Types and prevalence of extended-spectrum beta-lactamase producing Enterobacteriaceae in poultry

Multi-drug resistant (MDR) Gram-negative pathogenic bacteria isolated from poultry in the Noakhali region of Bangladesh

Rapidly increasing antibiotic-resistant bacterial strains in Bangladesh's food and farm animals stem from the excessive and inappropriate use of antibiotics. To assess the prevalence of multi-drug resistant (MDR) Gram-negative bacteria in poultry chicks, we sought to isolate and identify strains carrying antimicrobial resistance genes. Isolation and identification involved biochemical tests, 16S rRNA sequencing, and PCR screening of species-specific genes. MDR patterns were evaluated using CLSI guidelines with seventeen antibiotics across twelve classes. Targeted gene sequences were amplified for the detection of Extended-spectrum β-Lactamase (ESBL), carbapenem, tetracycline, sulfonamide, and colistin resistance genes. Common isolates, such as Escherichia coli, Klebsiella pneumoniae, Proteus penneri, and Enterobacter hormaechei, exhibited average Multiple Antimicrobial Resistance (MAR) indices of 0.66, 0.76, 0.8, 0.84, and 0.81, 0.76, 0.84, 0.41 for broiler and layer chicken, respectively. Providencia stuartii and Salmonella enterica, exclusive to broiler samples, had MAR indices of 0.82 and 0.84, respectively. Additional isolates Morganella morganii, Aeromonas spp., and Wohlfahrtiimonas chitiniclastica were found in layers (Average MAR indices: 0.73, 0.71, and 0.91). Notably, M. morganii, E. hormaechei and W. chitiniclastica were identified for the first time in Bangladeshi poultry chicken, although their evolution is yet to be understood. In this study, Pan-drug resistance was observed in one P. stuartii (broiler) and one Aeromonas spp. (layer) with a MAR index 1, while all isolates exhibited MAR indices >0.2, indicating MDR. Antimicrobial resistance (AMR) gene screening identified blaTEM, blaSHV, tetA, and sul1 in a majority of the MDR strains. Interestingly, E. coli (lactose positive and negative) and E. hormaechei were exclusively found to possess the tetB gene. In addition, E. coli (lactose negative), Klebsiella pneumoniae, Enterobacter hormaechei, M. morganii, and P. stuartii were observed to carry the colistin-resistant mcr-1 gene, whereas sul2 was detected in E. coli (lactose positive and negative), E. hormaechei, P. stuartii, and P. penneri. These findings emphasize the health risk of our consumers of both broiler and layer chickens as they have turned into a potent reservoir of various AMR gene carrying MDR and Pan-drug resistant bacteria.

Levels of Different Microbial Groups on Inert Surfaces of Poultry Slaughterhouses: Identification Using Matrix-Assisted Laser Desorption Ionization Time-of-Flight and Detection of Extended-Spectrum Beta-Lactamase- and Carbapenemase-Producing Enterobacteria

Knowledge of the microbiota present in food processing environments is a significant advance that will allow for better evaluation of the risk of food contamination and a better design of the procedures for sanitization. The levels of microbial group indicators of hygienic quality were determined in different areas of the slaughter lines of two poultry slaughterhouses in the northwest of Spain (22 surfaces in each slaughterhouse were studied). The average microbial levels (cfu/cm2) were 2.15 × 102 ± 4.26 × 102 (total aerobic counts, TAC), 1.99 × 102 ± 5.00 × 102 (psychrotrophic microorganisms), 3.10 × 100 ± 1.37 × 101 (enterobacteria), 3.96 × 100 ± 2.55 × 101 (coliforms), 1.80 × 10-1 ± 7.79 × 10-1 (enterococci), and 1.12 × 10-1 ± 3.35 × 10-1 (vancomycin-resistant enterococci, VRE). TAC and psychrotrophic microorganisms were the most abundant groups in all samples (p < 0.05). The counts of both microbial groups were higher (p < 0.05) in samples of Slaughterhouse A than in those of Slaughterhouse B. Microbial loads for the rest of the bacteria were not influenced by the slaughterhouse sampled (p > 0.05). All 44 samples showed TAC and psychrotrophic microorganisms. Colonies of the rest of the microbial groups were only found in 26 samples (59.1% of the total). The isolates (one from each sample) were identified with MALDI-TOF and PCR. Gram-negative bacteria (all Enterobacteriaceae) were isolated in 23 samples, and Gram-positive bacteria were isolated in 16 (9 Enterococcus spp., 2 Enterococcus spp. and VRE, 3 VRE, 1 Enterococcus spp. and Listeria spp., and 1 Listeria spp.). The resistance of the strains to 11 (Enterococcus spp.) or 17 (Enterobacteriaceae) antibiotics was determined (disk diffusion, CLSI), finding an average of 2.05 ± 2.06 resistances per strain (3.46 ± 2.27 if reduced susceptibility reactions are included). A total of 37.3% of the Enterobacteriaceae isolates had a gene for resistance to beta-lactam antibiotics (blaTEM, blaCTX-M-15, blaKPC, blaCMY-2 or blaNDM). The high prevalence of resistant bacteria and resistance genes highlights the need to establish measures to control the spread of antibiotic resistance in poultry slaughterhouses. The findings of this work could contribute to the design of more effective sanitation procedures.

Antibiotic Resistance Profile and Bio-Control of Multidrug-Resistant Escherichia coli Isolated from Raw Milk in Vietnam Using Bacteriophages

E. coli is an important zoonotic pathogen capable of causing foodborne illness and bovine mastitis. Bacteriophages have been increasingly considered a promising tool to control unwanted bacteria. The aim of this study is to determine the antibiotic resistance profile of E. coli isolated from raw milk and the efficacy of phage in controlling multidrug-resistant E. coli in raw milk. Antibiotic susceptibility testing showed the highest resistance rates of E. coli isolates to co-trime (27.34%) and ampicillin (27.34%), followed by streptomycin (25.18%), tetracycline (23.02%), and the lowest resistance rates to ciprofloxacin, gentamycin, and ceftazidime, all at a rate of 2.16%. All isolates were susceptible to meropenem. Of the 139 E. coli isolates, 57 (41.01%) were resistant to at least one antibiotic, and 35 (25.18%) were classified as MDR strains. Molecular characterization indicated that 5 (3.6%) out of the 139 isolates were STEC strains carrying stx1 gene. Seven (5.04%) isolates were phenotypically identified as ESBLEC, and four isolates (2.88%) were resistant to colistin. The results of the genotypic test revealed that four out of seven ESBLEC strains carried both blaTEM and blaCTX-M-1, two harbored blaTEM, and one possessed blaCTX-M-1, while mcr-1 was detected in all four colistin-resistant E. coli isolates. In particular, one isolated E. coli strain (EM148) was determined to be a multidrug-resistant strain simultaneously carrying blaTEM, blaCTX-M-1, and mcr-1. A total of eight phages were successfully recovered from raw milk. The application of phage PEM3 significantly reduced viable counts of multidrug-resistant host EM148 in raw milk by at least 2.31 log CFU/mL at both 24 °C and 4 °C.

Widespread prevalence of plasmid-mediated blaCTX-M type extended-spectrum beta-lactamase Escherichia coli in backyard broiler production systems in the United States

Extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) is an emerging pathogen of high concern given its resistance to extended-spectrum cephalosporins. Broiler chicken, which is the number one consumed meat in the United States and worldwide, can be a reservoir of ESBL E. coli. Backyard poultry ownership is on the rise in the United States, yet there is little research investigating prevalence of ESBL E. coli in this setting. This study aims to identify the prevalence and antimicrobial resistance profiles (phenotypically and genotypically) of ESBL E. coli in some backyard and commercial broiler farms in the U.S. For this study ten backyard and ten commercial farms were visited at three time-points across flock production. Fecal (n = 10), litter/compost (n = 5), soil (n = 5), and swabs of feeders and waterers (n = 6) were collected at each visit and processed for E. coli. Assessment of ESBL phenotype was determined through using disk diffusion with 3rd generation cephalosporins, cefotaxime and ceftazidime, and that with clavulanic acid. Broth microdilution and whole genome sequencing were used to investigate both phenotypic and genotypic resistance profiles, respectively. ESBL E. coli was more prevalent in backyard farms with 12.95% of samples testing positive whereas 0.77% of commercial farm samples were positive. All isolates contained a blaCTX-M gene, the dominant variant being blaCTX-M-1, and its presence was entirely due to plasmids. Our study confirms concerns of growing resistance to fourth generation cephalosporin, cefepime, as roughly half (51.4%) of all isolates were found to be susceptible dose-dependent and few were resistant. Resistance to non-beta lactams, gentamicin and ciprofloxacin, was also detected in our samples. Our study identifies prevalence of blaCTX-M type ESBL E. coli in U.S. backyard broiler farms, emphasizing the need for interventions for food and production safety.

Detection of Extended-Spectrum Beta-Lactamase (ESBL)-Producing Enterobacteriaceae from Diseased Broiler Chickens in Lusaka District, Zambia

Poultry products in Zambia form an integral part of the human diet in many households, as they are cheap and easy to produce. The burden of poultry diseases has, however, remained a major challenge. Growing consumer demand for poultry products in Zambia has resulted in non-prudent antimicrobial use on farms, intending to prevent and treat poultry diseases for growth optimisation and maximising profits. This cross-sectional study aimed to identify the different types of bacteria causing diseases in chickens in Lusaka and to detect the extended-spectrum lactamase (ESBL)-encoding genes. We collected 215 samples from 91 diseased chickens at three post-mortem facilities and screened them for Gram-negative bacteria. Of these samples, 103 tested positive for various clinically relevant Enterobacteriaceae, including Enterobacter (43/103, 41.7%), Escherichia coli (20/103, 19.4%), Salmonella (10/103, 9.7%), and Shigella (8/103, 7.8%). Other isolated bacteria included Yersinia, Morganella, Proteus, and Klebsiella, which accounted for 21.4%. E. coli, Enterobacter, Salmonella, and Shigella were subjected to antimicrobial susceptibility testing. The results revealed that E. coli, Enterobacter, and Shigella were highly resistant to tetracycline, ampicillin, amoxicillin, and trimethoprim-sulfamethoxazole, while Salmonella showed complete susceptibility to all tested antibiotics. The observed resistance patterns correlated with antimicrobial usage estimated from sales data from a large-scale wholesale and retail company. Six (6/14, 42.9%) E. coli isolates tested positive for blaCTX-M, whilst eight (8/14, 57.1%) Enterobacter samples tested positive for blaTEM. Interestingly, four (4/6, 66.7%) of the E. coli isolates carrying blaCTX-M-positive strains were also positive for blaTEM. Sanger sequencing of the PCR products revealed that five (5/6, 83.3%) of the abovementioned isolates possessed the blaCTX-M-15 allele. The results suggest the presence of potentially pathogenic ESBL-producing Enterobacteriaceae in poultry, threatening public health.

Genomic surveillance of extended-spectrum cephalosporin-resistant Escherichia coli isolated from poultry in the UK from 2016 to 2020

Introduction

Surveillance is vital for monitoring the increasing risk of antimicrobial resistance (AMR) in bacteria leading to failures in humans and animals to treat infections. In a One Health context, AMR bacteria from livestock and food can transfer through the food chain to humans, and vice versa, which can be characterized in detail through genomics. We investigated the critical aspects of AMR and the dynamics of AMR in poultry in the UK.

Methods

In this study, we performed whole genome sequencing for genomic characterization of 761 extended-spectrum cephalosporinases (ESCs) harboring Escherichia coli isolated from poultry caeca and meat through EU harmonized monitoring of AMR in zoonotic and commensal bacteria from 2016 and 2018 and UK national monitoring in 2020.

Results

The most common ESC in 2016 and 2018 was blaCTX-M-1; however, 2020 had a greater diversity of ESCs with blaCTX-M-55 dominant in chickens and blaCTX-M-15 more prevalent in turkeys. Co-resistance to sulphonamides, tetracycline, and trimethoprim was widespread, and there were several positive correlations between the sequence types (STs) and ESC genes. We identified certain AMR genotypes and STs that were frequent each year but not as successful in subsequent years, e.g., ST350 harboring blaCTX-M-1, sul2, and tetA-v4.Phylogenetic comparison of isolates prevalent in our panel with global ones from the same STs available in public databases showed that isolates from the UK generally clustered together, suggesting greater within-country than between-country transmission.

Discussion

We conclude that future genomic surveillance of indicator organisms will be invaluable as it will enable detailed comparisons of AMR between and within neighboring countries, potentially identifying the most successful sequence types, plasmids, or emerging threats.

CTX-M-55-type ESBL-producing fluoroquinolone-resistant Escherichia coli sequence type 23 repeatedly caused avian colibacillosis in Kagoshima Prefecture, Japan

OBJECTIVES

The production of expanded-spectrum beta-lactamases (ESBLs) and fluoroquinolone resistance in Enterobacteriaceae has become a global concern. The aim of this study was to investigate the spread of ESBL-producing and fluoroquinolone-resistant avian pathogenic Escherichia coli (APEC) in Kagoshima, a prefecture with the largest amount of poultry in Japan.

METHODS

The antimicrobial susceptibility and genetic characteristics of 228 APEC strains isolated from 57 farms in Kagoshima Prefecture, Japan, between 2005 and 2017 were analysed. Information about the companies with hatcheries connected to the farms was also collected, and the epidemiologic relatedness of APEC strains and the processes of adopting chicks were compared.

RESULTS

Seven CTX-M-type ESBL genes, blaCTX-M-1, blaCTX-M-2, blaCTX-M-14, blaCTX-M-15, blaCTX-M-25, blaCTX-M-55, and blaCTX-M-65, were found in 60 (26.3%) of the 228 APEC strains. The ciprofloxacin-resistant strains belonged to 10 different sequence types (ST10, ST23, ST93, ST155, ST156, ST350, ST359, ST602, ST648, and ST9479), and the two ST602 strains showed remarkably high ciprofloxacin resistance (MIC: 128 µg/mL) and had amino acid mutations in GyrA (S83L and D87N), ParC (S80I), and ParE (E460A). A CTX-M-55-type ESBL-producing fluoroquinolone-resistant Og78-ST23 strain was isolated multiple times over two years on a farm. Furthermore, epidemiologically closely related strains were isolated from different farms that used the same common hatcheries.

CONCLUSIONS

APEC is often transferred from hatcheries to farms via healthy chicks, and the prudent use of antimicrobials and careful monitoring of resistant strains on poultry farms and hatcheries are important in preventing the selection and spread of high-risk APEC strains such as CTX-M-55-type ESBL-producing Og78-ST23.

Prevalence and Transmission of Extended-Spectrum Cephalosporin (ESC) Resistance Genes in Escherichia coli Isolated from Poultry Production Systems and Slaughterhouses in Denmark

The emergence of extended-spectrum cephalosporin (ESC)-resistant Escherichia coli is a global concern. This study aimed to assess the prevalence and transmission of ESC-resistant E. coli in the Danish broiler production system. Samples from two vertically integrated Production Systems (1 and 2) and two slaughterhouses (A and B) were analyzed (n = 943) for the occurrence of ESC-resistant E. coli from 2015 to 2018. ESC-resistant E. coli isolates were whole-genome sequenced (WGS) for characterization of the multi-locus sequence type (MLST), antibiotic resistance genes, virulence genes, and plasmid replicon types. An ad hoc core genome (cg) MLST based on 2513 alleles was used to examine the genetic relatedness among isolates. The prevalence of ESC-resistant E. coli in the conventional Production System 1 was 2.7%, while in Production System 2 the prevalence was 26.7% and 56.5% for samples from the conventional and organic production, respectively. The overall prevalence of ESC-resistant E. coli in broiler thigh and fecal samples ranged from 19.3% in Slaughterhouse A to 22.4% in Slaughterhouse B. In total, 162 ESC-resistant E. coli were isolated and shown to belong to 16 different sequence types (STs). The most prevalent STs were ST2040 (n = 85) and ST429 (n = 22). Seven ESC resistance genes were detected: blaCMY-2 (n = 119), blaTEM-52B (n = 16), blaCTX-M-1 (n = 5), blaTEM-52C (n = 3), blaCTX-M-14 (n = 1), blaSHV-12 (n = 1), and up-regulation of ampC (n = 16), with an unknown resistance gene in one isolate (n = 1). The carriage of blaCMY-2 in 119 isolates was primarily associated with IncI1 (n = 87), and IncK plasmids (n = 31). Highly similar blaCMY-2 carrying E. coli isolates from ST429 were found in production systems as well as in slaughterhouses. In conclusion, findings from this study indicate that ESC-resistant E. coli are transferred vertically from farms in the production systems to slaughterhouses with the potential to enter the food supply.

Multidrug-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae isolated from chicken droppings in poultry farms at Gondar City, Northwest Ethiopia

BACKGROUND

The poultry sector is one of the largest and fastest-growing agricultural sub-sector, especially in developing countries like Ethiopia. In poultry production, poultry farmers use sub-optimum doses of antibiotics for growth promotion and disease prevention purpose. This indiscriminate use of antibiotics in poultry farms contributes to the emergence of antibiotic-resistant bacteria, which has adverse implications for public health. Therefore, this study is aimed to assess multidrug resistance and extended-spectrum beta-lactamase-producing Enterobacteriaceae from chicken droppings in poultry farms.

METHODS

A total of 87 pooled chicken-dropping samples were collected from poultry farms from March to June 2022. Samples were transported with buffered peptone water. Selenite F broth was used for the enrichment and isolation of Salmonella spp. Isolates were cultured and identified by using MacConkey agar, Xylose lysine deoxycholate agar, and routine biochemical tests. Kirby-Bauer disk diffusion technique and combination disk test were used for antibiotic susceptibility testing and confirmation of extended-spectrum beta-lactamase production, respectively. Data were entered using Epi-data version 4.6 and then exported to SPSS version 26 for analysis.

RESULT

Out of 87 pooled chicken droppings, 143 Enterobacteriaceae isolates were identified. Of these, E. coli accounts for 87 (60.8%), followed by Salmonella spp. 23 (16.1%), P. mirabilis 18 (12.6%) and K. pneumoniae 11 (7.7%). A high resistance rate was observed for ampicillin 131 (91.6%), followed by tetracycline 130 (90.9), and trimethoprim-sulfamethoxazole 94 (65.7%). The overall multidrug resistance rate was 116/143 (81.1%; 95% CI: 74.7-87.5). A total of 12/143 (8.4%; CI: 3.9-12.9) isolates were extended-spectrum beta-lactamase producers, with 11/87 (12.6%) E. coli and 1/11 (9.1%) K. pneumoniae.

CONCLUSION AND RECOMMENDATIONS

High prevalence of multi-drug resistant isolates was observed. This study alarms poultry as a potential reservoir of extended-spectrum beta-lactamase-producing Enterobacteriaceae, which might shed and contaminate the environment through faecal matter. Prudent use of antibiotics should be implemented to manage antibiotic resistance in poultry production.

Enumeration, antimicrobial resistance and genomic characterization of extended-spectrum β-lactamases producing Escherichia coli from supermarket chicken meat in the United Arab Emirates

The occurrence and counts of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in retail chicken sold in the United Arab Emirates (UAE) were investigated in this study. Results indicated that 79.68 % of chicken carcasses (251/315) sampled from UAE supermarkets harbored ESBL-producing E. coli. About half (51.75 % [163/315]) of the tested samples had an ESBL-producing E. coli count range between ≥3 log₁₀ and < 5 log₁₀ CFU/g. The antimicrobial resistance profiles of a subset of 100 isolates showed high rates of non-susceptibility to clinically significant antibiotics, particularly ciprofloxacin (80 %) and cefepime (46 %). Moreover, 7 % of the isolates exhibited resistance to colistin, with PCR-based screening revealing the presence of the mcr-1 gene in all colistin-resistant isolates. Multiplex PCR screening identified bla_CTX-M and bla_TEM genes as the most frequently presented genes among the phenotypically confirmed ESBL-producing E. coli. Further whole-genome sequencing and bioinformatic analysis of 27 ESBL-producing E. coli isolates showed that the gene family bla_CTX group 1 was the most prevalent, notably CTX-M-55 (55.55 % [15/27]), followed by CTX-M-15 (22.22 % [6/27]). The most common sequence types (STs) were ST359 and ST1011, with three evident clusters identified based on phylogenomic analysis, aligned with isolates from specific production companies. Analysis of plasmid incompatibility types revealed IncFIB, IncFII, Incl2, and IncX1 as the most commonly featured plasmids. The findings of this study indicate a noticeable prevalence and high counts of ESBL-producing E. coli in chicken sampled from supermarkets in the UAE. The high rates of antimicrobial resistance to clinically important antibiotics highlight the potential public health risk associated with consuming chicken contaminated with ESBL-producing E. coli. Overall, this study emphasizes the importance of continued antimicrobial resistance monitoring in the UAE food chain and calls for further exposure risk assessment of the consumption of ESBL-producing E. coli via chicken meat.

Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line

The presence of mobile genetic elements in Salmonella isolated from a chicken farm constitutes a potential risk for the appearance of emerging bacteria present in the food industry. These elements contribute to increased pathogenicity and antimicrobial resistance through genes that are related to the formation of biofilms and resistance genes contained in plasmids, integrons, and transposons. One hundred and thirty-three Salmonella isolates from different stages of the production line, such as feed manufacturing, hatchery, broiler farm, poultry farm, and slaughterhouse, were identified, serotyped and sequenced. The most predominant serotype was Salmonella Infantis. Phylogenetic analyses demonstrated that the diversity and spread of strains in the pipeline are serotype-independent, and that isolates belonging to the same serotype are very closely related genetically. On the other hand, Salmonella Infantis isolates carried the pESI IncFIB plasmid harboring a wide variety of resistance genes, all linked to mobile genetic elements, and among carriers of these plasmids, the antibiograms showed differences in resistance profiles and this linked to a variety in plasmid structure, similarly observed in the diversity of Salmonella Heidelberg isolates carrying the IncI1-Iα plasmid. Mobile genetic elements encoding resistance and virulence genes also contributed to the differences in gene content. Antibiotic resistance genotypes were matched closely by the resistance phenotypes, with high frequency of tetracycline, aminoglycosides, and cephalosporins resistance. In conclusion, the contamination in the poultry industry is described throughout the entire production line, with mobile genetic elements leading to multi-drug resistant bacteria, thus promoting survival when challenged with various antimicrobial compounds.

β-Lactam resistance genes present in UK pheasants and red-legged partridges

BACKGROUND

Despite considerable recent reductions in antimicrobial use, the UK gamebird industry continues to struggle with production diseases during the rearing season, necessitating significant antibiotic use. This observational study investigated the presence of genes conferring resistance to β-lactam antibiotics within industry-reared pheasants and red-legged partridges in the UK.

METHODS

DNA was extracted from 60 pooled caecal samples collected from gamebirds at routine postmortem examinations during the rearing season. Genes encoding extended-spectrum β-lactamases (ESBL) were detected by PCR and the corresponding alleles were determined.

RESULTS

Over half (53%) of the samples harboured genes encoding blaTEM resistance, with blaSHV identified in 20% of samples. The blaTEM gene was more common on sites with higher antibiotic use, whereas blaSHV was predominantly found in birds younger than 5 weeks. Genotyping of the identified resistance genes revealed the presence of blaTEM-1 , blaSHV-1 and blaSHV-11 alleles.

LIMITATIONS

This was a small-scale study conducted at four sites in southern England.

CONCLUSION

This is the first report of the presence of ESBL genes in gamebirds, highlighting the need for further research into antimicrobial resistance in UK gamebirds.

Exploring broilers and native fowls of Andaman and Nicobar Islands as a source of β-lactamase-producing Enterobacteriaceae even with limited anthropogenic activities and docking-based identification of catalytic domains in novel β-lactamase variants

Objectives

The present study was conducted to detect the occurrence of β-lactamase and biofilm-producing Escherichia coli, Salmonella, and Klebsiella in broilers and native fowl reared in the Andaman and Nicobar Islands, India. The study also included molecular docking experiments to confirm the nature of the catalytic domains found in the β-lactamase variants obtained and to reveal the clonal relationship of the isolates with human clinical strains from the database.

Materials and methods

A total of 199 cloacal swabs were collected from five poultry breeds/varieties (broiler, Vanraja, Desi, Nicobari, and layer) in three districts of the Andaman and Nicobar Islands. E. coli, Salmonella enterica, and Klebsiella pneumoniae were isolated by standard techniques and confirmed by PCR. Phenotypical β-lactamase producers were identified by a double-disc test. The genes (bla _CTX, bla _SHV, bla _TEM , and bla _AmpC) were screened, and selected sequences of β-lactamase variants were submitted to DDBJ. Homology modeling, model validation, and active site identification of different β-lactamase variants were done by the SWISS-MODEL. Molecular docking was performed to identify the catalytic domains of the β-lactamase variants. The selected β-lactamase sequences were compared with the Indian ESBL sequences from human clinical strains in NCBI-GenBank.

Results

In total, 425 Enterobacteriaceae strains were isolated from the collected samples. Klebsiella pneumoniae (42.58%) was found to be the most prevalent, followed by Salmonella enterica (30.82%) and E. coli (26.58%). The phenotypical antibiogram of all 425 isolates showed the highest resistance against oxytetracycline (61-76%) and the lowest against gentamicin (15-20%). Phenotypical production of β-lactamase enzymes was observed in 141 (33.38%) isolates. The isolation rate of β-lactamase producing E. coli, Salmonella enterica, and Klebsiella pneumoniae was significantly higher (p < 0.05) in the birds reared in the South Andaman district (25.6, 17.5, and 18.7%, respectively) than in Nicobar (11.5, 7.6, 7.1%, respectively). Genotyping of the β-lactamase-producing isolates revealed the maximum possession of bla _TEM, followed by bla _SHV and bla _{CTX - M}. The nucleotide sequences were found to be similar with bla _{CTX - M-15}, bla _{SHV - 11}, bla _{SHV - 27}, bla _{SHV - 228}, bla _{TEM - 1}, and bla _AmpC in BLAST search. Distribution of studied biofilm-associated genes in Enterobacteriaceae strains from different varieties of the birds revealed that the layer birds had the maximum possession, followed by Vanraja, Desi, broilers, and Nicobari fowls. The phylogenetic analysis of selected sequences revealed a partial clonal relationship with human clinical strains of the Indian subcontinent. Molecular docking depicted the Gibbs free energy release for 10 different macromolecules (proteins) and ligand (antibiotic) complexes, ranging from -8.1 (SHV-27 + cefotaxime) to -7 (TEM-1 + cefotaxime) kcal/mol.

Conclusion and relevance

The study revealed β-lactamase variants circulating in the fowl population of the Andaman and Nicobar Islands (India), even in remote places with low anthropogenic activity. Most of the strains possessed bla _{TEM - 1}, followed by bla _{CTX - M-15}. Possession of bla _{SHV - 11}, bla _{SHV - 27}, and bla _{SHV - 228} in poultry Enterobacteriaceae strains was not reported earlier from any part of the world. The phylogenetic analysis revealed a partial clonal relationship of β-lactamase sequences with the human clinical strains isolated from the Indian subcontinent.

Integrated surveillance of extended-spectrum beta-lactamase (ESBL)-producing Salmonella and Escherichia coli from humans and animal species raised for human consumption in Canada from 2012 to 2017

Resistance to beta-lactam antimicrobials caused by extended-spectrum beta-lactamase (ESBL)-producing organisms is a global health concern. The objectives of this study were to (1) summarise the prevalence of potential ESBL-producing Escherichia coli (ESBL-EC) and Salmonella spp. (ESBL-SA) isolates from agrifood and human sources in Canada from 2012 to 2017, and (2) describe the distribution of ESBL genotypes among these isolates. All data were obtained from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). CIPARS analysed samples for the presence of ESBLs through phenotypic classification and identified beta-lactamase genes (bla_TEM, bla_SHV, bla_CTX, bla_OXA, bla_CMY-2) using polymerase chain reaction (PCR) and whole genome sequencing (WGS). The prevalence of PCR-confirmed ESBL-EC in agrifood samples ranged from 0.5% to 3% across the surveillance years, and was detected most frequently in samples from broiler chicken farms. The overall prevalence of PCR-confirmed ESBL-SA varied between 1% and 4% between 2012 and 2017, and was most frequently detected in clinical isolates from domestic cattle. The TEM-CMY2 gene combination was the most frequently detected genotype for both ESBL-EC and ESBL-SA. The data suggest that the prevalence of ESBL-EC and ESBL-SA in Canada was low (i.e. <5%), but ongoing surveillance is needed to detect emerging or changing trends.

Effects of a Specific Pre- and Probiotic Combination and Parent Stock Vaccination on Performance and Bacterial Communities in Broilers Challenged with a Multidrug-Resistant Escherichia coli

Antibiotic resistance poses a risk for human and animal health, leading to a growing demand for effective alternatives. Combining nutritional tools and parent stock vaccination could be an approach to achieve sufficient protection against bacterial infections in poultry. In an Escherichia coli O1/O18 challenge trial, we investigated the protective effects of feeding diets containing Enterococcus faecium DSM 7134 and fructooligosaccharides (FOS) combined with specific parent stock vaccination in 225 ROSS 308 broilers. Data on performance parameters, intestinal microbial composition and metabolites, and antibiotic resistance genes (sul1-3, dhfr1a, SHV-12) were obtained. E. faecium and FOS combined with parent stock vaccination led to the highest body weights, which were significantly higher than those of controls throughout the experiment and decreased the relative abundance of Proteobacteria in the crop digesta compared to that in the positive control. However, cumulative feed conversation remained unaffected by the strategies. Birds receiving the pre-/probiotic combination showed lower cecal pH levels and higher crop L-lactate concentrations than the controls, whereas copy numbers of dhfr1a (trimethoprim resistance) and SHV-12 (extended-spectrum beta-lactamase) genes were only decreased in broilers from vaccinated hens compared to those in the challenged control. In conclusion, prophylactic administration of E. faecium and FOS in combination with parent stock vaccination can have complementary effects by improving broiler weight gain and stimulating intestinal bacterial metabolism, which may be beneficial for maintaining gut health in terms of Escherichia coli infection.

Prevalence and multidrug resistance of Enterococcus species isolated from chickens at slaughterhouses in Nakhon Ratchasima Province, Thailand

Background and Aim

Enterococcus is a commensal bacteria found in humans and animals, which can cause human nosocomial infections. One of the most contaminated enterococcal sources is poultry meat. Therefore, this study estimated the prevalence and antimicrobial resistance (AMR) profile of Enterococcus from chickens and their meat products at local slaughterhouses in Nakhon Ratchasima Province, Thailand.

Materials and Methods

From January 2021 to March 2022, 558 samples from 279 cloacal swabs and breast meat were collected from 31 local slaughterhouses in the area. Then, the samples were screened for Enterococcus using modified de Man, Rogosa, and Sharpe agar. Next, selected Gram-positive, catalase-negative, and cocci-shaped colonies were investigated for enterococcal confirmation using Enterococcosel Agar (EA). We also cultivated the samples directly on EA. However, the disk diffusion method was used to investigate positive Enterococcus resistance profiles to 16 antimicrobial agents. Finally, selected phenotypic multidrug-resistant (MDR) Enterococcus isolates were further assessed to identify AMR genes by polymerase chain reaction.

Results

Investigations showed that the prevalence of Enterococcus isolates from the chicken cloacal swabs and meat samples were 29.75% (83/279) and 28.32% (78/279), respectively. Most Enterococcus positive isolates were resistant to colistin, followed by cefoxitin, cephalexin, and streptomycin. These isolates also showed a prevalence of MDR species (65.22%; 105/161) and 66 patterns. Furthermore, selected MDR Enterococcus (MDRE) from cloacal swabs and breast meat were positive for the resistant extended-spectrum beta-lactamase TEM genes at 71.43% (20/28) and 78.26% (18/23), respectively, whereas other AMR genes detected in the selected MDR enterococci from the cloacal swabs and breast meat were beta-lactamase TEM (bla _TEM [0%, 1.96%]), Class 1 integrase (intI1 [14.28%, 0%]), colistin (mrc-1 [3.57%, 0%]), and vancomycin (vanA [14.28%, 0%]).

Conclusion

This study indicated that phenotypic MDRE correlated with extended-spectrum beta-lactamase TEM gene presence, leading to an AMR reservoir that can be transferred to other bacteria.

Antibiotic Susceptibility Profiles and Resistance Mechanisms to β-Lactams and Polymyxins of Escherichia coli from Broilers Raised under Intensive and Extensive Production Systems

The intensive and extensive broiler production systems imply different veterinary interventions, including the use of antimicrobials. This study aimed to compare the antimicrobial susceptibility profiles of Escherichia coli isolated from both systems, characterize resistance mechanisms to β-lactams and polymyxins, and identify genetic elements such as integrons. E. coli isolates recovered from broiler cecal samples were assayed for antimicrobial susceptibility through the broth microdilution technique. The molecular characterization of acquired resistance mechanisms to β-lactams and colistin and the detection of integrons was performed by a multiplex PCR. For most antibiotics tested, the prevalence of reduced susceptibility is higher in commensal and extended-spectrum β-lactamases (ESBL)/AmpC producers from broilers raised in the intensive system, compared with those raised under extensive conditions. SHV-12 was the most common ESBL enzyme found in both production systems. Other ESBL variants such as CTX-M-1, CTX-M-55, CTX-M-14, CTX-M-32, CTX-M-9, TEM-52, and plasmid-encoded AmpC enzyme CMY-2 were also present. MCR-1 was identified in a colistin-resistant isolate from broilers raised under the intensive system. This study highlights the differences in E. coli antibiotic susceptibility from both production types and emphasizes that a great deal of work remains to decrease consumption and antimicrobial resistance levels.

A One Health Genomic Investigation of Gentamicin Resistance in Escherichia coli from Human and Chicken Sources in Canada, 2014 to 2017

We investigated whether gentamicin resistance (Gen^r) in Escherichia coli isolates from human infections was related to Gen^r E. coli in chicken and whether resistance may be due to coselection from use of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on 483 Gen^r E. coli isolates isolated between 2014 and 2017. These included 205 human-source isolates collected by the Canadian Ward (CANWARD) program and 278 chicken-source isolates: 167 from live/recently slaughtered chickens (animals) and 111 from retail chicken meat collected by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). The predominant Gen^r gene was different in human and chicken sources; however, both sources carried aac(3)-IId, aac(3)-VIa, and aac(3)-IVa. Forty-one percent of human clinical isolates of Gen^r E. coli contained a bla_CTX-M extended-spectrum beta-lactamase (ESBL) gene (84/205), and 53% of these were sequence type 131 (ST131). Phylogenomic analysis revealed a high diversity of Gen^r isolates; however, there were three small clusters of closely related isolates from human and chicken sources. Gen^r and spectinomycin resistance (Spec^r) genes were colocated in 148/167 (89%) chicken animal isolates, 94/111 (85%) chicken retail meat isolates, and 137/205 (67%) human-source isolates. Long-read sequencing of 23 isolates showed linkage of the Gen^r and Spec^r genes on the same plasmid in 14/15 (93%) isolates from chicken(s) and 6/8 (75%) isolates from humans. The use of lincomycin-spectinomycin on farms may be coselecting for gentamicin-resistant plasmids in E. coli in broiler chickens; however, Gen^r isolates and plasmids were mostly different in chickens and humans.

Characterization of plasmid-mediated quinolone resistance genes and extended-spectrum beta-lactamases in non-typhoidal Salmonella enterica isolated from broiler chickens

Background and Aim:

Antibiotic-resistant Salmonella is a public health concern. Fluoroquinolones and extended-spectrum beta-lactams are widely used for the treatment of Salmonella infections. This study focused on the detection of plasmid-mediated quinolone resistance (PMQR) and extended-spectrum beta-lactamase (ESBL) genes among multidrug-resistant (MDR) Salmonella enterica isolated from broilers.

Materials and Methods:

A total of 40 non-typhoidal S. enterica isolates were collected from 28 broiler chicken farms in four Iraqi Governorates. These isolates were examined for their susceptibility to 10 antimicrobial agents by disk-diffusion method followed by polymerase chain reaction assay for the detection of PMQR determinants and ESBLs genes.

Results:

Salmonella strains revealed high levels of resistance to the following antibiotics: Nalidixic acid 100%, levofloxacin (LEV) 97.5%, amoxicillin-clavulanic acid 95.0%, tetracycline 92.5%, and nitrofurantoin 80.0%. Otherwise, all isolates were susceptible to cefotaxime and ceftriaxone. All isolates were MDR, with 15 different profiles observed. Among 38 amoxicillin/clavulanic acid-resistant Salmonella isolates, 20 (52.6%) had the blaTEM gene, while blaSHV, blaCTX-M, and blaOXA genes were not detected. Only 5 (12.8%) out of 39 LEV-resistant isolates were positive for qnrB, three of which had blaTEM. No qnrC or qnrD, qnrS, aac(6`)-Ib-cr, qunA, and oqxAB genes were found in any of the tested isolates.

Conclusion:

This study demonstrates that broiler chickens may be considered a potential source for spreading MDR non-typhoidal Salmonella and ESBL traits in poultry production. Therefore, it is important to continuously monitor ESBL and PMQR genes to avoid the spread of resistant strains in the food chain and impact public health.

A Review of Current Bacterial Resistance to Antibiotics in Food Animals

The overuse of antibiotics in food animals has led to the development of bacterial resistance and the widespread of resistant bacteria in the world. Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in food animals are currently considered emerging contaminants, which are a serious threat to public health globally. The current situation of ARB and ARGs from food animal farms, manure, and the wastewater was firstly covered in this review. Potential risks to public health were also highlighted, as well as strategies (including novel technologies, alternatives, and administration) to fight against bacterial resistance. This review can provide an avenue for further research, development, and application of novel antibacterial agents to reduce the adverse effects of antibiotic resistance in food animal farms.

Transferability of ESBL-encoding IncN and IncI1 plasmids among field strains of different Salmonella serovars and Escherichia coli

OBJECTIVES

This study aimed to sequence, assemble and annotate three plasmids (two IncN and one IncI1) carrying the bla_CTX-M-1 gene and assess their transmissibility rates between homologous and heterologous serovars and/or species of bacteria.

METHODS

First, the plasmids were sequenced, assembled, and annotated. They were then transferred from three donor strains (E. coli/IncN, S. Heidelberg/IncN, and S. Heidelberg/IncI1) into nine recipient strains (S. Enteritidis, S. Heidelberg, S. Saint Paul, S. Cero, S. Infantis, S. Braenderup, E. coli 50, and E. coli 2010). The bla_CTX-M-1 gene PCR, plasmid isolation, and antimicrobial susceptibility testing were used on the transconjugants to confirm the successful transfer of ESBL plasmids into the recipient strains.

RESULTS

Both IncN plasmids were 42,407 bp in size and showed >99.4% similarity to the S. Bredeney pET1.2-IncN (GenBank accession CP043224.1) whereas the IncI1 plasmid was 107,635 bp in size and demonstrated >99.9% similarity to the E. coli pCOV33 plasmid (GenBank accession MG649046.1). Successful plasmid transfer was observed between donor ​E. coli (IncN) and all recipient strains except for E. coli 50 and between donor S. Heidelberg (IncN) and all recipient strains. Successful plasmid transfer was also observed between S. Heidelberg (IncI1) and E. coli 50.

CONCLUSIONS

Transfer of the bla _CTX-M-1 encoding IncN and IncI1 plasmids via conjugation is possible yet occurs at different frequencies depending on the donor strain of bacteria with S. Heidelberg (IncN) having the highest donor-dependent transfer frequency, followed by E. coli 9079 (IncN) and S. Heidelberg (IncI1).

Fecal Shedding of Multidrug Resistant Escherichia coli Isolates in Dogs Fed with Raw Meat-Based Diets in Brazil

The practice of feeding dogs raw meat-based diets (RMBDs) is growing in several countries, and the risks associated with the ingestion of pathogenic and antimicrobial-resistant Escherichia coli in dogs fed these diets are largely unknown. We characterized E. coli strains isolated from dogs fed either an RMBD or a conventional dry feed, according to the phylogroup, virulence genes, and antimicrobial susceptibility profiles of the bacteria. Two hundred and sixteen E. coli strains were isolated. Dogs fed RMBDs shed E. coli strains from the phylogroup E more frequently and were positive for the E. coli heat-stable enterotoxin 1-encoding gene. Isolates from RMBD-fed dogs were also frequently positive for multidrug-resistant E. coli isolates including extended-spectrum beta-lactamase (ESBL) producers. Whole-genome sequencing of seven ESBL-producing E. coli strains revealed that they predominantly harbored blaCTX-M-55, and two strains were also positive for the colistin-resistant gene mcr-1. These results suggest that feeding an RMBD can affect the dog’s microbiota, change the frequency of certain phylogroups, and increase the shedding of diarrheagenic E. coli. Also, feeding an RMBD seemed to be linked with the fecal shedding of multidrug-resistant E. coli, including the spread of strains harboring mobilizable colistin resistance and ESBL genes. This finding is of concern for both animal and human health.

Prevalence and characterisation of antimicrobial resistance genes and class 1 and 2 integrons in multiresistant Escherichia coli isolated from poultry production

A global increase in the populations of drug resistant bacteria exerts negative effects on animal production and human health. Our study has been focused on the assessment of resistance determinants in relation to phenotypic resistance of the 74 commensal E. coli isolates present in different ecological environments. The samples were collected from poultry litter, feces, and neck skin. Among the microorganisms isolated from the poultry litter (group A), the highest resistance was noted against AMP and DOX (100%). In the E. coli extracts from the cloacal swabs (group B), the highest resistance was observed against AMP (100%) and CIP (92%). The meat samples (group C) were characterized by resistance to AMP (100%) and STX (94.7%). Genes encoding resistance to β-lactams (bla_TEM, bla_CTX-M), fluoroquinolones (qnrA, qnrB, qnrS), aminoglycosides (strA-strB, aphA1, aac(3)-II), sulfonamides (sul1, sul2, sul3), trimethoprim (dfr1, dfr5, dfr7/17) and tetracyclines (tetA, tetB) were detected in the studied bacterial isolates. The presence of class 1 and 2 integrons was confirmed in 75% of the MDR E. coli isolates (plasmid DNA), of which 60% contained class 1 integrons, 15% contained class 2 integrons, and 11.7% carried integrons of both classes. Thus, it may be concluded that integrons are the common mediators of antimicrobial resistance among commensal multidrug resistant Escherichia coli at important stages of poultry production.

Antimicrobial resistance profiles of Escherichia coli and prevalence of extended‐spectrum beta‐lactamase‐producing Enterobacteriaceae in calves from organic and conventional dairy farms in Switzerland

This study compared the antimicrobial resistance (AMR) among commensal Escherichia coli in the fecal microbiota of young calves raised on organic and on conventional dairy farms in Switzerland. Further, fecal carriage of extended‐spectrum beta‐lactamase (ESBL) producing Enterobacteriaceae was assessed for calves from both farming systems. Where possible, data on antimicrobial usage (AMU) were obtained. Antimicrobial susceptibility testing was performed on a total of 71 isolates using the disk diffusion method. ESBL producers were characterized by polymerase chain reaction‐based multilocus sequence typing and sequencing of the bla_ESBL genes. Organically raised calves were significantly more likely to harbor E. coli that showed AMR to ampicillin (odds ratio [OR]: 2.78, 95% confidence interval [CI]: 1.02–7.61, p = 0.046), streptomycin (OR: 3.22, 95% CI: 1.17–8.92, p = 0.046), kanamycin (OR: 11.3, 95% CI: 2.94–43.50, p < 0.001), and tetracycline (OR: 3.25, 95% CI: 1.13–9.31, p = 0.028). Calves with reported AMU were significantly more likely to harbor E. coli with resistance to ampicillin (OR: 3.91, 95% CI: 1.03–14.85, p = 0.045), streptomycin (OR: 4.35, 95% CI: 1.13–16.7, p = 0.045), and kanamycin (OR: 8.69, 95% CI: 2.01–37.7, p = 0.004). ESBL‐producing Enterobacteriaceae (18 E. coli and 3 Citrobacter braakii) were detected exclusively among samples from conventionally farmed calves (OR: infinity [∞], 95% CI: 2.3–∞, p < 0.0013). The observations from this study suggest that AMR is highly prevalent among commensal E. coli in young dairy calves, irrespective of the farm management system, with proportions of certain resistance phenotypes higher among organic calves. By contrast, the occurrence of ESBL producers among young dairy calves may be linked to factors associated with conventional farming.

The Impact of Pre- and Probiotic Product Combinations on Ex vivo Growth of Avian Pathogenic Escherichia coli and Salmonella Enteritidis

Due to the global spread of antibiotic resistance, there is a strong demand to replace antimicrobial growth promotors in livestock. To identify suitable additives that inhibit the growth of avian pathogenic Escherichia coli O1/O18 and Salmonella enterica serotype Enteritidis strains, an ex vivo screening was performed. Inulin and fructooligosaccharides (FOS) were investigated as prebiotics. Enterococcus faecium and Bacillus coagulans served as probiotic strains. Firstly, the pathogen was anaerobically incubated in caecal digesta from different broiler breeder flocks with the addition of feed additives. Secondly, subsamples of these suspensions were incubated in an antibiotic medium for selective growth of the pathogen. During this step, turbidity was recorded, and lag times were calculated for each pathogen as readout of growth inhibition. Combinations of E. faecium with inulin or FOS significantly extended the lag time for E. coli compared to control. Moreover, older age was a significant factor to enhance this inhibitory effect. In contrast, the combination of FOS and B. coagulans showed shorter lag times for S. Enteritidis. Our results indicate that the E. faecium strain with prebiotics may inhibit the pathogen proliferation in the studied poultry flocks. Furthermore, our results suggest that prophylactic treatments should be assigned by feed additive, age and animal origin.

Prevalence of poultry Escherichia coli isolates producing extended-spectrum beta-lactamases and their public health importance

Recently, different reports highlighted the problem with dissemination of Escherichia coli producing extended spectrum beta-lactamases (ESBL) in poultry farms in Europe. The high incidence of Escherichia coli among poultry in Europe harbouring blaCTX-M-1 and the occurrence of ESBL and AmpC-producing Escherichia coli in raw meat samples collected from slaughterhouses in Europe have been discussed. ESBL-producing Enterobacteriaceae can be transmitted along the broiler production chain. Plasmids responsible for ESBL production frequently carry genes coding resistance to other antimicrobial classes, such as fluoroquinolones, aminoglycosides, sulphonamides. Resistance to cephalosporins in Enterobacteriaceae is of special concern for public health, because these anti­microbial agents are critically important. The aim of this mini review was to describe the mechanisms of resistance and prevalence of ESBL-producing E. coli. It is important to investigate the spread of these bacteria among poultry, the role of farm birds as reservoir of E. coli and the risk for people.

The Magnitude of Carbapenemase and ESBL Producing Enterobacteriaceae Isolates from Patients with Urinary Tract Infections at Tikur Anbessa Specialized Teaching Hospital, Addis Ababa, Ethiopia

BACKGROUND

The emergence of multidrug-resistant organisms, such as extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE), and carbapenemase-producing Enterobacteriaceae (CPE) is a public health concern. Therefore, this study aimed to determine the magnitude of carbapenemase and ESBL producing bacteria isolated from patients affected by Urinary Tract Infection (UTI).

METHODS

A cross-sectional study was conducted from December 2018 to March 2019 at Tikur Anbessa Specialized Hospital. A total of 120 Enterobacteriaceae isolates from UTI patients were collected and identified on species level using standard microbiological methods. Antimicrobial susceptibility test was determined according to the guidelines of the Clinical and Laboratory Standards Institute. Detection of ESBL production was carried out by using ESBL ChromoSelect Agar medium and the combined disk diffusion. Production of carbapenemase was determined by using Hodge-test and modified carbapenem inactivation method as described in CLSI guidelines.

RESULTS

Out of the total 120 Enterobacteriaceae isolates, 74 (61.7%) were ESBL-producers, and 8 (6.7%) were carbapenemase producers. The most common ESBL producing isolate was E.coli 38 (51.4%) and the most common carbapenemase-producing isolate was K.pneumoniae five (62.5%). Most of the ESBL and carbapenemase-producing isolates were recovered from hospitalized patients 46 (62.2%) and 7 (87.5%) respectively. The rate of ESBL and CPE production was observed high among patients taking antibiotics 64.8% (59/91) and 7.7% (7/91) respectively, but no significant association was observed p > 0.05. Furthermore, about 1.7% (2/120) isolates were found both ESBL and carbapenemase producers. Significant resistances rates were observed in ESBL and CPE isolates.

CONCLUSION

Enterobacteriaceae isolates showed a significantly higher rate of ESBL production. A significant figure of carbapenemase production was observed among Enterobacteriaceae isolates causing UTI. The production of ESBL and CPE enhanced for an increased rate of MDR patterns. Efforts need to be made to introduce a system for tracking and detecting ESBL-PE and CPE-producing bacteria in hospitals, and monitoring dissemination of ESBL and CPE-producing Enterobacteriaceae is strongly recommended.

Antimicrobial resistance genes and genetic characteristics of multidrug-resistant Escherichia coli in a veterinary hospital in Taiwan

Introduction. Antimicrobial resistance associated with animal hosts is easily transmitted to humans either by direct contact with resistant organisms or by transferring resistance genes into human pathogens.Gap statement. There are limited studies on antimicrobial resistance genes and genetic elements of multidrug-resistant (MDR) Escherichia coli in veterinary hospitals in Taiwan.Aim. The aim of this study was to investigate antimicrobial resistance genes in multidrug-resistant Escherichia coli from animals.Methodology. Between January 2014 and August 2015, 95 multidrug-resistant Escherichia coli isolates were obtained from pigs (n=66), avians (n=18), and other animals (n=11) in a veterinary hospital in Taiwan. Susceptibility testing to 24 antimicrobial agents of 14 antimicrobial classes was performed. Antimicrobial resistance genes, integrons, and insertion sequences were analysed by polymerase chain reaction and nucleotide sequencing. Pulsed-field gel electrophoresis (PFGE), and multi-locus sequence typing were used to explore the clonal relatedness of the study isolates.Results. Different antimicrobial resistance genes found in these isolates were associated with resistance to β-lactams, tetracycline, phenicols, sulfonamides, and aminoglycosides. Fifty-five of 95 E. coli isolates (55/95, 57.9 %) were not susceptible to extended-spectrum cephalosporins, and bla _CTX-M-55 (11/55, 20.0 %) and bla _CMY-2 (40/55, 72.7 %) were the most common extended-spectrum β-lactamase (ESBL) and AmpC genes, respectively. Both bla _CTX-M and bla _CMY-2 were present on conjugative plasmids that contained the insertion sequence ISEcp1 upstream of the bla genes. Plasmid-mediated FOX-3 β-lactamase-producing E. coli was first identified in Taiwan. Forty isolates (40/95, 42 %) with class 1 integrons showed seven resistance phenotypes. Genotyping of 95 E. coli isolates revealed 91 different XbaI pulsotypes and 52 different sequence types. PFGE analysis revealed no clonal outbreaks in our study isolates.Conclusion. This study showed a high diversity of antimicrobial resistance genes and genotypes among MDR E. coli isolated from diseased livestock in Taiwan. To our knowledge, this is the first report of plasmid-mediated ESBL in FOX-3 β-lactamase-producing E. coli isolates in Taiwan. MDR E. coli isolates from animal origins may contaminate the environment, resulting in public health concerns, indicating that MDR isolates from animals need to be continuously investigated.

Isolation of Ciprofloxacin and Ceftazidime-Resistant Enterobacterales From Vegetables and River Water Is Strongly Associated With the Season and the Sample Type

The dissemination of antibiotic-resistant bacteria (ARB) from water used for crop irrigation to vegetables is poorly studied. During a year, five farmer markets in a city in Central Chile were visited, and 478 vegetable samples (parsleys, corianders, celeries, lettuces, chards, and beets) were collected. Simultaneously, 32 water samples were collected from two rivers which are used to irrigate the vegetables produced in the area. Resistant Enterobacterales were isolated and identified. Colistin resistance gene mcr-1 and extended spectrum β-lactamases (ESBL) were molecularly detected. The association of environmental factors was evaluated, with the outcomes being the presence of Enterobacterales resistant to four antibiotic families and the presence of multidrug resistance (MDR) phenotypes. Parsley, coriander, and celery showed the highest prevalence of resistant Enterobacterales (41.9% for ciprofloxacin and 18.5% for ceftazidime). A total of 155 isolates were obtained, including Escherichia coli (n=109), Citrobacter sp. (n=20), Enterobacter cloacae complex (n=8), Klebsiella pneumoniae (n=8), and Klebsiella aerogenes (n=1). Resistance to ampicillin (63.2%) and ciprofloxacin (74.2%) was most frequently found; 34.5% of the isolates showed resistance to third-generation cephalosporins, and the MDR phenotype represented 51.6% of the isolates. In two E. coli isolates (1.29%), the gene mcr-1 was found and ESBL genes were found in 23/62 isolates (37%), with bla_CTX-M being the most frequently found in 20 isolates (32%). Resistant Enterobacterales isolated during the rainy season were less likely to be MDR as compared to the dry season. Understanding environmental associations represent the first step toward an improved understanding of the public health impact of ARB in vegetables and water.

Occurrence of Escherichia coli producing extended spectrum β-lactamases in food-producing animals

Multidrug resistance due to the production of extended-spectrum beta-lactamases (ESBLs) is a major problem in human as well as in veterinary medicine. These strains appear in animal and human microbiomes and can be the source of infection both in animal and in human healthcare, in accordance with the One Health theorem. In this study we examined the prevalence of ESBL-producing bacteria in food-producing animals. We collected 100 porcine and 114 poultry samples to examine the prevalence of ESBL producers. Isolates were identified using the MALDI-TOF system and their antibiotic susceptibility was tested using the disk diffusion method. ESBL gene families and phylogroups were detected by polymerase chain reactions. The prevalence of ESBL producers was relatively high in both sample groups: 72 (72.0%) porcine and 39 (34.2%) poultry isolates were ESBL producers. Escherichia coli isolates were chosen for further investigations. The most common ESBL gene was CTX-M-1 (79.3%). Most of the isolates belong to the commensal E. coli phylogroups. The porcine isolates could be divided into three phylogroups, while the distribution of the poultry isolates was more varied. In summary, ESBL-producing bacteria are prevalent in the faecal samples of the examined food-producing animals, with a dominance of the CTX-M-1 group enzymes and commensal E. coli phylogroups.

Inhibition of Antimicrobial-Resistant Escherichia coli Using a Broad Host Range Phage Cocktail Targeting Various Bacterial Phylogenetic Groups

Antimicrobial-resistant (AMR) commensal Escherichia coli is a major reservoir that disseminates antimicrobial resistance to humans through the consumption of contaminated foods, such as retail poultry products. This study aimed to control AMR E. coli on retail chicken using a broad host range phage cocktail. Five phages (JEP1, 4, 6, 7, and 8) were isolated and used to construct a phage cocktail after testing infectivity on 67 AMR E. coli strains isolated from retail chicken. Transmission electron microscopic analysis revealed that the five phages belong to the Myoviridae family. The phage genomes had various sizes ranging from 39 to 170 kb and did not possess any genes associated with antimicrobial resistance and virulence. Interestingly, each phage exhibited different levels of infection against AMR E. coli strains depending on the bacterial phylogenetic group. A phage cocktail consisting of the five phages was able to infect AMR E. coli in various phylogenetic groups and inhibited 91.0% (61/67) of AMR E. coli strains used in this study. Furthermore, the phage cocktail was effective in inhibiting E. coli on chicken at refrigeration temperatures. The treatment of artificially contaminated raw chicken skin with the phage cocktail rapidly reduced the viable counts of AMR E. coli by approximately 3 log units within 3 h, and the reduction was maintained throughout the experiment without developing resistance to phage infection. These results suggest that phages can be used as a biocontrol agent to inhibit AMR commensal E. coli on raw chicken.

Bacillus pumilus and Bacillus subtilis Promote Early Maturation of Cecal Microbiota in Broiler Chickens

Mature and stable intestinal microbiota in chickens is essential for health and production. Slow development of microbiota in young chickens prolongs the precarious period before reaching mature configuration. Whether probiotics can play a role in the early maturation of intestinal microbiota is unknown. To address this, day-old chicks were assigned into six groups: NC (basal diet), PC (virginiamycin), low (BPL) and high-dose (BPH) of Bacillus pumilus, and low (BSL) and high-dose (BSH) of Bacillus subtilis. Cecal contents at days 7, 14, 28 and 42 were used to analyze the treatment and time effects on the diversity and composition of microbiota. Overall, the alpha diversity was significantly decreased in the NC group between days 7 and 14, while this decline was prevented in the Bacillus subtilis probiotic (BSL and BSH) and even reversed in the BPH group. The beta-diversity showed significant responses of microbial communities to probiotics in first two weeks of life. Analyses of the abundance of microbiota reflected that members of the family Ruminococcaceae (Ruminnococcus, Oscillospira, Faecalibacterium, Butyricicoccus, and Subdoligranulum), which were dominant in mature microbiota, were significantly higher in abundance at day 14 in the probiotic groups. Conversely, the abundance of genera within the family Lachnospiraceae (Ruminococcus, Blautia, and Coprococcus) was dominant in early dynamic microbiota but was significantly lower in the probiotic groups at day 14. The Lactobacillus and Bifidobacterium abundance was higher, while the Enterobacteriaceae abundance was lower in the probiotic groups. In summary, the probiotics efficiently helped the cecal microbiota reach mature configuration earlier in life. These results could be used for the future manipulation of microbiota from the perspective of improving poultry performance.

Isolation of third generation cephalosporin resistant Enterobacteriaceae from retail meats and detection of extended spectrum beta-lactamase activity

Various methods have been described to isolate third generation cephalosporin (3GC) resistant Enterobacteriaceae from foods, but it is not known how comparable they are between studies. Here, the performance of five enrichment broths and two selective agars are compared for their ability to isolate 3GC resistant Enterobacteriaceae from retail chicken, beef, pork, and veal samples. The results showed equivalence between Enterobacteriaceae enrichment broth (EE), lauryl sulfate broth (LST), and modified typtone soy broth (mTSB). Lower isolation rates were observed when LST and mTSB were supplemented with the 3GC antibiotic cefotaxime. The overall performance of MacConkey agar supplemented with cefotaxime and a proprietary selective agar (ESBL CHROMagar) was equivalent, although differences linked to the microbiota of specific meat commodities were noted. Regardless of the isolation method, further screening was required to confirm the taxonomy and resistance of the presumptive positive strains. Approximately 40% of confirmed 3GC resistant foodborne Enterobacteriaceae strains tested positive for extended spectrum beta-lactamase (ESBL) activity. Strains that were resistant to ceftriaxone and susceptible to cefoxitin were more likely to test positive for ESBL activity, as were strains that possessed either of two ESBL genes (bla_SHV or bla_TEM). Based on our results, we recommend using an antibiotic-free enrichment broth, two selective agars, and an isolate screening strategy to isolate 3GC resistant Enterobacteriaceae from retail meats. Antibiotic susceptibility testing and/or PCR screening for bla_SHV or bla_TEM can then be used to identify ESBL producing strains among the 3GC resistant meat isolates. The adoption of this approach by the research community will enable more effective monitoring of antibiotic resistance rates and trends among foodborne Enterobacteriaceae over time and across jurisdictions.

Risk Factors for Antimicrobial Resistance in Turkey Farms: A Cross-Sectional Study in Three European Countries

Food-producing animals are an important reservoir and potential source of transmission of antimicrobial resistance (AMR) to humans. However, research on AMR in turkey farms is limited. This study aimed to identify risk factors for AMR in turkey farms in three European countries (Germany, France, and Spain). Between 2014 and 2016, faecal samples, antimicrobial usage (AMU), and biosecurity information were collected from 60 farms. The level of AMR in faecal samples was quantified in three ways: By measuring the abundance of AMR genes through (i) shotgun metagenomics sequencing (n = 60), (ii) quantitative real-time polymerase chain reaction (qPCR) targeting ermB, tetW, sul2, and aph3'-III; (n = 304), and (iii) by identifying the phenotypic prevalence of AMR in Escherichia coli isolates by minimum inhibitory concentrations (MIC) (n = 600). The association between AMU or biosecurity and AMR was explored. Significant positive associations were detected between AMU and both genotypic and phenotypic AMR for specific antimicrobial classes. Beta-lactam and colistin resistance (metagenomics sequencing); ampicillin and ciprofloxacin resistance (MIC) were associated with AMU. However, no robust AMU-AMR association was detected by analyzing qPCR targets. In addition, no evidence was found that lower biosecurity increases AMR abundance. Using multiple complementary AMR detection methods added insights into AMU-AMR associations at turkey farms.

Prevalence and risk factors for faecal carriage of multidrug resistant Escherichia coli among slaughterhouse workers

The increasing occurrence of antimicrobial-resistant Escherichia coli in human and animal population has become a global public health problem that requires immediate intervention. We aimed to investigate prevalence and risk factors for faecal carriage of drug-resistant E. coli among slaughterhouse workers. We conducted this cross-sectional study among 118 apparently healthy workers in the largest slaughterhouses in Abuja and Lagos from July to December 2020. E. coli was isolated from stool samples of slaughterhouse workers and antimicrobial susceptibility testing performed using the Kirby-Bauer disk diffusion method. Multi-drug resistance (MDR) was defined as resistance to three or more classes of antibiotics. Majority were males: 88.1% (n = 104), aged > 41 years: 28.8% (n = 34), married: 70.3% (n = 83), and were butchers: 53.4% (n = 63). Prevalence of MDR E. coli was 50% (n = 59), highest among butchers compared to slaughterhouse cleaners. Of 75 E. coli isolates identified, 25.3% (n = 19) were ESBL producers; 78.7% (n = 59) were MDR. Keeping animals (p = 0.01); eating at the slaughterhouse (p = 0.03) and collecting waste (p = 0.02) remained independent risk factors for acquiring MDR E. coli. Prevalence of resistant E. coli was highest among butchers and associated with keeping animals at home, eating at work, and waste-collection. Hand-hygiene and responsible use of antibiotics among slaughterhouse workers should be encouraged.

Risk factors for faecal carriage of multidrug-resistant Escherichia coli in a college community: a penalised regression model

OBJECTIVES

Bacterial antimicrobial resistance is a serious global public-health threat. Intestinal commensal drug-resistant bacteria have been suggested as an important reservoir of antimicrobial resistance genes (ARGs), which may be acquired via food. We aimed to identify risk factors associated with faecal carriage of drug-resistant commensal Escherichia coli among healthy adults focused on their dietary habits.

METHODS

We conducted a cross-sectional study targeting healthy adult volunteers in a college community. Faecal samples and questionnaires were obtained from 113 volunteers. We conducted backward elimination logistic regression and least absolute shrinkage and selection operator (LASSO) methods to identify risk factors.

RESULTS

We analysed responses from 81 of 113 volunteers who completed the questionnaire. The logistic regression and LASSO methods identified red meat consumption to be associated with an increased risk [OR = 6.13 (95% CI 1.83-24.2) and 1.82, respectively] and fish consumption with a reduced risk [OR = 0.27 (95% CI 0.08-0.85) and 0.81] for carriage of multidrug-resistant (MDR) E. coli, adjusted for biological sex, employment status, frequently used supermarket and previous travel.

CONCLUSION

Dietary habits are associated with risk of faecal carriage of MDR E. coli. This study supports the growing evidence that food may be an important source of ARGs present in human commensal E. coli.

Transmission of Similar Mcr-1 Carrying Plasmids among Different Escherichia coli Lineages Isolated from Livestock and the Farmer

Colistin use has mostly been stopped in human medicine, due to its toxicity. However, nowadays, it still is used as a last-resort antibiotic to treat hospital infections caused by multi-drug resistant Enterobacteriaceae. On the contrary, colistin has been used in veterinary medicine until recently. In this study, 210 fecal samples from pigs (n = 57), calves (n = 152), and the farmer (n = 1) were collected from a farm where E. coli harboring mcr-1–mcr-3 was previously detected. Samples were plated, and mcr-genes presence was confirmed by multiplex-PCR. Hybrid sequencing which determined the presence and location of mcr-1, other antibiotic resistance genes, and virulence factors. Eighteen colistin resistant isolates (13 from calves, four from pigs, and one from the farmer) contained mcr-1 associated with plasmids (IncX4, IncI2, and IncHI2), except for two that yielded mcr-1 in the chromosome. Similar plasmids were distributed in different E. coli lineages. Transmission of mcr-1 to the farmer most likely occurred by horizontal gene transfer from E. coli of calf origin, since plasmids were highly similar (99% coverage, 99.97% identity). Moreover, 33 virulence factors, including stx2 for Shiga toxin E. coli (STEC) were detected, highlighting the role of livestock as a reservoir of pathotypes with zoonotic potential.

Rapid detection of extended spectrum β-lactamase producing Escherichia coli isolated from fresh pork meat and pig cecum samples using multiplex recombinase polymerase amplification and lateral flow strip analysis

The emergence and dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is a global health issue. Food-producing animals, including pigs, are significant reservoirs of antimicrobial resistance (AMR), which can be transmitted to humans. Thus, the rapid detection of ESBLs is required for efficient epidemiological control and treatment. In this study, multiplex recombinase polymerase amplification (RPA) combined with a single-stranded tag hybridization chromatographic printed-array strip (STH-PAS), as a lateral flow strip assay (LFA), was established for the rapid and simultaneous detection of multiple bla genes in a single reaction. Visible blue lines, indicating the presence of the bla_CTX-M, bla_SHV, and bla_OXA genes, were observed within 10 min by the naked eye. The limit of detection of all three genes was 2.5 ng/25 μL, and no cross-reactivity with seven commensal aerobic bacteria was observed. A total of 93.9% (92/98) and 96% (48/50) of the E. coli isolates from pork meat and fecal samples, respectively, expressed an ESBL-producing phenotype. Nucleotide sequencing of the PCR amplicons showed that bla_CTX-M was the most prevalent type (91.3–95.83%), of which the main form was bla_CTX-M-55. The sensitivity and specificity of the RPA-LFA were 99.2% and 100%, respectively, and were in almost perfect agreement (κ = 0.949–1.000) with the results from PCR sequencing. Thus, the RPA-LFA is a promising tool for rapid and equipment-free ESBL detection and may facilitate clinical diagnosis in human and veterinary medicine, as well as AMR monitoring and surveillance.

The Escherichia coli Sequence Type 131 Harboring Extended-Spectrum Beta-Lactamases and Carbapenemases Genes from Poultry Birds

Background and Aim

The extended-spectrum beta-lactamases (ESBLs), as well as carbapenemases, are considered as the foremost resistance determinants throughout the world. However, the relevant data especially related to the sequence types of ESBL and carbapenemases producing Escherichia coli from the poultry is limited from Pakistan. Here, we present the data on the genetic diversity of E. coli strains isolated from the poultry birds from the poultry farms located in Islamabad, Pakistan, and the underlying resistance mechanisms to beta-lactam agents.

Methods

Of 250 broilers from 25 different farms (10 birds from each farm), the cecal samples were obtained and analyzed for the presence of ESBLs producing E. coli (ESBL-Ec) as well as carbapenemases producing E. coli (CPEc) strains using selective agar for ESBL and carbapenemases screening. The susceptibility profiling of the ESBL-Ec and CPEc isolates was evaluated followed by multi-locus sequence typing.

Results

A total of 119 strains were positive for ESBL production whereas 37 strains were found positive to produce carbapenemases in addition to ESBLs. The MLST analysis has shown a diversity of isolates as the E. coli isolates from poultry birds correspond to a total of 16 sequence types (STs). The ST131 (22/48, 46%) followed by ST8051 (10/48, 21%) were the main STs in this study. The bla_CTX-M gene was detected in all the poultry E. coli strains whereas the bla_TEM was found in 45.5% of strains. The bla_VIM was found in all 37 CPEc isolates whereas the bla_NDM and bla_IMP were found in 31/37 (83.8%) and 16/37 (43.2%) CPEc isolates respectively.

Conclusion

The overall results have shown the prevalence of diverse genotypes among the ESBL-Ec and carbapenemase-producing E. coli (CPEC) from poultry. Furthermore, the study documents poultry birds as a persisting reservoir of extensively antimicrobial-resistant E. coli ST131 in Pakistan, suggesting a potential threat to public health.

16S rRNA Sequencing Analysis of the Gut Microbiota in Broiler Chickens Prophylactically Administered with Antimicrobial Agents

In poultry production, gut microbiota (GM) plays a pivotal role and influences different host functions related to the efficiency of production performances. Antimicrobial (AM) use is one of the main factors affecting GM composition and functions. Although several studies have focused their attention on the role of AMs as growth promoters in the modulation of GM in broilers, the consequences of higher AM concentrations administered during prophylactic treatments need to be better elucidated. For this purpose, 16S rRNA gene sequencing was performed to evaluate the impact of different prophylactic AM protocols on the composition and diversity of the broiler GM. Diversity analysis has shown that AM treatment significantly affects alpha diversity in ileum and beta diversity in both ileum and caecum. In ileal samples, the Enterobacteriaceae family has been shown to be particularly affected by AM treatments. AMs have been demonstrated to affect GM composition in broiler. These findings indicate that withdrawal periods were not enough for the restoral of the original GM. Further studies are needed for a better elucidation of the negative effects caused by an altered GM in broilers.

Genetic Features of Extended-Spectrum β-Lactamase-Producing Escherichia coli from Poultry in Mayabeque Province, Cuba

A total of 434 poultry cloacal samples were collected from seven different farms in different years (2013–2015) in the Cuban province of Mayabeque and analyzed for the presence of third-generation cephalosporin-resistant Escherichia coli (3GC-R-Ec). Sixty-two 3GC-R-Ec isolates were recovered in total from the farms, with detection rates of 2.9% in 2013, 10.3% in 2014, and 28.7% in 2015. Characterization of 32 3GC-R-Ec isolates revealed the presence of the extended-spectrum β-lactamase (ESBL) genes bla_CTX-M-1 (n = 27), bla_CTX-M-15 (n = 4), and bla_CTX-M-1 together with bla_LAP-2 (n = 1). The isolates also contained different proportions of genes conferring decreased susceptibility to sulfonamides (sul1, sul2, sul3), trimethoprim (dfrA1, dfrA7, dfrA12, dfrA14, dfrA17), tetracyclines (tet(A), tet(B)), aminoglycosides (aac(6′)-Ib-cr, strA, strB), chloramphenicol (cmlA1, floR), macrolides (mph(A), mph(D)), and quinolones (qnrS, qnrB, aac(6′)-Ib-cr) as well as mutations in the fluoroquinolone-resistance determining regions of GyrA (S83L, D87N, D87Y) and ParC (S80I, E84G). The isolates belonged to 23 different sequence types and to phylogroups A (n = 25), B1 (n = 5), and D (n = 2), and they contained plasmid-associated incompatibility groups FII, X1, HI1, HI2, N, FIA, and FIB. These findings reveal a genetically diverse population of multiresistant ESBL-producing E. coli in poultry farms in Cuba, which suggests multiple sources of contamination and the acquisition of antibiotic resistance genes.

Detection of ESBL/AmpC-Producing and Fosfomycin-Resistant Escherichia coli From Different Sources in Poultry Production in Southern Brazil

This study discussed the use of antimicrobials in the commercial chicken production system and the possible factors influencing the presence of Extended-spectrum β-lactamase (ESBL)/AmpC producers strains in the broiler production chain. The aim of this study was to perform longitudinal monitoring of ESBL-producing and fosfomycin-resistant Escherichia coli from poultry farms in southern Brazil (Paraná and Rio Grande do Sul states) and determine the possible critical points that may be reservoirs for these strains. Samples of poultry litter, cloacal swabs, poultry feed, water, and beetles (Alphitobius sp.) were collected during three distinct samplings. Phenotypic and genotypic tests were performed for characterization of antimicrobial resistant strains. A total of 117 strains were isolated and 78 (66%) were positive for ESBL production. The poultry litter presented ESBL positive strains in all three sampled periods, whereas the cloacal swab presented positive strains only from the second period. The poultry litter represents a significant risk factor mainly at the beginning poultry production (odds ratio 6.43, 95% confidence interval 1-41.21, p < 0.05). All beetles presented ESBL positive strains. The predominant gene was bla CTX-M group 2, which occurred in approximately 55% of the ESBL-producing E. coli. The cit gene was found in approximately 13% of the ESBL-producing E. coli as AmpC type determinants. A total of 19 out of 26 fosfomycin-resistant strains showed the fosA3 gene, all of which produced ESBL. The correlation between fosA3 and bla CTX-M group 1 (bla CTX-M55 ) genes was significant among ESBL-producing E. coli isolated from Paraná (OR 3.66, 95% CI 1.9-9.68) and these genetic determinants can be transmitted by conjugation to broiler chicken microbiota strains. Our data revealed that poultry litter and beetles were critical points during poultry production and the presence of fosfomycin-resistant strains indicate the possibility of risks associated with the use of this antimicrobial during production. Furthermore, the genetic determinants encoding CTX-M and fosA3 enzymes can be transferred to E. coli strains from broiler chicken microbiota, thereby creating a risk to public health.

Molecular analysis of blaSHV, blaTEM, and blaCTX-M in extended-spectrum β-lactamase producing Enterobacteriaceae recovered from fecal specimens of animals

Colonization of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae as animal gut microbiota is a substantial global threat. This study aimed to determine the molecular characterization of blaSHV, blaTEM, and blaCTX-M variants in animals, as well as to evaluate the antimicrobial resistance conferred by these genes. We prospectively analyzed 1273 fecal specimens of farm and domestic animals for the isolation of enterobacteria that had the ESBL phenotype by using biochemical methods. The extracted genes were amplified by polymerase chain reaction and sequenced for the characterization of blaSHV, blaTEM, and blaCTX-M variants. The drug-resistance spectrum and hierarchical clusters were analyzed against 19 antibacterial agents. Out of 245 (19.2%) ESBL enterobacteria, 180 (75.5%) Escherichia coli and 34 (13.9%) Klebsiella pneumoniae were prevalent species. A total of 73.9% blaCTX-M, 26.1% blaTEM, and 14.2% blaSHV were found among the enterobacteria; however, their association with farm or domestic animals was not statistically significant. The distribution of bla gene variants showed the highest number of blaCTX-M-1 (133; 54.3%), followed by blaCTX-M-15 (28; 11.4%), blaTEM-52 (40; 16.3%), and blaSHV-12 (22; 9%). In addition, 84.5% of the enterobacteria had the integrons intI1. We observed ±100% enterobacteria resistant to cephalosporin, 7 (2.9%) to colistin (minimum inhibitory concentration breakpoint ≥4 μg/mL), 9 (3.7%) to piperacillin-tazobactam, 11 (4.5%) to imipenem, 14 (5.7%) to meropenem, and 18 (7.3%) to cefoperazone-sulbactam, without statistically significant association. Animal gut microbiota contain a considerable number of blaCTX-M, blaTEM, blaSHV, and integrons, which are a potential source of acquired extensive drug resistance in human strains and leaves fewer therapeutic substitutes.

Longitudinal monitoring of multidrug resistance in Escherichia coli on broiler chicken fattening farms in Shandong, China

The extensive use of antibiotics has, in recent years, caused antimicrobial resistance and multidrug resistance in Escherichia coli to gradually develop into a worldwide problem. These resistant E. coli could be transmitted to humans through animal products and animal feces in the environment, thereby creating a problem for bacterial treatment for humans and animals and resulting in a public health issue. Monitoring the resistance of E. coli throughout the broiler fattening period is therefore of great significance for both the poultry industry and public health. In this longitudinal study, samples were taken from 6 conventional broiler fattening farms in Shandong Province, China, at 3 different times within 1 fattening period. The overall isolation rate of E. coli was 53.04% (375/707). Antibiotic resistance was very common in the E. coli isolated from these farms, and differed for different antibiotics, with ampicillin having the highest rate (92.86%) and cefoxitin the lowest (10.12%). Multidrug resistance was as high as 91.07%. More importantly, both the resistance rate of E. coli to the different drugs and the detection rate of drug resistance genes increased over time. The mobile colistin resistance (mcr-1) gene was detected in 24.40% of the strains, and these strains often carried other drug resistance genes, such as those conferring aminoglycoside, β-lactamase, tetracycline, and sulfonamide resistance. Antimicrobial resistance and drug resistance genes in E. coli were least common in the early fattening stage. The individual detection rates of sul1, sul3, aacC4, aphA3, and mcr-1 were significantly lower (P < 0.05) for the early fattening stage than for the middle and late stages. The rational use of antibiotics, in conjunction with the improvement of the breeding environment during the entire broiler fattening cycle, will be helpful in the development of the poultry industry and the protection of public health.

Broiler Farms and Carcasses Are an Important Reservoir of Multi-Drug Resistant Escherichia coli in Ecuador

Antimicrobial resistance (AMR) is a major health threat for public and animal health in the twenty-first century. In Ecuador, antibiotics have been used by the poultry industry for decades resulting in the presence of multi-drug resistant (MDR) bacteria in the poultry meat production chain, with the consequent risk for public health. This study evaluated the prevalence of ESBL/AmpC and mcr genes in third-generation cephalosporin-resistant Escherichia coli (3GC-R E. coli) isolated from broiler farms (animal component), broiler carcasses (food component), and human enteritis (human component) in Quito-Ecuador. Samples were collected weekly from November 2017 to November 2018. For the animal, food, and human components, 133, 335, and 302 samples were analyzed, respectively. Profiles of antimicrobial resistance were analyzed by an automated microdilution system. Resistance genes were studied by PCR and Sanger sequencing. From all samples, 122 (91.7%), 258 (77%), and 146 (48.3%) samples were positive for 3GC-R E. coli in the animal, food, and human components, respectively. Most of the isolates (472/526, 89.7%) presented MDR phenotypes. The ESBL bla_CTX-M-55, bla_CTX-M-3, bla_CTX-M-15, bla_CTX-M-65, bla_CTX-M-27, and bla_CTX-M-14 were the most prevalent ESBL genes while bla_CMY-2 was the only AmpC detected gene. The mcr-1 gene was found in 20 (16.4%), 26 (10.1%), and 3 (2.1%) of isolates from animal, food, and human components, respectively. The implication of poultry products in the prevalence of ESBL/AmpC and mcr genes in 3GC-R must be considered in the surveillance of antimicrobial resistance.