of Escherichia coli from duck farms in Zhanjiang, China. INTRODUCTION: The widespread use of antibiotics in animal agriculture has increased the resistance of Escherichia coli, and pathogenic E. coli often harbor complex virulence factors. Antimicrobial resistance in pathogenic bacteria can cause public health problems. Correlation analyses of the resistance, virulence, and serotype data from the pathogenic bacteria found on farms and in the surrounding environment can thus provide extremely valuable data to help improve public health management. METHODS: In this investigation, we have assessed the drug resistance and virulence genes as well as the molecular typing characteristics of 30 E. coli strains isolated from duck farms in the Zhanjiang area of China. Polymerase chain reaction was used to detect the drug resistance and virulence genes as well as serotypes, and whole-genome sequencing was used to analyze the multilocus sequence typing. RESULTS: The detection rates for the oqxA resistance gene and fimC virulence gene were highest (93.3%, respectively). There were no correlations between the drug resistance and virulence gene numbers in the same strain. The epidemic serotype was O81 (5/24), ST3856 was an epidemic sequence type, and strains I-9 and III-6 carried 11 virulence genes. The E. coli strains from the duck farms in the Zhanjiang area were thus found to have a broad drug resistance spectrum, various virulence genes, complex serotypes, and certain pathogenicity and genetic relationship. DISCUSSION: Monitoring the spread of pathogenic bacteria and the provision of guidance regarding the use of antibiotics in the livestock and poultry industries will be required in the future in the Zhanjiang area.202337396302
193550.9998Antibiotic Susceptibility Profile and Tetracycline Resistance Genes Detection in Salmonella spp. Strains Isolated from Animals and Food. Salmonella spp. is among the leading causes of foodborne infections in humans and a large number of animals. Salmonella spp. is a pathogen involved in the dissemination of antimicrobial resistance because it can accumulate antibiotic resistance genes (ARGs). In this study, the antibiotic resistance profile to 15 antibiotics, belonging to six different classes, of 60 strains of Salmonella spp. collected from pets, farm animals, wildlife, and food in Sicily (Italy) was investigated by the Kirby-Bauer method. Given that almost 33.3% of the Salmonella spp. strains were resistant to tetracycline, Real-Time PCR analysis was applied on all the 60 strains to detect the presence of eight selected tet resistance genes. Besides, the presence of the int1 gene, related to the horizontal gene transfer among bacteria, was also investigated in all the strains by Real-Time PCR analysis. Our data showed that 56% of the isolated strains harbored one or more tet resistance genes and that these strains were most frequently isolated from animals living in close contact with humans. Concerning int1, 17 strains (28.3%) harbored this genetic element and eight of these simultaneously contained tet genes. The results of this study highlight the importance of using a molecular approach to detect resistance genetic determinants, whose spread can increase the diffusion of multidrug-resistant strains. Besides, the study of zoonotic bacteria such as Salmonella spp. which significantly contribute to ARGs dissemination should always follow a One Health approach that considers the health of humans, animals, and the environment to be closely related.202134356729
573660.9998Comparative Genomic Analysis and Antimicrobial Resistance Profile of Enterococcus Strains Isolated from Raw Sheep Milk. The role of Enterococcus spp. in food is debated since this group of lactic acid bacteria contains opportunistic pathogenic strains, some of which exhibit a multidrug-resistant profile. In livestock farms, the use of antibiotics is the most common practice to deal with mastitis-causing bacteria. However, the heavy usage and/or misuse of antibiotics has led to the emergence of antibiotic resistance. This study aimed to genetically and phenotypically characterize Enterococcus strains isolated from raw sheep milk. Samples were collected over one year from the bulk tank of a dairy sheep farm and cultured on selective media. Isolates were purified and analyzed by whole-genome sequencing and antimicrobial susceptibility testing. The isolates were divided into clusters and the corresponding species were identified along with their genes related to virulence and antibiotic resistance. The pan-, core- and accessory-genomes of the strains were determined. Finally, the antibiotic-resistant profile of selected strains was examined and associated with their genomic characterization. These findings contribute to a better understanding of Enterococci epidemiology, providing comprehensive profiles of their virulence and resistance genes. The presence of antibiotic-resistant bacteria in raw sheep milk destined for the production of cheese should raise awareness.202540872636
561370.9998Characterizing Antimicrobial Resistance in Clinically Relevant Bacteria Isolated at the Human/Animal/Environment Interface Using Whole-Genome Sequencing in Austria. Antimicrobial resistance (AMR) is a public health issue attributed to the misuse of antibiotics in human and veterinary medicine. Since AMR surveillance requires a One Health approach, we sampled nine interconnected compartments at a hydrological open-air lab (HOAL) in Austria to obtain six bacterial species included in the WHO priority list of antibiotic-resistant bacteria (ARB). Whole genome sequencing-based typing included core genome multilocus sequence typing (cgMLST). Genetic and phenotypic characterization of AMR was performed for all isolates. Eighty-nine clinically-relevant bacteria were obtained from eight compartments including 49 E. coli, 27 E. faecalis, 7 K. pneumoniae and 6 E. faecium. Clusters of isolates from the same species obtained in different sample collection dates were detected. Of the isolates, 29.2% were resistant to at least one antimicrobial. E. coli and E. faecalis isolates from different compartments had acquired antimicrobial resistance genes (ARGs) associated with veterinary drugs such as aminoglycosides and tetracyclines, some of which were carried in conjugative and mobilizable plasmids. Three multidrug resistant (MDR) E. coli isolates were found in samples from field drainage and wastewater. Early detection of ARGs and ARB in natural and farm-related environments can identify hotspots of AMR and help prevent its emergence and dissemination along the food/feed chain.202236232576
192580.9998Camel Milk Resistome in Kuwait: Genotypic and Phenotypic Characterization. Antimicrobial resistance (AMR) is one of the major global health and economic threats. There is growing concern about the emergence of AMR in food and the possibility of transmission of microorganisms possessing antibiotic resistance genes (ARGs) to the human gut microbiome. Shotgun sequencing and in vitro antimicrobial susceptibility testing were used in this study to provide a detailed characterization of the antibiotic resistance profile of bacteria and their ARGs in dromedary camel milk. Eight pooled camel milk samples, representative of multiple camels distributed in the Kuwait desert, were collected from retail stores and analyzed. The genotypic analysis showed the presence of ARGs that mediate resistance to 18 classes of antibiotics in camel milk, with the highest resistance to fluoroquinolones (12.48%) and disinfecting agents and antiseptics (9%). Furthermore, the results pointed out the possible transmission of the ARGs to other bacteria through mobile genetic elements. The in vitro antimicrobial susceptibility testing indicated that 80% of the isolates were resistant to different classes of antibiotics, with the highest resistance observed against three antibiotic classes: penicillin, tetracyclines, and carbapenems. Multidrug-resistant pathogens including Klebsiella pneumoniae, Escherichia coli, and Enterobacter hormaechei were also revealed. These findings emphasize the human health risks related to the handling and consumption of raw camel milk and highlight the necessity of improving the hygienic practices of farms and retail stores to control the prevalence of ARGs and their transmission.202438786109
561890.9998An Epidemiological Study on Salmonella in Tibetan Yaks from the Qinghai-Tibet Plateau Area in China. Salmonella is an important foodborne pathogen that can cause a range of illnesses in humans; it has also been a key focus for monitoring in the field of public health, including gastroenteritis, sepsis, and arthritis, and can also cause a decline in egg production in poultry and diarrhea and abortion in livestock, leading to death in severe cases, resulting in huge economic losses. This study aimed to investigate the isolation rate, antimicrobial resistance, serotypes, and genetic diversity of Salmonella isolated from yak feces in various regions on the Qinghai-Tibet Plateau. A total of 1222 samples of yak dung were collected from major cities in the Qinghai-Tibet Plateau area, and the sensitivity of the isolated bacteria to 10 major classes of antibiotics was determined using the K-B paper disk diffusion method for drug susceptibility. Meanwhile, the serotypes of the isolated bacteria were analyzed using the plate agglutination test for serum antigens, and their carriage of drug resistance and virulence genes was determined using PCR and gel electrophoresis experiments. The isolated bacteria were also classified using MLST (Multi-Locus Sequence Typing). The overall isolation rate for Salmonella was 18.25% (223/1222), and the results of the antibiotic susceptibility tests showed that 98.65% (220/223) of the isolated bacteria were resistant to multiple antibiotics. In the 223 isolates of Salmonella, eight classes of 20 different resistance genes, 30 serotypes, and 15 different types of virulence genes were detected. The MLST analysis identified 45 distinct sequence types (STs), including five clonal complexes, of which ST34, ST11, and ST19 were the most common. These findings contribute valuable information about strain resources, genetic profiles, and typing data for Salmonella in the Qinghai-Tibet Plateau area, facilitating improved bacterial surveillance, identification, and control in yak populations. They also provide certain data supplements for animal Salmonella infections globally, filling research gaps.202439765601
5515100.9998Wildlife Waterfowl as a Source of Pathogenic Campylobacter Strains. BACKGROUND: The aim of the study was to determine whether free-living birds belonging to game species whose meat is used for human consumption can constitute a reservoir of pathogenic Campylobacter strains, spreading these bacteria to other hosts or directly contributing to human infection. METHODS: A total of 91 cloacal swabs were taken from different species of wildlife waterfowl to estimate the Campylobacter prevalence, the genetic diversity of the isolates, and the presence of virulence genes and to evaluate the antimicrobial resistance. RESULTS: The presence of Campylobacter spp. was confirmed in 32.9% of samples. Based on flaA-SVR sequencing, a total of 19 different alleles among the tested Campylobacter isolates were revealed. The virulence genes involved in adhesion were detected at high frequencies among Campylobacter isolates regardless of the host species. The highest resistance was observed for ciprofloxacin. The resistance rates to erythromycin and tetracycline were observed at the same level. CONCLUSIONS: These results suggest that wildlife waterfowl belonging to game species may constitute a reservoir of Campylobacter, spreading these bacteria to other hosts or directly contributing to human disease. The high distribution of virulence-associated genes among wildlife waterfowl Campylobacter isolates make them potentially able to induce infection in humans.202235215056
1926110.9998Whole genome sequencing revealed high occurrence of antimicrobial resistance genes in bacteria isolated from poultry manure. BACKGROUND: Global demand for food has driven expansion and intensification of livestock production, particularly in developing nations where antibiotic use is often routine. Waste from poultry production, including manure, is commonly utilized as fertilizers in agroecosystems, risking environmental contamination with potentially zoonotic bacteria and antimicrobial resistance genes (ARGs). METHODS: Here, 33 bacterial isolates were recovered from broiler (n = 17) and layer (n = 16) chicken manure by aerobic culture using Luria Bertani agar. Antimicrobial susceptibility testing (AST) was performed using disc diffusion method. MALDI-ToF and 16S rRNA sequencing were used to identify and compare a subset of antibiotic-resistant isolates (n = 13). Comparison of whole genome sequence assemblies and phenotypic assays were used to assess capacity for biofilm formation, heavy metal tolerance and virulence. RESULTS: AST by disc diffusion revealed all isolates were resistant to a minimum of three antibiotics, with resistance to ampicillin, co-trimoxazole, fluoroquinolones, tetracyclines, streptomycin, rifampicin and/or chloramphenicol detected. Stutzerimonas sp. and Acinetobacter sp. were the common genera observed in this study. Genome sequencing of each selected isolate revealed carriage of multiple ARGs capable of conferring resistance to many antimicrobials commonly employed in poultry production and human medicine, including tetracyclines, quinolones, macrolides, sulfonamide and cephalosporins. CONCLUSIONS: The high occurrence of ARGs in studied bacterial isolates confirms that poultry manure could act as a source of genetic material that could be transferred to commensal microbiota and opportunistic pathogens of humans. Understanding the complex resistome interplay between humans, animals, and the environment requires a One Health approach, with implications for agricultural settings and public health.202539880102
5560120.9998Linezolid- and Multidrug-Resistant Enterococci in Raw Commercial Dog Food, Europe, 2019-2020. We describe enterococci in raw-frozen dog food commercialized in Europe as a source of genes encoding resistance to the antibiotic drug linezolid and of strains and plasmids enriched in antibiotic-resistance and virulence genes in hospitalized patients. Whole-genome sequencing was fundamental to linking isolates from dog food to human cases across Europe.202134287135
5610130.9998Characterization of antimicrobial resistance profiles in Escherichia coli isolated from captive mammals in Ecuador. BACKGROUND: This study focuses on the AMR profiles in E. coli isolated from captive mammals at EcoZoo San Martín, Baños de Agua Santa, Ecuador, highlighting the role of wildlife as reservoirs of resistant bacteria. AIMS: The aim of this research is to investigate the antimicrobial resistance profiles of E. coli strains isolated from various species of captive mammals, emphasizing the potential zoonotic risks and the necessity for integrated AMR management strategies. MATERIALS & METHODS: A total of 189 fecal samples were collected from 70 mammals across 27 species. These samples were screened for E. coli, resulting in 90 identified strains. The resistance profiles of these strains to 16 antibiotics, including 10 β-lactams and 6 non-β-lactams, were determined using the disk diffusion method. Additionally, the presence of Extended-Spectrum Beta-Lactamase (ESBL) genes and other resistance genes was analyzed using PCR. RESULTS: Significant resistance was observed, with 52.22% of isolates resistant to ampicillin, 42.22% to ceftriaxone and cefuroxime, and 27.78% identified as ESBL-producing E. coli. Multiresistance (resistance to more than three antibiotic groups) was found in 35.56% of isolates. Carnivorous and omnivorous animals, particularly those with prior antibiotic treatments, were more likely to harbor resistant strains. DISCUSSION: These findings underscore the role of captive mammals as indicators of environmental AMR. The high prevalence of resistant E. coli in these animals suggests that zoos could be significant reservoirs for the spread of antibiotic-resistant bacteria. The results align with other studies showing that diet and antibiotic treatment history influence resistance profiles. CONCLUSION: The study highlights the need for an integrated approach involving veterinary care, habitat management, and public awareness to prevent captive wildlife from becoming reservoirs of antibiotic-resistant bacteria. Improved waste management practices and responsible antibiotic use are crucial to mitigate the risks of AMR in zoo environments and reduce zoonotic threats.202439016692
5611140.9998Antibiotic-Resistant Bacteria Dissemination in the Wildlife, Livestock, and Water of Maiella National Park, Italy. Antimicrobial resistance (AMR) is a global health concern that has been linked to humans, animals, and the environment. The One Health approach highlights the connection between humans, animals, and the environment and suggests that a multidisciplinary approached be used in studies investigating AMR. The present study was carried out to identify and characterize the antimicrobial resistance profiles of bacteria isolated from wildlife and livestock feces as well as from surface water samples in Maiella National Park, Italy. Ecological and georeferenced data were used to select two sampling locations, one where wildlife was caught within livestock grazing areas (sympatric group) and one where wildlife was caught outside of livestock grazing areas (non-sympatric group). Ninety-nine bacterial isolates from 132 feces samples and seven isolates from five water samples were collected between October and December 2019. The specimens were examined for species identification, antibiotic susceptibility and molecular detection of antibiotic resistance. Forty isolates were identified as Escherichia coli, forty-eight as Enterococcus spp., eight as Streptococcus spp. and ten as other gram-negative bacteria. Phenotypic antibiotic resistance to at least one antimicrobial agent, including some antibiotics that play a critical role in human medicine, was detected in 36/106 (33.9%, 95% CI: 25-43) isolates and multidrug resistance was detected in 9/106 isolates (8.49%, 95% CI: 3.9-15.5). In addition, genes associated with antibiotic resistance were identified in 61/106 (57.55%, 95% CI: 47.5-67) isolates. The samples from sympatric areas were 2.11 (95% CI: 1.2-3.5) times more likely to contain resistant bacterial isolates than the samples from non-sympatric areas. These data suggest that drug resistant bacteria may be transmitted in areas where wildlife and livestock cohabitate. This emphasizes the need for further investigations focusing on the interactions between humans, wildlife, and the environment, the results of which can aid in the early detection of emerging AMR profiles and possible transmission routes.202336766321
5729150.9997Virulome and genome analyses identify associations between antimicrobial resistance genes and virulence factors in highly drug-resistant Escherichia coli isolated from veal calves. Food animals are known reservoirs of multidrug-resistant (MDR) Escherichia coli, but information regarding the factors influencing colonization by these organisms is lacking. Here we report the genomic analysis of 66 MDR E. coli isolates from non-redundant veal calf fecal samples. Genes conferring resistance to aminoglycosides, β-lactams, sulfonamides, and tetracyclines were the most frequent antimicrobial resistance genes (ARGs) detected and included those that confer resistance to clinically significant antibiotics (blaCMY-2, blaCTX-M, mph(A), erm(B), aac(6')Ib-cr, and qnrS1). Co-occurrence analyses indicated that multiple ARGs significantly co-occurred with each other, and with metal and biocide resistance genes (MRGs and BRGs). Genomic analysis also indicated that the MDR E. coli isolated from veal calves were highly diverse. The most frequently detected genotype was phylogroup A-ST Cplx 10. A high percentage of isolates (50%) were identified as sequence types that are the causative agents of extra-intestinal infections (ExPECs), such as ST69, ST410, ST117, ST88, ST617, ST648, ST10, ST58, and ST167, and an appreciable number of these isolates encoded virulence factors involved in the colonization and infection of the human urinary tract. There was a significant difference in the presence of multiple accessory virulence factors (VFs) between MDR and susceptible strains. VFs associated with enterohemorrhagic infections, such as stx, tir, and eae, were more likely to be harbored by antimicrobial-susceptible strains, while factors associated with extraintestinal infections such as the sit system, aerobactin, and pap fimbriae genes were more likely to be encoded in resistant strains. A comparative analysis of SNPs between strains indicated that several closely related strains were recovered from animals on different farms indicating the potential for resistant strains to circulate among farms. These results indicate that veal calves are a reservoir for a diverse group of MDR E. coli that harbor various resistance genes and virulence factors associated with human infections. Evidence of co-occurrence of ARGs with MRGs, BRGs, and iron-scavenging genes (sit and aerobactin) may lead to management strategies for reducing colonization of resistant bacteria in the calf gut.202235298535
5734160.9997Escherichia coli Strains Originating from Raw Sheep Milk, with Special Reference to Their Genomic Characterization, Such as Virulence Factors (VFs) and Antimicrobial Resistance (AMR) Genes, Using Whole-Genome Sequencing (WGS). The objective of this work was to deliver a comprehensive genetic characterization of a collection of E. coli strains isolated from raw sheep milk. To complete our purpose, the technique of whole-genome sequencing, coupled with bioinformatics and phenotypic characterization of antimicrobial resistance, was performed. These Gram-negative, facultative anaerobic bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Shigella spp. and Salmonella spp. Genetic analysis was carried out on all strains (phylogram, sequence types, VFs, AMR genes, and pangenome). The results showed the presence of various genetic traits that are related to virulence factors contributing to their pathogenic potential. In addition, genes conferring resistance to antibiotics were also detected and confirmed using phenotypic tests. Finally, the genome of the E. coli strains was characterized by the presence of several mobile genetic elements, thus facilitating the exchange of various genetic elements, associated with virulence and antimicrobial resistance, within and beyond the species, through horizontal gene transfer. Contaminated raw sheep milk with pathogenic E. coli strains is particularly alarming for cheese production in artisan dairies.202540872695
5577170.9997Study on Bacteria Isolates and Antimicrobial Resistance in Wildlife in Sicily, Southern Italy. Wild environments and wildlife can be reservoirs of pathogens and antibiotic resistance. Various studies have reported the presence of zoonotic bacteria, resistant strains, and genetic elements that determine antibiotic resistance in wild animals, especially near urban centers or agricultural and zootechnical activities. The purpose of this study was the analysis, by cultural and molecular methods, of bacteria isolated from wild animals in Sicily, Italy, regarding their susceptibility profile to antibiotics and the presence of antibiotic resistance genes. Bacteriological analyses were conducted on 368 wild animals, leading to the isolation of 222 bacterial strains identified by biochemical tests and 16S rRNA sequencing. The most isolated species was Escherichia coli, followed by Clostridium perfringens and Citrobacter freundii. Antibiograms and the determination of resistance genes showed a reduced spread of bacteria carrying antibiotic resistance among wild animals in Sicily. However, since several wild animals are becoming increasingly close to residential areas, it is important to monitor their health status and to perform microbiological analyses following a One Health approach.202133478101
5621180.9997Comparative Genomics of DH5α-Inhibiting Escherichia coli Isolates from Feces of Healthy Individuals Reveals Common Co-Occurrence of Bacteriocin Genes with Virulence Factors and Antibiotic Resistance Genes. Background/Objectives: The presence of multi-drug-resistant (MDR) bacteria in healthy individuals poses a significant public health concern, as these strains may contribute to or even facilitate the dissemination of antibiotic resistance genes (ARGs) and virulence factors. In this study, we investigated the genomic features of antimicrobial-producing Escherichia coli strains from the gut microbiota of healthy individuals in Singapore. Methods: Using a large-scale screening approach, we analyzed 3107 E. coli isolates from 109 fecal samples for inhibitory activity against E. coli DH5α and performed whole-genome sequencing on 37 representative isolates. Results: Our findings reveal genetically diverse strains, with isolates belonging to five phylogroups (A, B1, B2, D, and F) and 23 unique sequence types (STs). Bacteriocin gene clusters were widespread (92% of isolates carried one or more bacteriocin gene clusters), with colicins and microcins dominating the profiles. Notably, we identified an hcp-et3-4 gene cluster encoding an effector linked to a Type VI secretion system. Approximately 40% of the sequenced isolates were MDR, with resistance for up to eight antibiotic classes in one strain (strain D96). Plasmids were the primary vehicles for ARG dissemination, but chromosomal resistance determinants were also detected. Additionally, over 55% of isolates were classified as potential extraintestinal pathogenic E. coli (ExPEC), raising concerns about their potential pathogenicity outside the intestinal tract. Conclusions: Our study highlights the co-occurrence of bacteriocin genes, ARGs, and virulence genes in gut-residing E. coli, underscoring their potential role in shaping microbial dynamics and antibiotic resistance. While bacteriocin-producing strains show potential as probiotic alternatives, careful assessment of their safety and genetic stability is necessary for therapeutic applications.202541009839
2534190.9997Prevalence, antibiotic resistance, and virulence gene profile of Escherichia coli strains shared between food and other sources in Africa: A systematic review. BACKGROUND AND AIM: Foodborne diseases caused by Escherichia coli are prevalent globally. Treatment is challenging due to antibiotic resistance in bacteria, except for foodborne infections due to Shiga toxin-producing E. coli, for which treatment is symptomatic. Several studies have been conducted in Africa on antibiotic resistance of E. coli isolated from several sources. The prevalence and distribution of resistant pathogenic E. coli isolated from food, human, and animal sources and environmental samples and their virulence gene profiles were systematically reviewed. MATERIALS AND METHODS: Bibliographic searches were performed using four databases. Research articles published between 2000 and 2022 on antibiotic susceptibility and virulence gene profile of E. coli isolated from food and other sources were selected. RESULTS: In total, 64 articles were selected from 14 African countries: 45% of the studies were conducted on food, 34% on animal samples, 21% on human disease surveillance, and 13% on environmental samples. According to these studies, E. coli is resistant to ~50 antimicrobial agents, multidrug-resistant, and can transmit at least 37 types of virulence genes. Polymerase chain reaction was used to characterize E. coli and determine virulence genes. CONCLUSION: A significant variation in epidemiological data was noticed within countries, authors, and sources (settings). These results can be used as an updated database for monitoring E. coli resistance in Africa. More studies using state-of-the-art equipment are needed to determine all resistance and virulence genes in pathogenic E. coli isolated in Africa.202338023276