Genetic elements associated with antimicrobial resistance among avian pathogenic Escherichia coli

Prevalence of specific serogroups, antibiotic resistance and virulence factors of avian pathogenic Escherichia coli (APEC) isolated from clinical cases: A systematic review and meta-analysis

Pathogenic strains of Escherichia coli infecting poultry, commonly called avian pathogenic E. coli (APEC) present significant risks, to the health of both poultry and the general public. This systematic review aimed to examine the prevalence of APEC serotypes, sequence types (ST), phylogenetic groups, virulence factors and antibiotic resistance patterns based on 189 research papers sourced from PubMed, Web of Science, and ProQuest. Then, data were extracted from the selected studies and analyzed to assess the global distribution and characteristics of APEC strains. The metaprop codes in the Meta and Metafor packages of R as implemented in RStudio were then used to conduct meta-analysis. Among APEC strains identified from these different research reports serogroup O78 had the highest overall prevalence (16 %), followed by serogroups O2 (10 %), and O117 (8 %). The most common ST profiles were ST117 (20 %), ST140 (15 %), ST95 (12 %), and ST131 (9 %). ST117 and ST140 are known reservoirs for pathogenic E. coli in humans. Moreover, phylogenetic assessment highlighted the prevalence of phylogroups A, A1, F, D, and B2 among APEC strains indicating diversity in phylogenetic origin within poultry populations. The presence of antimicrobial resistance was notable among APEC strains against antibiotics such as tetracyclines, penicillins, and cephalosporins. This resistance may be linked to use of antimicrobials in poultry production in certain regions presenting challenges for both animal health management and human infection control. Analysis of sequences linked to adherence or virulence indicated that genes encoding adhesins (csg, fimC), iron/metal uptake (sitB, sitC, iroD) and cytotoxicity (estB, hlyF), and serum resistance (traT, iss) were highly prevalent. These factors have been reported to contribute to APEC host colonization and virulence in poultry. In summary, this overview of the characteristics of APEC highlights the pressing importance of monitoring and implementing management approaches to reduce antimicrobial resistance considering that a phylogenetic diversity of E. coli strains causes infections in both poultry and humans and represents a risk to both animal and public health. Further, determining the major conserved aspects and predominant mechanisms of virulence of APEC is critical for improving diagnostics and developing preventative measures to reduce the burden of infection caused by pathogenic E. coli in poultry and lower risks associated with foodborne transmission of E. coli to humans through poultry and poultry products.

The synergy effect of matrine and berberine hydrochloride on treating colibacillosis caused by an avian highly pathogenic multidrug-resistant Escherichia coli

Infection by multidrug-resistant avian pathogenic Escherichia coli (APEC) in chickens always leads to the uselessness of antibiotics, highlighting the need for alternative antibacterial agents. Sophora flavescens and Coptis chinensis have been a classical combination used together in Traditional Chinese Medicine (TCM) formulas to treat diseases with similar symptoms to colibacillosis for an extended period, but the effect of their active ingredients' combination on APEC infection remains unstudied. The objective of this study was to explore the synergistic effect of matrine and berberine hydrochloride on colibacillosis caused by an isolated multidrug-resistant APEC. In this study, a highly pathogenic E. coli was isolated from the liver of a diseased chicken in a farm suspected of colibacillosis, and it was resistant to multiple antibiotics. The LD50 of the strain was approximately 3.759×108 CFU/mL. The strain harbored several antibiotic resistance genes and virulence genes. Matrine and berberine hydrochloride have synergistic antibacterial effect against the isolated strain in vitro. The combined use of matrine and berberine hydrochloride exhibited synergistic effects in the treatment of APEC infection by regulating the organ indices, improving the pathological situation, decreasing the bacterial load, and regulating the inflammatory factors to enhance the survival rate of chickens in vivo. These results provided a foundation for revealing the effective effects and possible mechanisms of matrine and berberine hydrochloride as potential antimicrobial agents on diseases caused by multidrug-resistant APEC in chickens.

Unveiling the traits of antibiotic resistance and virulence in Escherichia coli obtained from poultry waste

Antibiotic resistance and virulence factors in avian pathogenic Escherichia coli (APEC) have become significant concerns, contributing to adverse environmental effects. The extensive use of antibiotics in poultry farming has resulted in the emergence of antibiotic-resistant APEC strains. This study prioritizes the molecular screening of APEC to uncover their antibiotic resistance and virulence attributes, with specific attention to their environmental impact. To address the imperative of understanding APEC pathogenesis, our study analyzed 50 poultry waste samples including 10 poultry litter, 15 fecal matter, 15 wastewater, and 10 anatomical waste samples. For the presence of virulence genes, 35 Escherichia coli isolates were subjected to molecular characterization. Amongst these, 27 were APEC strains demonstrating the presence of at least four virulence genes each. Notably, virulence genes such as fimH, ompA, ybjX, waaL, cvaC, hlyF, iss, ompT, and iroN were observed among all the E. coli isolates. Furthermore, eleven of the APEC strains exhibited resistance to tetracycline, ampicillin, sulphonamides, and fluoroquinolones.These findings highlight the role of APEC as a potential source of environmental pollution serving as a reservoir for virulence and resistance genes. Understanding the dynamics of antibiotic resistance and virulence in APEC is essential due to its potential threat to broiler chickens and the broader population through the food chain, intensifying concerns related to environmental pollution. Recognizing the ecological impact of APEC is essential for developing effective strategies to mitigate environmental pollution and safeguard the health of ecosystems and human populations.

Unveiling the landscape of resistance against high priority critically important antimicrobials in food-producing animals across Africa: A scoping review

The rapid population growth in Africa is associated with an increasing demand for livestock products which in turn can lead to antimicrobial use. Antimicrobial usage in animals contributes to the emergence and selection of resistant bacteria which constitutes a serious public health threat. This study aims to review and summarize the available information on highest priority critically important antimicrobials (HPCIAs) resistance in livestock production in Africa. This work will help to inform future policies for controlling antimicrobial resistance (AMR) in the food production chain. A scoping review was conducted according to the Cochrane handbook and following PRISMA 2020 guidelines for reporting. Primary research studies published after 1999 and reporting resistance of Escherichia coli, Enterococcus spp, Staphylococcus aureus, Salmonella spp, and Campylobacter spp to HPCIAs in poultry, cattle, pigs, goats, and sheep in Africa were searched in four databases. A total of 312 articles were included in the review. The majority of the studies (40.7) were conducted in North African countries. More than 49.0% of included studies involved poultry and 26.2% cattle. Cephalosporins and quinolones were the most studied antimicrobial classes. Of the bacteria investigated in the current review, E. coli (41.7%) and Salmonella spp (24.9%) represented the most commonly studied. High levels of resistance against erythromycin in E. coli were found in poultry (MR 96.1%, IQR 83.3-100.0%), cattle (MR 85.7%, IQR 69.2-100.0%), and pigs (MR 94.0%, IQR 86.2-94.0%). In sheep, a high level of resistance was observed in E. coli against nalidixic acid (MR 87.5%, IQR 81.3-93.8%). In goats, the low level of sensibility was noted in S. aureus against streptomycin (MR 86.8%, IQR 19.4-99.0%). The study provides valuable information on HPCIAs resistance in livestock production in Africa and highlights the need for further research and policies to address the public health risk of AMR. This will likely require an investment in diagnostic infrastructure across the continent. Awareness on the harmful impact of AMR in African countries is a requirement to produce more effective and sustainable measures to curb AMR.

Antimicrobial resistance of avian pathogenic Escherichia coli isolated from broiler, layer, and breeder chickens

Background and Aim

Antimicrobials are extensively used in poultry production for growth promotion as well as for the treatment and control of diseases, including avian pathogenic Escherichia coli (APEC). Poor selection, overuse, and misuse of antimicrobial agents may promote the emergence and dissemination of antimicrobial resistance (AMR) in APEC. This study aimed to assess antimicrobial susceptibility patterns and detect antibiotic resistance genes (ARGs) in APEC isolated from clinical cases of colibacillosis in commercial broiler, layer, and breeder chickens.

Materials and Methods

A total of 487 APEC were isolated from 539 across 300 poultry farms in various regions of Nepal. Antimicrobial susceptibility patterns was determined using the Kirby-Bauer disk diffusion and broth microdilution methods. The index of AMR, such as multiple antibiotic resistance (MAR) index, resistance score (R-score), and multidrug resistance (MDR) profile, were determined. Polymerase chain reaction was employed to detect multiple ARGs and correlations between phenotypic and genotypic resistance were analyzed.

Results

The prevalence of APEC was 91% (487/539). All of these isolates were found resistant to at least one antimicrobial agent, and 41.7% of the isolates were resistant against 8-9 different antimicrobials. The antibiogram of APEC isolates overall showed the highest resistance against ampicillin (99.4%), whereas the highest intermediate resistance was observed in enrofloxacin (92%). The MAR index and R-score showed significant differences between broiler and layers, as well as between broiler breeder and layers. The number of isolates that were resistant to at least one agent in three or more antimicrobial categories tested was 446 (91.6%) and were classified as MDR-positive isolates. The ARGs were identified in 439 (90.1%) APEC isolates, including the most detected mobilized colistin resistance (mcr1) which was detected in the highest (52.6%) isolates. Overall, resistance gene of beta-lactam (blaTEM), mcr1, resistance gene of sulphonamide (sul1) and resistance gene of tetracycline (tetB) (in broiler), were detected in significantly higher than other tested genes (p < 0.001). When examining the pair-wise correlations, a significant phenotype-phenotype correlation (p < 0.001) was observed between levofloxacin and ciprofloxacin, chloramphenicol and tetracycline with doxycycline. Similarly, a significant phenotype-genotype correlation (p < 0.001) was observed between chloramphenicol and the tetB, and colistin with blaTEM and resistance gene of quinolone (qnrA).

Conclusion

In this study, the current state of APEC AMR in commercial chickens is revealed for the first time in Nepal. We deciphered the complex nature of AMR in APEC populations. This information of molecular surveillance is useful to combat AMR in APEC and to contribute to manage APEC associated diseases and develop policies and guidelines to enhance the commercial chicken production.

Phenotypic and genotypic characterization of extended spectrum beta-lactamase producing E. coli harboring carbapenem and colistin-resistant genes from poultry farms in Egypt

Background

eEscherichia coli (E. coli) bacteria that produce extended spectrum beta-lactamase (ESBL) is associated with a high prevalence of human illnesses worldwide. The emergence of resistance to carbapenem and colistin compounds poses further challenges to the treatment options for these illnesses. This study aimed to evaluate the phenotypic and genotypic pattern of resistance to carbapenem and colistin in ESBL-producing E. coli. Escherichia coli isolates collected from the respiratory tract of chickens in El-Sharkia government, Egypt.

Methods

A total of 250 lung samples were collected from 50 poultry farms. These samples were then subjected to isolation, identification, and serotyping of E. coli. The presence of antimicrobial resistance was identified by disc diffusion testing. The occurrence of ESBL phenotypes was also assessed using the double disc synergy method. PCR/sequencing techniques were employed to examine the presence of ESBL (β-lactamase (bla)-TEM, blaSHV, and blaCTX-M), colistin (mcr-1), and carbapenem (blaNDM, blaVIM, and blaKPC) resistance genes.

Results

The findings revealed that 140 out of 250 (56%) were identified as E. coli. All E. coli isolates had a high level of multi-antimicrobial resistance (MAR) with an index value greater than 0.2, and 65.7% of them were confirmed to produce ESBL. Out of the 92 ESBL phenotypes, 55 (59.7%), 32 (34.7%), 18 (19.6%), and 37 (40.2%) isolates harbor b laTEM-3, b laSHV-4, b laCTX-M-1, a nd blaCTX-M-14 genes, respectively. The blaNDM-1 gene was identified in all 40 phenotypes that exhibited resistance to carbapenem, accounting for 28.5% of all strains of E. coli and 43.4% of ESBL isolates. The VIM and KPC genes were not detected in any of the samples. Furthermore, there was a significant prevalence of the mobilized colistin resistance (mcr)-1 gene, with 64 (69.5%) of the ESBL isolates exhibiting this gene.

Conclusion

The prevalence of ESBL-producing E. coli, particularly those resistant to carbapenem and colistin, poses a significant public health risk in society.

Comparative meta-analysis of antimicrobial resistance from different food sources along with one health approach in the Egypt and UK

BACKGROUND

Antimicrobial resistance (AMR) is a critical global issue that poses significant threats to human health, animal welfare, and the environment. With the increasing emergence of resistant microorganisms, the effectiveness of current antimicrobial medicines against common infections is diminishing. This study aims to conduct a competitive meta-analysis of surveillance data on resistant microorganisms and their antimicrobial resistance patterns in two countries, Egypt and the United Kingdom (UK).

METHODS

Data for this study were obtained from published reports spanning the period from 2013 to 2022. In Egypt and the UK, a total of 9,751 and 10,602 food samples were analyzed, respectively. Among these samples, 3,205 (32.87%) in Egypt and 4,447 (41.94%) in the UK were found to contain AMR bacteria.

RESULTS

In Egypt, the predominant resistance was observed against β-lactam and aminoglycosides, while in the United Kingdom, most isolates exhibited resistance to tetracycline and β-lactam. The findings from the analysis underscore the increasing prevalence of AMR in certain microorganisms, raising concerns about the development of multidrug resistance.

CONCLUSION

This meta-analysis sheds light on the escalating AMR problem associated with certain microorganisms that pose a higher risk of multidrug resistance development. The significance of implementing One Health AMR surveillance is emphasized to bridge knowledge gaps and facilitate accurate AMR risk assessments, ensuring consumer safety. Urgent actions are needed on a global scale to combat AMR and preserve the effectiveness of antimicrobial treatments for the well-being of all living beings.

Identification, Typing, and Drug Resistance Analysis of Escherichia coli in Two Different Types of Broiler Farms in Hebei Province

Hebei Province is an important area for breeding broiler chickens in China, but the antimicrobial resistance and prevalence of Escherichia coli (E. coli) are still unclear. A total of 180 cloacal samples from broiler farms in Hebei Province were collected and used for the isolation and identification of E. coli. The isolates were subjected to resistance phenotyping, resistance profiling, and genotyping, and some multiresistant strains were subjected to multilocus sequence typing (MLST). The results showed that 175 strains were isolated. Among both types of broiler farms, the ampicillin resistance rate was the highest, and the meropenem resistance rate was the lowest. Serious multiresistance was present in both types of broiler farms. Thirty strains of multidrug-resistant E. coli were typed by MLST to obtain a total of 18 ST types, with ST10 being the most prevalent. This study was to simply analyze the antimicrobial resistance and prevalence of E. coli in broiler chickens in Hebei Province after the implementation of the pilot work program of action to reduce the use of veterinary antimicrobials in standard farms (SFs) and nonstandard farms (NSFs). This study will provide a research basis and data support for the prevention and control of E. coli in Hebei.

Genomic Analysis of Multidrug-Resistant Escherichia coli Strains Isolated in Tamaulipas, Mexico

The global spread of antimicrobial resistance genes (ARGs) is a major public health concern. Mobile genetic elements (MGEs) are the main drivers of this spread by horizontal gene transfer (HGT). Escherichia coli is widespread in various environments and serves as an indicator for monitoring antimicrobial resistance (AMR). Therefore, the objective of this work was to evaluate the whole genome of multidrug-resistant E. coli strains isolated from human clinical, animal, and environmental sources. Four E. coli strains previously isolated from human urine (n = 2), retail meat (n = 1), and water from the Rio Grande River (n = 1) collected in northern Tamaulipas, Mexico, were analyzed. E. coli strains were evaluated for antimicrobial susceptibility, followed by whole genome sequencing and bioinformatic analysis. Several ARGs were detected, including blaCTX-M-15, blaOXA-1, blaTEM-1B, blaCMY-2, qnrB, catB3, sul2, and sul3. Additionally, plasmid replicons (IncFIA, IncFIB, IncFII, IncY, IncR, and Col) and intact prophages were also found. Insertion sequences (ISs) were structurally linked with resistance and virulence genes. Finally, these findings indicate that E. coli strains have a large repertoire of resistance determinants, highlighting a high pathogenic potential and the need to monitor them.

Molecular mechanism of antimicrobial co-resistance Colistin (mcr-1) and ESBLs genes among Escherichia coli isolates from commercial chickens in Pakistan

Emergence of plasmid mediated colistin and extended spectrum β-lactamases (ESBL) resistant genes has been impacted the efficacy of colistin and β-lactams drugs like 3rd, 4th generation cephalosporin. Current study was aimed to investigate antimicrobial resistance genes (ARGs) among Escherichia coli isolates from meat producing commercial broilers in Pakistan. Two hundred (n=200) fecal samples were collected during January-2018 to August-2019. For isolation of E. coli, pink colonies on MacConkey agar were transferred to EMB agar. Metallic sheen color colonies were tested biochemically using API-20E kit. The molecular identification of E. coli (n=153) was targeted by amplification of uid gene through polymerase chain reaction (PCR) and different ARGs i.e. gentamicin, streptomycin, tetracycline, colistin, β-lactams drugs, quinolone and ampicillin followed by sequence analysis. Genotypically, followed by phenotypically of resistant ARGs of isolated PCR-confirmed E. coli (153) shoed resistant against gentamicin (aac(3)-IV), streptomycin (aadA1), tetracycline (tetA), colistine (mcr-1), ampicillin (bla-TEM) and bla-CTX-M were 86%, 88%, 86%, 88%, 83% & 77% respectively. 33/38 (86%) of the isolate was positive for quinolone resistance. Colistine (mcr-1), ESBLs (bla-TEM) and (bla-CTX-M) resistance genes were 88%, 83% and 77% respectively. About 33 isolated E. coli harbored the both mcr-1 and ESBLs genes. All of E. coli isolates were found sensitive to ceftriaxone (CTX-30) and imipenem (IMP-10). The Isolated E. coli showed single or multi clade decadency. The E. coli and ARGs sequences showed single or multi clade decadency. This is first comprehensive study from Pakistan that described the molecular evidences of ARGs and their co-existence in single isolates originated from commercial poultry. Commercial chicken (Broilers) can act as melting pot of antibiotic resistance genes for human being. It is alarming situation for surveillance of antibiotic resistance program because of more regulated prescription of antimicrobial agents in Pakistan.

Antimicrobial resistance, virulence associated genes and phylogenetic background versus plasmid replicon types: the possible associations in avian pathogenic Escherichia coli (APEC)

BACKGROUND

Antimicrobial resistance (AMR) in bacterial isolates from food producing animals not only challenges the preventive and therapeutic strategies in veterinary medicine, but also threatens public health. Genetic elements placed on both chromosome and plasmids could be involved in AMR. In the present study, the associations of genomic backbone and plasmids with AMR were evaluated. We also provided some primary evidences that which genetic lineages potentially host certain groups of plasmids.

RESULTS

In the current study, 72 avian pathogenic Escherichia coli (APEC) strains were examined. Isolates resistant to tetracycline and trimethoprim-sulfamethoxazole (87.5%; each), and harboring bla_TEM (61.1%) were dominant. Moreover, phylogroup D was the most prevalent phylogroup in total (23.6%), and among multidrug-resistant (MDR) isolates (14/63). The most prevalent Inc-types were also defined as follows: IncP (65.2%), IncI1 (58.3%), and IncF group (54.1%). Significant associations among phylogroups and AMR were observed such as group C to neomycin (p = 0.002), gentamicin (p = 0.017) and florfenicol (p = 0.036). Furthermore, group D was associated with bla_CTX. In terms of associations among Inc-types and AMR, resistance to aminoglycoside antibiotics was considerably linked with IncP (p = 0.012), IncI1 (p = 0.038) and IncA/C (p = 0.005). The bla_TEM and bla_CTX genes presence were connected with IncI1 (p = 0.003) and IncFIC (p = 0.013), respectively. It was also shown that members of the D phylogroup frequently occured in replicon types FIC (8/20), P (13/47), I1 (13/42), HI2 (5/14) and L/M (3/3).

CONCLUSIONS

Accorging to the results, it seems that group D strains have a great potential to host a variety of plasmids (Inc-types) carrying different AMR genes. Thus, based on the results of the current study, phyogroup D could be a potential challenge in dealing with AMR in poultry. There were more strong correlations among Inc-types and AMR compared to phylotypes and AMR. It is suggested that in epidemiological studies on AMR both genomic backbone and major plasmid types should be investigated.

Characterizing 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.

Comparative Characteristics and Pathogenic Potential of Escherichia coli Isolates Originating from Poultry Farms, Retail Meat, and Human Urinary Tract Infection

The pathogenicity of many bacterial strains is determined by the acquisition of virulence genes and depends on many factors. The aim of this study was to analyse the phylogenetic background, virulence patterns, and drug susceptibility of 132 E. coli isolates tested in the context of the ExPEC (Extraintestinal Pathogenic E. coli) pathotype and the correlation of these features with bacterial isolation source: food (retail meat), poultry farms (AFEC—Avian Faecal E. coli), and patients with UTI (urinary tract infection) symptoms. The drug-susceptibility results of tested E. coli isolates obtained indicate that the resistance profile—ampicillin/tetracycline/trimethoprim+sulfamethoxazole/ciprofloxacin (AMP/TE/SXT/CIP)—was most frequently observed. The multidrug resistance (MDR) phenotype was found in 31.8% of isolates from poultry farms, 36.8% of strains isolated from food, and 20% of clinical samples. The greatest similarity of virulence profiles applied to isolates derived from poultry farms and food. Most of the AFEC from poultry farms and food-derived isolates belonged to commensals from phylogroups A and B1, while among the isolates from patients with UTI symptoms, the most common was the B2 phylogroup. The collective analysis showed similarity of the three studied groups of E. coli isolates in terms of the presented patterns of antimicrobial resistance, while the virulence profiles of the isolates studied showed great diversity. The phylogroup analysis showed no similarity between the poultry/food isolates and the UTI isolates, which had significant pathogenic potential.

Combating Bovine Mastitis in the Dairy Sector in an Era of Antimicrobial Resistance: Ethno-veterinary Medicinal Option as a Viable Alternative Approach

Bovine mastitis (BM) is the traditional infectious condition in reared cattle which may result in serious repercussions ranging from animal welfare to economic issues. Owing to the high costs associated with preventative practices and therapeutic measures, lower milk output, and early culling, bovine mastitis is accountable for most of the financial losses suffered in cattle farming. Streptococcus agalactiae, Staphylococcus aureus, Streptococcus dysgalactiae and coliform bacteria are the predominant pathogens for bovine mastitis. In addition, the occurrence of BM has been linked to lactation stage and poor management, in the latter case, the poor stabling conditions around udder hygiene. BM occurs throughout the world, with varying rates of Streptococcus agalactiae infection in different regions. Despite the modern techniques, such as the appropriate milking practices that are applied, lower levels of pathogen vulnerability may help to prevent the development of the disease, BM treatment is primarily reliant on antibiotics for both prophylactic and therapeutic purposes. Nevertheless, as a result of the proliferation of bacterial agents to withstand the antibiotic effects, these therapies have frequently proven ineffectual, resulting in persistent BM. Consequently, alternative medicines for the management of udder inflammation have been researched, notably natural compounds derived from plants. This review focuses on BM in terms of its risk factors, pathogenesis, management, the molecular identification of causative agents, as well as the application of ethno-veterinary medicine as an alternative therapy.

Public health implications of plasmid-mediated quinolone and aminoglycoside resistance genes in Escherichia coli inhabiting a major anthropogenic river of India

Presence of antimicrobial resistance (AMR) genes in Escherichia coli inhabiting anthropogenic rivers is an important public health concern because plasmid-mediated AMR genes can easily spread to other pathogens by horizontal gene transfer. Besides β -lactams, quinolones and aminoglycosides are the major antibiotics against E. coli. In the present study, we have investigated the presence of plasmid-mediated quinolone resistance (PMQR) and aminoglycoside resistance genes in E. coli isolated from a major river of northern India. Our results revealed that majority of the strains were phenotypically susceptible for fluoroquinolones and some aminoglycosides like amikacin, netilmicin, tobramycin and gentamicin. However, 16.39% of the strains were resistant for streptomycin, 8.19% for kanamycin and 3.30% for gentamicin. Of the various PMQR genes investigated, only qnrS1 was present in 24.59% of the strains along with ISEcl2 . Aminoglycoside-resistance genes like strA-strB were found to be present in 16.39%, aphA1 in 8.19% and aacC 2 in only 3.30% of the strains. Though, no co-relation was observed between phenotypic resistance for fluorquinolones and presence of PMQR genes, phenotypic resistance for streptomycin, kanamycin and gentamicin exactly co-related with the presence of the genes strA-strB , aphA1 and aacC2 , respectively. Moreover, all the AMR genes discerned in aquatic E. coli were found to be situated on conjugative plasmids and, thus easily transferrable. Our study accentuates the importance of routine surveillance of urban rivers to curtail the spread of AMR genes in aquatic pathogens.

Evaluation of phenotypic and genotypic patterns of aminoglycoside resistance in the Gram-negative bacteria isolates collected from pediatric and general hospitals

The purpose of the current study was to evaluate the phenotypic and genotypic patterns of aminoglycoside resistance among the Gram-negative bacteria (GNB) isolates collected from pediatric and general hospitals in Iran. A total of 836 clinical isolates of GNB were collected from pediatric and general hospitals from January 2018 to the end of December 2019. The identification of bacterial isolates was performed by conventional biochemical tests. Susceptibility to aminoglycosides was evaluated by the disk diffusion method (DDM). The frequency of genes encoding aminoglycoside-modifying enzymes (AMEs) was screened by the PCR method via specific primers. Among all pediatric and general hospitals, the predominant GNB isolates were Acinetobacter spp. (n = 327) and Escherichia coli (n = 144). However, E. coli (n = 20/144; 13.9%) had the highest frequency in clinical samples collected from pediatrics. The DDM results showed that 64.3% of all GNB were resistant to all of the tested aminoglycoside agents. Acinetobacter spp. and Klebsiella pneumoniae with 93.6%, Pseudomonas aeruginosa with 93.4%, and Enterobacter spp. with 86.5% exhibited very high levels of resistance to gentamicin. Amikacin was the most effective antibiotic against E. coli isolates. In total, the results showed that the aac (6')-Ib gene with 59% had the highest frequency among genes encoding AMEs in GNB. The frequency of the surveyed aminoglycoside-modifying enzyme genes among all GNB was found as follows: aph (3')-VIe (48.7%), aadA15 (38.6%), aph (3')-Ia (31.3%), aph (3')-II (14.4%), and aph (6) (2.6%). The obtained data demonstrated that the phenotypic and genotypic aminoglycoside resistance among GNB was quite high and it is possible that the resistance genes may frequently spread among clinical isolates of GNB.

Multidrug resistance, biofilm formation, and virulence genes of Escherichia coli from backyard poultry farms

Background and Aim:

Backyard chicken flocks have traditionally been regarded as an essential food source in developed countries; however, they may act as reservoirs and spread various zoonotic bacterial pathogens. This study was designed to investigate the prevalence, phenotypic resistance, biofilm formation (BF), and pathotypes of Escherichia coli isolates from backyard poultry farms.

Materials and Methods:

Cloacal swabs (n=150) and internal organs (n=150) were collected from 30 backyard chicken flocks; 20 of them were experiencing systemic infection, and the other ten were apparently healthy. Samples were bacteriologically examined for E. coli isolation. Isolates were identified biochemically by the VITEK^® 2 COMPACT system (BioMérieux, France). For molecular identification, 16S rRNA was amplified and sequenced. Ten antimicrobials were selected for E. coli antimicrobial susceptibility testing. The minimum inhibitory concentration for each antimicrobial was determined. The extended-spectrum β-lactamase activity in isolates was investigated using cephalosporin/clavulanate combination disks. The ability of isolates for BF was determined by the microtiter plate method. Thirteen virulence genes linked to different E. coli pathotypes and two serotype-related genes were investigated by real-time polymerase chain reaction.

Results:

Eighty-six E. coli strains were isolated from 30 backyard chicken flocks. The isolates were biochemically identified to the species level. Genetically, sequences of the 16S rRNA gene showed >98% identity with E. coli in the National Center for Biological Information database. The frequency of isolation from diseased flocks was significantly higher (p<0.05) than apparently healthy flocks; 63.9% of the isolates were recovered from cloacal swabs and 36.04% were recovered from internal organs. E. coli isolates showed high resistance to ampicillin (AMP; 75.6%), gentamicin (39.5%), and tetracycline (29.1%). However, none of the isolates were resistant to imipenem. A variable drug resistance profile for E. coli isolates was reported. Twenty-one (24.4%) isolates were sensitive to all ten antimicrobials. Seven (8.1%) isolates were resistant only to AMP, and 28 (32.6%) were resistant to two antimicrobials, whereas the remaining 30 (34.9%) isolates showed multidrug resistance (MDR). Of the 86 isolates, 8 (9.3%) were confirmed as extended-spectrum β-lactamase (ESBL)-producing E. coli by the combination disk diffusion method. All ESBL isolates were MDR with an MDR index of 0.5-0.6. Fifty-seven (66.3%) isolates were capable of forming biofilms; 22 (25.6%) of them were strong biofilm producers, 24 (27.9%) moderate producers, and 11 (12.8%) weak producers. A statistically significant pairwise correlation was obtained for MDR versus BF (r=0.512) and MDR index versus BF (r=0.556). Based on virulence gene profiles, five pathotypes were identified, including enteropathogenic E. coli (39.5%), avian pathogenic E. coli (32.53%), enterohemorrhagic E. coli (EHEC; 9.3%), enterotoxigenic E. coli (ETEC; 5.8%), and enteroaggregative E. coli (EAEC; 1.2%). The lower frequency of EAEC and ETEC was statistically significant than other pathotypes. Three isolates were identified as O157 based on the detection of the rbfO157 gene.

Conclusion:

This study reported a high prevalence of MDR, suggesting the misuse of antimicrobials in backyard chicken farms. The emergence of ESBL and EHEC isolates in backyard chickens is a public health concern. Furthermore, the backyard flocks environment may harbor different pathogenic bacteria that may enhance the persistence of infection and the transmission to in-contact humans. Regular monitoring for the occurrence of MDR and the zoonotic pathotypes among E. coli in backyard chicken flocks is recommended, as these bacteria can transmit to humans through food products or contaminated environments.

High incidence of multi-drug resistance and heterogeneity of mobile genetic elements in Escherichia coli isolates from diseased ducks in Sichuan province of China

Harmonious ecological environment is a major concern with rising feeding and consumption of ducks, as these waterfowl birds can promote the spread of antibiotic resistant genes (ARGs). Therefore, this study was conducted to know diversity of antimicrobial resistance (AMR), integrons, and mobile genetic elements (MGEs) in Escherichia coli (E. coli) isolated from intestinal contents or pericardial effusion of diseased ducks from 2018 to 2020 in Sichuan, China. The AMR phenotype was determined via disk diffusion test in 165 E. coli isolates. Further, the integrase genes of integron (intI1, intI2 and intI3 genes), gene cassettes (GCs) and MGEs were screened by PCR and sequencing. The results indicated 100% isolates were resistant to at least one antibiotic and 98.8% were multidrug-resistant strains. Highest AMR phenotype was recorded to rifampin (97.0%) followed by ampicillin (95.8%), chloramphenicol (89.7%), trimethoprim-sulfamethoxazole (84.2%), ciprofloxacin (83.0%), cefotaxime (80.0%), streptomycin (75.8%), doxycycline (49.7%), amikacin (10.3%), amoxicillin/clavulanic acid (3.6%), polymyxin B (1.2%) and ertapenem (0.6%). Further, class 1 and 2 integrons were found in 87.3% and 17.6% isolates, respectively. All isolates were negative for intI3 gene. The variable region of class 1 and 2 integrons contained total 13 different GCs, including arr-3+dfrA27, dfrA1+aadA1, dfrA17+aadA5, dfrA12, dfrA1+sat2+aadA1, dfrA12+aadA2, dfrA5, aadA2+ere(A)+dfrA32, aac(6')-Ib-cr, aadA22, aadA5, dfrA17, and dfrA27. Moreover, 13 MGEs in 69 different combinations were observed with predominance of IS26 followed by tnpA/Tn21, trbC, ISEcp1, merA, ISAba1, tnsA, tnsB, tnsC, IS1133, tnsD, ISCR3/14, and tnsE. Thus, the monitoring of integrons, MGEs and ARGs is important to understand the complex mechanism of AMR, which might help to introduce interventions for prevention and control of AMR in duck farms in China.

The Avian Pathogenic Escherichia coli (APEC) pathotype is comprised of multiple distinct, independent genotypes

Avian Pathogenic E. coli (APEC) is the causative agent of avian colibacillosis, resulting in economic losses to the poultry industry through morbidity, mortality and carcass condemnation, and impacts the welfare of poultry. Colibacillosis remains a complex disease to manage, hampered by diagnostic and classification strategies for E. coli that are inadequate for defining APEC. However, increased accessibility of whole genome sequencing (WGS) technology has enabled phylogenetic approaches to be applied to the classification of E. coli and genomic characterization of the most common APEC serotypes associated with colibacillosis O1, O2 and O78. These approaches have demonstrated that the O78 serotype is representative of two distinct APEC lineages, ST-23 in phylogroup C and ST-117 in phylogroup G. The O1 and O2 serotypes belong to a third lineage comprised of three sub-populations in phylogroup B2; ST-95, ST-140 and ST-428/ST-429. The frequency with which these genotypes are associated with colibacillosis implicates them as the predominant APEC populations and distinct from those causing incidental or opportunistic infections. The fact that these are disparate clusters from multiple phylogroups suggests that these lineages may have become adapted to the poultry niche independently. WGS studies have highlighted the limitations of traditional APEC classification and can now provide a path towards a robust and more meaningful definition of the APEC pathotype. Future studies should focus on characterizing individual APEC populations in detail and using this information to develop improved diagnostics and interventions.

A retrospective analysis of antimicrobial resistance in pathogenic Escherichia coli and Salmonella spp. isolates from poultry in Uganda

There are increasing reports of antimicrobial treatment failures for bacterial diseases of poultry in Uganda. The paucity of data on antimicrobial resistance (AMR) of pathogenic bacteria in Uganda is a major setback to AMR control. This study investigated the occurrence of fowl typhoid, colibacillosis, and AMR in associated pathogens from 2012 to 2018. Laboratory records from the Central Diagnostic Laboratory (CDL), a National Veterinary Diagnostic Facility located at Makerere University, were reviewed. Archived isolates of the causative bacteria for the two diseases were also evaluated for AMR. The frequencies of the two disease conditions, their clinical and necropsy presentations and the demographic data of the diagnostic samples were summarized from the records. Archived bacterial isolates were revived before antimicrobial susceptibility testing. This was done on Mueller Hinton agar using the disk diffusion method, against 16 antimicrobials of medical and veterinary importance according to the Clinical Laboratory Standards Institute guidelines. A total of 697 poultry cases were presented for bacteriological investigations in the review period. Colibacillosis and salmonellosis had prevalence rates of 39.7% (277/697) and 16.2% (113/697), respectively. A total of 63 and 92 isolates of Escherichia coli and Salmonella spp., respectively, were archived but 43 (68.3%) E. coli and 47 (51.1%) Salmonella spp. isolates were recovered and evaluated for AMR. Multidrug resistance was more frequent in E. coli (38; 88.4%) than salmonellae (25; 53.2%), (p < 0.001). The high prevalence of colibacillosis, salmonellosis and the AMR of associated pathogens warrants immediate institution of appropriate disease control measures.

High incidence of multidrug resistance and class 1 and 2 integrons in Escherichia coli isolated from broiler chickens in South of Iran

The objective was to investigate the multidrug resistance and presence of class 1 and 2 integrons in 300 Escherichia coli isolates obtained from 20 broiler farms during three rearing periods (one-day-old chicks, thirty-day-old chickens, and one day before slaughter) in Fars, South Iran. Results showed that 81.00%, 82.00%, and 85.00% of isolates were multidrug-resistant on the first day, thirty-day-old chickens, and one day before slaughter, respectively. Multidrug-resistant E. coli isolates were further examined for the presence of class 1 and 2 integrons using PCR assay. The existence of class 1 integron-integrase gene (intI1) was confirmed in 68.40%, 72.70%, and 60.90% of multidrug-resistant isolates from stage 1, stage 2, and stage 3 of the rearing period, respectively. The frequency of class 2 integron-integrase gene (intI2) during the first to the third stage of sampling was 2.60%, 25.50%, and 30.40%. Also, sequence analysis of the cassette arrays within class 1 integron revealed the presence of the genes associated with resistance for trimethoprim (dfrA), streptomycin (aadA), erythromycin (ereA), and orfF genes. The results revealed that percentages of antimicrobial resistance in E. coli isolates were significantly higher in the middle and end stages of the rearing period. In conclusion, widespread dissemination of class 1 integrons in all three stages and rising trends of class 2 integrons existence in E. coli isolates during the rearing period of broiler chickens could exacerbate the spread of resistance factors among bacteria in the poultry industry. Future research is needed to clarify its implication for human health.

Characterizing avian pathogenic Escherichia coli (APEC) from colibacillosis cases, 2018

Colibacillosis caused by avian pathogenic Escherichia coli (APEC) is a devastating disease of poultry that results in multi-million-dollar losses annually to the poultry industry. Disease syndromes associated with APEC includes colisepticemia, cellulitis, air sac disease, peritonitis, salpingitis, omphalitis, and osteomyelitis among others. A total of 61 APEC isolates collected during the Fall of 2018 (Aug-Dec) from submitted diagnostic cases of poultry diagnosed with colibacillosis were assessed for the presence of 44 virulence-associated genes, 24 antimicrobial resistance genes and 17 plasmid replicon types. Each isolate was also screened for its ability to form biofilm using the crystal violet assay and antimicrobial susceptibility to 14 antimicrobials using the NARMS panel. Overall, the prevalence of virulence genes ranged from 1.6% to >90% with almost all strains harboring genes that are associated with the ColV plasmid-the defining trait of the APEC pathotype. Overall, 58 strains were able to form biofilms and only three strains formed negligible biofilms. Forty isolates displayed resistance to antimicrobials of the NARMS panel ranging from one to nine agents. This study highlights that current APEC causing disease in poultry possess virulence and resistance traits and form biofilms which could potentially lead to challenges in colibacillosis control.

Impact of Probiotic B. infantis EVC001 Feeding in Premature Infants on the Gut Microbiome, Nosocomially Acquired Antibiotic Resistance, and Enteric Inflammation

Background: Preterm birth is a major determinant of neonatal survival and morbidity, but the gut microbiome and associated enteric inflammation are also key factors in neonatal development and the risk of associated morbidities. We prospectively and longitudinally followed two cohorts of preterm infants, one of which was fed activated Bifidobacterium longum subsp. infantis (B. infantis) EVC001 8 × 109 CFU daily, and the other was not fed a probiotic. Hospital feeding protocol assigned all infants born at <1500 g and/or < 32 weeks corrected gestational age to the probiotic feeding protocol, whereas infants born at >1500 g and/or >32 weeks corrected gestational age were not fed a probiotic. Fecal samples were opportunistically collected from 77 infants throughout the hospital stay, and subjected to shotgun metagenomic sequencing and quantification of enteric inflammation. De-identified metadata was collected from patient medical records. Results: The gut microbiome of preterm infants was typified by a high abundance of Enterobacteriaceae and/or Staphylococcaceae, and multivariate modeling identified the probiotic intervention, rather than degree of prematurity, day of life, or other clinical interventions, as the primary source of change in the gut microbiome. Among infants fed B. infantis EVC001, a high abundance of total Bifidobacteriaceae developed rapidly, the majority of which was B. infantis confirmed via subspecies-specific qPCR. Associated with this higher abundance of Bifidobacteriaceae, we found increased functional capacity for utilization of human milk oligosaccharides (HMOs), as well as reduced abundance of antibiotic resistance genes (ARGs) and the taxa that harbored them. Importantly, we found that infants fed B. infantis EVC001 exhibited diminished enteric inflammation, even when other clinical variables were accounted for using multivariate modeling. Conclusion: These results provide an important observational background for probiotic use in a NICU setting, and describe the clinical, physiological, and microbiome-associated improvements in preterm infants associated with B. infantis EVC001 feeding.

The impact of essential oils on antibiotic use in animal production regarding antimicrobial resistance - a review

Population growth directly affects the global food supply, demanding a higher production efficiency without farmland expansion - in view of limited land resources and biodiversity loss worldwide. In such scenario, intensive agriculture practices have been widely used. A commonly applied method to maximize yield in animal production is the use of subtherapeutic doses of antibiotics as growth promoters. Because of the strong antibiotic selection pressure generated, the intense use of antibiotic growth promoters (AGP) has been associated to the rise of antimicrobial resistance (AMR). Also, cross-resistance can occur, leading to the emergence of multidrug-resistant pathogens and limiting treatment options in both human and animal health. Thereon, alternatives have been studied to replace AGP in animal production. Among such alternatives, essential oils and essential oil components (EOC) stand out positively from others due to, besides antimicrobial effectiveness, improving zootechnical indexes and modulating genes involved in resistance mechanisms. This review summarizes recent studies in essential oils and EOC for zoonotic bacteria control, providing detailed information about the molecular-level effects of their use in regard to AMR, and identifying important gaps to be filled within the animal production area.

Molecular Epidemiology of Antibiotic-Resistant Escherichia coli from Farm-To-Fork in Intensive Poultry Production in KwaZulu-Natal, South Africa

The increased use of antibiotics in food animals has resulted in the selection of drug-resistant bacteria across the farm-to-fork continuum. This study aimed to investigate the molecular epidemiology of antibiotic-resistant Escherichia coli from intensively produced poultry in the uMgungundlovu District, KwaZulu-Natal, South Africa. Samples were collected weekly between August and September 2017 from hatching to final retail products. E. coli was isolated on eosin methylene blue agar, identified biochemically, and confirmed using polymerase chain reaction (PCR). Susceptibility to 19 antibiotics was ascertained by the Kirby–Bauer disc diffusion method. PCR was used to test for resistance genes. The clonal similarity was investigated using enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR). In total, 266 E. coli isolates were obtained from all the samples, with 67.3% being non-susceptible to at least one antibiotic tested and 6.7% multidrug resistant. The highest non-susceptibility was to ampicillin (48.1%) and the lowest non-susceptibility to ceftriaxone and azithromycin (0.8%). Significant non-susceptibility was observed to tetracycline (27.4%), nalidixic acid (20.3%), trimethoprim-sulfamethoxazole (13.9%), and chloramphenicol (11.7%) which have homologues used in the poultry industry. The most frequently observed resistance genes were bla_CTX-M (100%), sul1 (80%), tetA (77%), and tetB (71%). ERIC-PCR grouped isolates into 27 clusters suggesting the spread of diverse clones across the farm-to-fork continuum. This reiterates the role of intensive poultry farming as a reservoir and a potential vehicle for the transmission of antibiotic resistance, with potentially severe public health implications, thus, requiring prompt and careful mitigation measures to protect human and environmental health.

Dissemination of antibiotic resistance genes (ARGs) via integrons in Escherichia coli: A risk to human health

With the induction of various emerging environmental contaminants such as antibiotic resistance genes (ARGs), environment is considered as a key indicator for the spread of antimicrobial resistance (AMR). As such, the ARGs mediated environmental pollution raises a significant public health concern worldwide. Among various genetic mechanisms that are involved in the dissemination of ARGs, integrons play a vital role in the dissemination of ARGs. Integrons are mobile genetic elements that can capture and spread ARGs among environmental settings via transmissible plasmids and transposons. Most of the ARGs are found in Gram-negative bacteria and are primarily studied for their potential role in antibiotic resistance in clinical settings. As one of the most common microorganisms, Escherichia coli (E. coli) is widely studied as an indicator carrying drug-resistant genes, so this article aims to provide an in-depth study on the spread of ARGs via integrons associated with E. coli outside clinical settings and highlight their potential role as environmental contaminants. It also focuses on multiple but related aspects that do facilitate environmental pollution, i.e. ARGs from animal sources, water treatment plants situated at or near animal farms, agriculture fields, wild birds and animals. We believe that this updated study with summarized text, will facilitate the readers to understand the primary mechanisms as well as a variety of factors involved in the transmission and spread of ARGs among animals, humans, and the environment.

Staphylococcus Spp. from Wild Mammals in Aragón (Spain): Antibiotic Resistance Status

Introduction

Antimicrobial resistance is a global health threat. It has been studied in humans and domestic animals, but there is a lack of data on wild animals. The objective of this study is the elucidation of its patterns in Staphylococcus spp. isolated from wild mammals of the Autonomous Community of Aragón (Spain).

Material and Methods

A total of 103 mammals (Artiodactyla, Carnivora, Chiroptera, Erinaceomorpha, and Lagomorpha) were studied. A recovery centre provided 32 and hunting 71. Nasal and faecal samples yielded 111 staphylococci, which were identified by matrix-assisted laser desorption/ionization–time of flight mass spectrometry. A susceptibility test to 11 antibiotics was carried out, and statistical analysis was performed.

Results

Some differences were detected in bacterial prevalence depending on how the mammal fed. Artiodactyla, mainly hunted, were predisposed to carry coagulase-positive staphylococci. The staphylococci species recovered were resistant to at least two classes of antibiotics, and were disseminated in all of the geographical areas studied.

Conclusion

Resistant staphylococci are widely distributed in the wild mammals in the areas of the study, but the resistance quantified in them is lower than that to be expected if the use of antibiotics in farms had a direct influence on the wildlife and its environment. On the other hand, resistance to antibiotics restricted to human use was widely disseminated in various wild animal species.

The role of Enterococcus faecalis during co-infection with avian pathogenic Escherichia coli in avian colibacillosis

Enterococcus spp. (ENT) are frequently co-isolated with avian pathogenic E. coli (APEC) from poultry with colibacillosis, a leading cause of flock mortality. Although largely overlooked, ENT may play an active role in these infections. To assess the frequency of ENT co-isolation in colibacillosis, cultures were collected from birds with gross lesions of omphalitis, polyserositis, and septicaemia over a 3-year period from three turkey flocks and three broiler flocks. In birds diagnosed with colibacillosis based on gross findings and isolation of E. coli, ENT were co-isolated with APEC in 35.7% (n = 41/115) of colibacillosis mortality and 3.7% of total mortality (n = 41/1122). Co-isolated APEC and ENT pairs (n = 41) were further characterized using antimicrobial resistance phenotyping and in vitro co-culture assays. E. faecalis (EF) was the most commonly co-isolated species (68% n = 28/41) and tetracycline resistance was the resistance phenotype most commonly found among APEC (51% n = 21/41) and ENT (93% n = 38/41). Under iron-restricted conditions, EF enhanced APEC growth in a proximity-dependent manner and APEC grown in mixed culture with EF exhibited a significant growth and survival advantage (P ≤ 0.01). In an embryo lethality assay, APEC co-infection with EF resulted in decreased survival of broiler embryos compared to mono-infections (P ≤ 0.05). These data demonstrate that EF augmented APEC survival and growth under iron limiting conditions, possibly translating to the increased virulence of APEC in broiler embryos. Thus, ENT co-infections may be a previously unrecognized contributor to colibacillosis-related mortality. Further investigations into the mechanism of this interaction are warranted. RESEARCH HIGHLIGHTS Enterococcus is frequently co-isolated with avian pathogenic E. coli (APEC). Enterococcus faecalis (EF) enhances survival of APEC in iron restricted conditions. EF co-infection increases APEC virulence in broiler embryos.

Antibiotic resistance and extended-spectrum β-lactamase in Escherichia coli isolates from imported 1-day-old chicks, ducklings, and turkey poults

Aim:

Antimicrobial resistance is a global health threat. This study investigated the prevalence of Escherichia coli in imported 1-day-old chicks, ducklings, and turkey poults.

Materials and Methods:

The liver, heart, lungs, and yolk sacs of 148 imported batches of 1-day-old flocks (chicks, 45; ducklings, 63; and turkey poults, 40) were bacteriologically examined for the presence of E. coli.

Results:

We isolated 38 E. coli strains from 13.5%, 6.7%, and 5.4% of imported batches of 1-day-old chicks, ducklings, and turkey poults, respectively. They were serotyped as O91, O125, O145, O78, O44, O36, O169, O124, O15, O26, and untyped in the imported chicks; O91, O119, O145, O15, O169, and untyped in the imported ducklings; and O78, O28, O29, O168, O125, O158, and O115 in the imported turkey poults. The E. coli isolates were investigated for antibiotic resistance against 16 antibiotics using the disk diffusion method and were found resistant to cefotaxime (60.5%), nalidixic acid (44.7%), tetracycline (44.7%), and trimethoprim-sulfamethoxazole (42.1%). The distribution of extended-spectrum β-lactamase (ESBL) and ampC β-lactamase genes was bla_TEM (52.6%), bla_SHV (28.9%), bla_CTX-M (39.5%), bla_OXA-1 (13.1%), and ampC (28.9%).

Conclusion:

Imported 1-day-old poultry flocks may be a potential source for the dissemination of antibiotic-resistant E. coli and the ESBL genes in poultry production.

Escherichia coli Isolated from Cases of Colibacillosis in Russian Poultry Farms (Perm Krai): Sensitivity to Antibiotics and Bacteriocins

Escherichia coli strains isolated from case of colibacillosis in Russian poultry farms in the region of Perm Krai were analyzed for their sensitivity to main antibiotics and bacteriocins. Sensitivity profiles for 9 antibiotics and 20 bacteriocins were determined with the disc diffusion method and the overlay test, respectively. Further, with the PCR the presence of several bla and integron 1 genes was revealed and the phylogenetic group for each strain determined. Among the 28 studied E. coli strains 85.7% were resistant to at least three antibiotics, 53.6% to five or more drugs, and 10.7% to eight antibiotics. PCR revealed that the bla_TEM gene was harbored by 71.4% of strains and the bla_CTX-M gene by 53.6% of strains. The class 1 integrons were found in 28.6% of strains. All of the studied strains were insensitive to ten or more bacteriocins. More than 90% of the studied strains were insensitive to pore-forming colicins of group A and B colicins, while 60.7% were insensitive to colicins with DNase and RNase activity. All of the analyzed strains were insensitive to at least two of the tested microcins. Neither the antibiotic resistance profile nor the bacteriocin resistance profile correlated with phylogenetic group of the strains. Thus, the studied strains were shown to possess high levels of multiple resistance to antibiotics and insensitivity to bacteriocins.

Co-occurrence of mcr-1 mediated colistin resistance and β-lactamase-encoding genes in multidrug-resistant Escherichia coli from broiler chickens with colibacillosis in Tunisia

OBJECTIVES

Colibacillosis caused by avian pathogenic Escherichia coli (APEC) is considered a major hindrance in poultry farming worldwide. This study aimed to characterize the genetic content and the relatedness between multidrug-resistant E. coli isolates from broiler chickens died due to colibacillosis from three farms from Tunisia.

METHODS

One hundred samples were collected from chickens' fresh carcasses from three poultry farms in Tunisia. E. coli isolation and identification were performed. Then, antimicrobial susceptibility regarding antibiotics, the ability to produce β-lactamases and minimum inhibitory concentration for colistin were determined according to Clinical and Laboratory Standards Institute guidelines. β-Lactam and non-β-lactam antimicrobial resistance genes, integrons, virulence genes, and phylogenetic groups were investigated using polymerase chain reaction. The genetic relatedness of the E. coli isolates was analysed by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).

RESULTS

A high infection rate of E. coli (50%) in infected organs of chickens was observed. The majority of E. coli isolates were multidrug resistant (96%); among them, 24% were colistin resistant and 30% were ESBL producing. Seven of 12 colistin-resistant isolates harboured the mcr-1 gene; among them, 10 were ESBL producing and carried bla_CTX-M-1, bla_TEM, and bla_SHV β-lactamase-encoding genes. E. coli isolates were assigned to different phylogroups but most of them (74%) belonged to the pathogenic phylogroup B2. Molecular typing by PFGE showed that some E. coli isolates harbouring ESBL-mcr-1 genes were clonally related. MLST revealed the presence of four different ST lineages among ESBL- and mcr-1-carrying E. coli: ST4187, ST3882; ST5693, and ST8932 with clonal dissemination of E. coli ST4187 between two of the farms.

CONCLUSION

This is the first report of ESBL-mcr-1-carrying E. coli isolates of a clinically relevant phylogenetic group (B2) from chickens that died due to colibacillosis in Tunisian poultry farms.

Genomic Characterization of Antibiotic Resistant Escherichia coli Isolated From Domestic Chickens in Pakistan

Poultry husbandry is important for the economic health of Pakistan, but the Pakistani poultry industry is negatively impacted by infections from Escherichia coli. We performed Illumina whole genome sequencing on 92 E. coli isolates obtained from the livers of deceased chickens originating in five Pakistani geographical regions. Our analysis indicates that the isolates are predominantly from the B1 and A clade and harbor a diverse number of antibiotic resistance and virulence genes, with no linkage between phylogeny and antibiotic resistance gene presence but some association between phylogeny and virulence gene and SNP presence for the B1 and E phylogroups. The colistin resistance gene mcr-1 and the quinolone resistance gene qnrS1 were both found in 13/92 isolates. Alarmingly, 82/92 of the E. coli strains characterized in this study are multidrug resistant with 100% (92/92) resistance to lincomycin, 81.5% (75/92) to streptomycin, 79.3% (73/92) to ampicillin and 66.3% (61/92) to ciprofloxacin. These results provide a high-resolution analysis of poultry-associated E. coli isolates in an area with a high endemic burden of antibiotic resistance. Surveillance of antibiotic resistance in poultry associated E. coli isolates is an important pillar of the One Health concept to integrate analysis of potential pathogens in human, animal, and environmental niches.

Identification of Escherichia coli from broiler chickens in Jordan, their antimicrobial resistance, gene characterization and the associated risk factors

BACKGROUND

Avian pathogenic Escherichia coli (APEC) is the principle cause of colibacillosis affecting poultry. The main challenge to the poultry industry is antimicrobial resistance and the emergence of multidrug resistant bacteria that threaten the safety of the food chain. Risk factors associated with emergence of antimicrobial resistance among avian pathogenic E. coli were correlated with the inappropriate use of antimicrobials along with inadequate hygienic practices, which encourages the selection pressure of antimicrobial resistant APEC. The aim of this study was to isolate, identify, serogroup and genotype APEC from broilers, assess their antibiotic resistance profile, expressed genes and the associated risk factors.

RESULTS

APEC was isolated from the visceral organs of sick chickens with a prevalence of 53.4%. The most prevalent serotypes were O1, O2, O25 and O78, in percentage of 14.8, 12.6, 4.4 and 23.7%, respectively. Virulence Associated Genes; SitA, iss, iucD, iucC, astA, tsh cvi and irp2 were detected in rate of 97.4, 93.3, 75, 74, 71, 46.5, 39 and 34%, respectively and 186 (69.2%) isolates possess > 5-10 genes. The highest resistance was found against sulphamethoxazole-trimethoprim, florfenicol, amoxicillin, doxycycline and spectinomycin in percentage; 95.5, 93.7, 93.3, 92.2 and 92.2%, respectively. Sixty-eight percent of APEC isolates were found to have at least 5 out of 8 antimicrobial resistant genes. The most predominant genes were Int1 97%, tetA 78.4%, bla TEM 72.9%, Sul1 72.4%, Sul2 70.2%. Two risk factors were found to be associated with the presence of multi-drug resistant APEC in broiler chickens, with a P value ≤0.05; the use of ground water as source of drinking water and farms located in proximity to other farms.

CONCLUSIONS

This study characterized the VAGs of avian pathogenic E. coli and establish their antimicrobial resistance patterns. The widespread of antimicrobial resistance of APEC isolates and detection of ARGs highlighted the need to monitor the spread of ARGs in poultry farms and the environment in Jordan. Use of ground water and closely located farms were significant risk factors associated with the presence of MDR APEC in broiler chickens in Jordan.

Intestinal gene expressions in broiler chickens infected with Escherichia coli and dietary supplemented with probiotic, acidifier and synbiotic

In this study, we investigated the effects of probiotic, acidifier and synbiotic supplementation on growth performance, mortality rate, intestinal gene expressions, fecal shedding, and organs colonization induced by Escherichia coli in broiler chickens. Six experimental groups were included; negative control group (NC), positive control group (PC), probiotic group (PR), acidifier group (AC), synbiotic group (SY) and colistin sulfate group (CS). Chickens in groups NC and PC were fed a basal diet, while chickens in groups PR, AC, SY, and CS were fed a basal diet containing probiotic, acidifier, synbiotic and colistin sulfate, respectively from the 1st day to the 28th day of age. At 7 days of age, all groups (not NC) were orally challenged with 0.5 ml (1.0 × 10⁹ CFU/ml) E. coli O78. The dietary supplementation of acidifier and synbiotic were sufficient to quell the devastating effects of E. coli infection in broilers. Growth performances represented by body weight gain, feed intake and feed conversion ratio were significantly improved as well as, mortalities were prevented whilst the ileal pro-inflammatory gene expressions (IL-6, IL-8, IL-13, TLR-4, IFN-γ, LITAF, AvBD-2, and AvBD-9) were significantly downregulated and the anti-inflammatory cytokine (IL-10) was significantly increased. In addition, E. coli fecal shedding and organs colonization was significantly diminished. It was concluded that the addition of both acidifier and synbiotic to the diet of broilers infected with E. coli could modulate the intestinal inflammatory responses induced by E. coli infection and minimized the inflammation-induced damage which resulted in improvement in growth performance, prevention of mortalities and reduction of E. coli environmental contamination.

Antimicrobial Resistance in Escherichia coli

Multidrug resistance in Escherichia coli has become a worrying issue that is increasingly observed in human but also in veterinary medicine worldwide. E. coli is intrinsically susceptible to almost all clinically relevant antimicrobial agents, but this bacterial species has a great capacity to accumulate resistance genes, mostly through horizontal gene transfer. The most problematic mechanisms in E. coli correspond to the acquisition of genes coding for extended-spectrum β-lactamases (conferring resistance to broad-spectrum cephalosporins), carbapenemases (conferring resistance to carbapenems), 16S rRNA methylases (conferring pan-resistance to aminoglycosides), plasmid-mediated quinolone resistance (PMQR) genes (conferring resistance to [fluoro]quinolones), and mcr genes (conferring resistance to polymyxins). Although the spread of carbapenemase genes has been mainly recognized in the human sector but poorly recognized in animals, colistin resistance in E. coli seems rather to be related to the use of colistin in veterinary medicine on a global scale. For the other resistance traits, their cross-transfer between the human and animal sectors still remains controversial even though genomic investigations indicate that extended-spectrum β-lactamase producers encountered in animals are distinct from those affecting humans. In addition, E. coli of animal origin often also show resistances to other-mostly older-antimicrobial agents, including tetracyclines, phenicols, sulfonamides, trimethoprim, and fosfomycin. Plasmids, especially multiresistance plasmids, but also other mobile genetic elements, such as transposons and gene cassettes in class 1 and class 2 integrons, seem to play a major role in the dissemination of resistance genes. Of note, coselection and persistence of resistances to critically important antimicrobial agents in human medicine also occurs through the massive use of antimicrobial agents in veterinary medicine, such as tetracyclines or sulfonamides, as long as all those determinants are located on the same genetic elements.

Molecular detection of genes encoding resistance to tetracycline and determination of plasmid-mediated resistance to quinolones in avian pathogenic Escherichia coli in Sukabumi, Indonesia

AIM

This study aimed to identify genes encoding resistance to tetracycline (TE) and plasmid-mediated resistance to quinolones in Escherichia coli isolates from clinical cases of avian colibacillosis in Sukabumi, Indonesia.

MATERIALS AND METHODS

A total of 25 E. coli archive isolates were collected in 2013-2017 from clinical cases of avian colibacillosis in Sukabumi, Indonesia. All isolates were tested for TE and quinolone resistance using the disk diffusion method. TE -resistant E. coli isolates were screened for the presence of tet(A) and tet(B) genes by single polymerase chain reaction (PCR). The qnr(A), qnr(B), and qnr(S) genes were detected by multiplex PCR in quinolone-resistant E. coli isolates.

RESULTS

Result of this study shows that 19 of 25 (76%) E. coli isolates are resistant to oxytetracycline and 64% are resistant to TE; among them, 63.2% and 31.5% were positive tet(A) and tet(B), respectively. 13 out of 25 (52%) are resistant to ciprofloxacin and 36% are resistant to enrofloxacin either norfloxacin; among them, 61.6% were positive qnr(A), 7.7% were positive qnr(B), 23% were positive qnr(S), and 7.7% were positive both of qnr(A) and qnr(S).

CONCLUSION

This study shows that a few pathogens of E. coli are resistant to TE and quinolone. The frequency of tet and qnr genes that are responsible for this resistance among avian pathogenic E. coli isolates in Sukabumi, Indonesia, was high.

Where Did They Come from-Multi-Drug Resistant Pathogenic Escherichia coli in a Cemetery Environment?

Human burial in cemeteries facilitates the decomposition of corpses without posing a public health danger. However, the role of cemeteries as potential environmental reservoirs of drug-resistant pathogens has not been studied. Thus, we investigated cemeteries as potential environmental reservoirs of multi-drug resistant (MDR) pathogenic Escherichia coli. E. coli isolates were obtained from water samples (collected from surface water bodies and boreholes in three cemeteries) after isolation using the Colilert^® 18 system. Pathogenic potentials of the isolates were investigated using real-time polymerase chain reactions targeting seven virulence genes (VGs) pertaining to six E. coli pathotypes. The resistance of isolates to eight antibiotics was tested using the Kirby–Bauer disc diffusion method. The mean E. coli concentrations varied from <1 most probable number (MPN)/100 mL to 2419.6 MPN/100 mL with 48% of 100 isolates being positive for at least one of the VGs tested. Furthermore, 87% of the isolates were resistant to at least one of the antibiotics tested, while 72% of the isolates displayed multi-drug resistance. Half of the MDR isolates harboured a VG. These results suggest that cemeteries are potential reservoirs of MDR pathogenic E. coli, originating from surrounding informal settlements, which could contaminate groundwater if the cemeteries are in areas with shallow aquifers.

Antibacterial activity of Thymus vulgaris essential oil alone and in combination with cefotaxime against blaESBL producing multidrug resistant Enterobacteriaceae isolates

The aim was to evaluate the susceptibility of bla_ESBL producing Enterobacteriaceae to Slovakian Thymus vulgaris essential oil (TVEO) alone and in combination with cefotaxime (CTX). TVEO composition was determined by gas chromatograph-mass spectrometer (GC/MS). Susceptibility to 21 antibiotics was determined by disc diffusion assay. Genes characterization for resistance to β-lactams was accomplished by polymerase chain reaction (PCR). The antibacterial activity was investigated by standard methods. The synergistic interaction was determined by checkerboard test. Thymol (34.5%), p-cymene (22.27%) and linalool (5.35%) were the major components present in the TVEO. The identified strains were multi-drug resistant (MDR). TVEO showed high activity against all MDR strains, including bla_ESBL producing isolates, with inhibition zones and MIC values in the range of 24-40 mm/10μL and 2.87-11.5 μg/mL, respectively. TVEO in combination with CTX showed a synergistic action against bla_SHV-12 producing Escherichia coli (FICI 0.28) and an additive effect vs ESBL producing Enterobacter cloacae (FICI 0.987).

Evaluation of the Genetics and Functionality of Plasmids in Incompatibility Group I1-Positive Salmonella enterica

Salmonella is a predominant foodborne pathogen in the United States and other countries. Mobile genetic elements such as plasmids allow Salmonella to adapt to external stress factors such as nutrient deprivation and host factors. Incompatibility group I1 (IncI1) plasmid-carrying Salmonella enterica strains were examined to determine the presence of plasmid-associated genes and their influence on phenotypic characteristics. The objective of this study was to understand the genetic determinants on IncI1 plasmids and their impact on antimicrobial susceptibility, competitive growth inhibition of Escherichia coli, and plasmid transfer. Primers were designed for genes that play a role in virulence, antimicrobial resistance, and plasmid transfer based on previously sequenced IncI1 plasmids. Polymerase chain reaction assays were conducted on 92 incompatibility group I1 (IncI1)-positive S. enterica strains. Phenotypic characterization included conjugation assays, antimicrobial susceptibility testing, and bacteriocin production based on the inhibition of growth of colicin-negative E. coli J53. The antimicrobial resistance genes aadA1, tetA, sul1, and bla_CMY were detected in 88%, 87%, 80%, and 48% of the strains, respectively. Over half of the strains were resistant or intermediately resistant to streptomycin (85%), sulfonamides (76%), tetracycline (74%), and ampicillin (68%) and 57% of the strains inhibited growth of E. coli J53 strain. Among putative virulence genes, colicin-associated colI and cib were detected in 23% and 35% of strains and imm and ccdA were present in 58% and 54% of strains, respectively. Approximately 61% of strains contained plasmids that conjugally transferred antimicrobial resistance, including 83% where the recipient received IncI1 plasmids. Most of the strains carried an assortment of transfer associated (pil and tra) genes with between 63% and 99% of strains being positive for individual genes. Taken together the study affirms that IncI1 plasmids likely play roles in the dissemination of antimicrobial resistance and virulence-associated factors among enteric organisms.

Phenotypic and genotypic characterization of antimicrobial susceptibility of avian pathogenic Escherichia coli isolated from broiler chickens

Aim:

Avian pathogenic Escherichia coli (APEC) is pathogenic strains of E. coli that are responsible for one of the most common bacterial diseases affecting poultry worldwide. This study was designed to determine the occurrence, antibiotic resistance profile, and antibiotic resistance genes of E. coli isolated from diseased and freshly dead broilers.

Materials and Methods:

In that context, a total of 200 broilers samples were examined by standard microbiological techniques for isolation of E. coli, and tested for their antimicrobial susceptibility against 15 antimicrobial agents using disc diffusion method. In addition, E. coli isolates were screened by multiplex polymerase chain reaction for detection of a number of resistance genes including aadA1 gene encodes streptomycin/neomycin, tetA encodes resistance to tetracycline, sul1 encodes sulfonamides, and β-lactamase encoding genes (bla_TEM and bla_SHV).

Results:

A total of 73 (36.5%) isolates were biochemically identified as E. coli strains. O78, O2, and O1 are the most prevalent serotypes detected. E. coli displayed a high resistance against penicillin (100%), followed by cefepime (95.8%) and a low resistance to norfloxacin (36.9%), and chloramphenicol (30%). Depending on the results of PCR, sul1 gene was the most predominant antibiotic resistant gene (87%) followed by bla_TEM (78%), tetA genes (60%), and aadA (54%). However, bla_SHV had the lowest prevalence (23%).

Conclusion:

The obtained results demonstrated the importance of studies on APEC and antibiotic resistance genes in our region which associated with intensive poultry industry, aiming to acquire preventive measures to minimize losses due to APEC and associated multidrug-resistance and resistance genes that of high significance to the rational use of antibiotics in clinical and public health.

Antimicrobial Resistance in Bacterial Poultry Pathogens: A Review

Antimicrobial resistance (AMR) is a global health threat, and antimicrobial usage and AMR in animal production is one of its contributing sources. Poultry is one of the most widespread types of meat consumed worldwide. Poultry flocks are often raised under intensive conditions using large amounts of antimicrobials to prevent and to treat disease, as well as for growth promotion. Antimicrobial resistant poultry pathogens may result in treatment failure, leading to economic losses, but also be a source of resistant bacteria/genes (including zoonotic bacteria) that may represent a risk to human health. Here we reviewed data on AMR in 12 poultry pathogens, including avian pathogenic Escherichia coli (APEC), Salmonella Pullorum/Gallinarum, Pasteurella multocida, Avibacterium paragallinarum, Gallibacterium anatis, Ornitobacterium rhinotracheale (ORT), Bordetella avium, Clostridium perfringens, Mycoplasma spp., Erysipelothrix rhusiopathiae, and Riemerella anatipestifer. A number of studies have demonstrated increases in resistance over time for S. Pullorum/Gallinarum, M. gallisepticum, and G. anatis. Among Enterobacteriaceae, APEC isolates displayed considerably higher levels of AMR compared with S. Pullorum/Gallinarum, with prevalence of resistance over >80% for ampicillin, amoxicillin, tetracycline across studies. Among the Gram-negative, non-Enterobacteriaceae pathogens, ORT had the highest levels of phenotypic resistance with median levels of AMR against co-trimoxazole, enrofloxacin, gentamicin, amoxicillin, and ceftiofur all exceeding 50%. In contrast, levels of resistance among P. multocida isolates were less than 20% for all antimicrobials. The study highlights considerable disparities in methodologies, as well as in criteria for phenotypic antimicrobial susceptibility testing and result interpretation. It is necessary to increase efforts to harmonize testing practices, and to promote free access to data on AMR in order to improve treatment guidelines as well as to monitor the evolution of AMR in poultry bacterial pathogens.