Comparative genetic characterization of third-generation cephalosporin-resistant Escherichia coli from chicken meat produced by integrated broiler operations in South Korea

Current status of β-lactam antibiotic use and characterization of β-lactam-resistant Escherichia coli from commercial farms by integrated broiler chicken operations in Korea

β-Lactam antibiotics are one of the most clinical importance in human and veterinary medicine because they are used for both preventive and therapeutic purposes against several gram-positive, gram-negative, and anaerobic organisms. In this study, it was confirmed that β-lactams (81.1%) were found to be significantly prescribed the most among 74 farms in 5 integrated broiler operations, and single prescription (84.6%), 2-day (41.5%) or 3-day (40.0%) administration, and 15 to 22 d of age (67.7%) administration was significantly higher in the farms (P < 0.05). Among the E. coli isolated from 74 farms in 5 integrated broiler operations, β-lactam-resistant E. coli isolates were detected more frequently in fecal sample (94.6%) than in dust sample (60.8%) (P < 0.05). The prevalence of MDR in β-lactam-resistant isolates, ranging from 88.1 to 96.5%, was significantly higher than that in non-β-lactam-resistant isolates (P < 0.05), without significant differences among operations. Of 466 β-lactam-resistant isolates, 432 (92.7%) isolates harbored β-lactamase genes. The non-extended-spectrum β-lactamase (ESBL) gene blaTEM-1 (81.8%) showed the highest prevalence among isolates, followed by the non-ESBL gene blaTEM-135 (6.4%) (P < 0.05). Five ESBL genes, SHV-12, OXA-1, CTX-M-27, CTX-M-55, and CTX-M-65, were found in 0.9 to 6.0% of the isolates. The pAmpC gene blaCMY-2 was detected in 17 isolates (3.6%). These results suggest that feces and dust are important reservoirs of antimicrobial-resistant bacteria, highlighting the need to strengthen farm management regulations, such as cleaning, disinfection, and litter disposal and to reduce the use of antibiotics in broiler operations.

Molecular Detection of Tetracycline-Resistant Genes in Multi-Drug-Resistant Escherichia coli Isolated from Broiler Meat in Bangladesh

This study aimed to estimate the antimicrobial resistance (AMR) patterns and tetracycline-resistant gene profiles of Escherichia coli (E. coli) from broiler meat and livers sourced from live bird markets (LBMs) and supermarkets (SMs) in Chattogram, Bangladesh. In total, 405 samples were collected from SMs and LBMs, comprising muscle (n = 215) and liver (n = 190) samples. Disc diffusion tests were used to determine antimicrobial susceptibility profiles. PCR was used to identify E. coli and tetracycline-resistant genes. Over half (57%) of the chicken product samples were positive for E. coli. The AMR profiling of these isolates showed that the highest prevalence of resistance was against sulphamethoxazole-trimethoprim (89%), followed by tetracycline (87%), ampicillin (83%), and ciprofloxacin (61%). Among the antimicrobials listed by the World Health Organization as critically important, E. coli isolates were found to be resistant to cephalexin (37%), gentamicin (32%), and colistin sulfate (21%). A large proportion of E. coli demonstrated multi-drug resistance (MDR). Most (84%) of the tetracycline-resistant isolates encoded tetA. Of the remaining isolates, 0.5% encoded tetC, 6.0% encoded two genes, and 3.6% of isolates were tetD, which was newly identified by this study in Bangladesh. Broiler products in Bangladesh are frequently contaminated with multi-drug-resistant E. coli, with differential carriage of tetracycline genes. The prevalence of tetracycline resistance among E. coli indicates a concern for poultry health and welfare regarding the management of colibacillosis. It also indicates growing public health risks of AMR among broiler-associated pathogens, which can be transferred to humans via the food chain. Appropriate control measures should be developed and implemented, focused on the rational use of antimicrobials in poultry farming systems, to mitigate risk from this drug-resistant zoonotic pathogen from foods of animal origin and to protect public health.

Genetic characterization of third- or fourth-generation cephalosporin-resistant avian pathogenic Escherichia coli isolated from broilers

The third- or fourth-generation cephalosporins (3GC or 4 GC) are classified as "critically important antimicrobials for human medicine" by WHO, but resistance to these drugs is increasing rapidly in avian pathogenic E. coli (APEC). This study investigated the distribution and genetic characteristics of 3GC- or 4 GC-resistant APEC isolates from five major integrated broiler operations in Korea. The prevalence of 3GC- or 4GC-resistant APEC isolates in 1-week-old broilers was the highest in farms of operation C (53.3%); however, the highest prevalence of these isolates in 4-week-old broilers was the highest on the farms of operation A (60.0%), followed by operations E (50.0%) and C (35.7%). All 49 3GC- or 4GC-resistant APEC isolates had at least one β-lactamase-encoding gene. The most common β-lactamase-encoding genes was extended-spectrum β-lactamase gene, bla CTX-M-15, detected in 24 isolates (49.0%), followed by bla TEM-1 (32.7%). Sixteen isolates (32.7%) harbored class 1 integrons, and four isolates (8.2%) showed different gene cassette-arrangements. However, only 1 of 26 isolates harboring class 2 integrons carried a gene cassette. Furthermore, both CRISPR 1 and 2 arrays were detected in most isolates (36 isolates; 73.5%), followed by CRISPR 2 (18.4%) and CRISPR 1 (4.1%). Interestingly, CRISPR 2 was significantly more prevalent in multidrug resistant (MDR)-APEC isolates than in non-MDR APEC isolates, whereas CRISPR 3 and 4 were significantly more prevalent in non-MDR APEC isolates (each 11.1%; p < 0.05). None of the protospacers of CRISPR arrays were directly associated with antimicrobial resistance. Our findings indicate that the distribution and characteristics of 3GC or 4GC-resistant APEC isolates differed among the integrated broiler operations; moreover, improved management protocols are needed to control the horizontal transmission of 3GC or 4GC-resistant APEC isolates.

Multidrug-Resistant and Genetic Characterization of Extended-Spectrum Beta-Lactamase-Producing E. coli Recovered from Chickens and Humans in Egypt

Simple Summary

Feeding food chain animals with sub-therapeutic doses for prophylaxis or for growth-promoting purposes has led to the emergence of resistant bugs such as ESBL-E. coli. Infections caused by these superbugs are tremendously associated with treatment failures and high morbidity/mortality rates. Scarce information is currently available on the relation between the incidence of ESBL-E. coli in human and food chain animals in Egypt. The current study analyzed chicken and human fecal samples for isolation and characterization of ESBL-producing E. coli followed by sequencing the isolates. Significant similarities were detected between human and chicken isolates, indicating the possibility of zoonotic transmission. In conclusion, the study encouraged managing the use of antibiotics in veterinary field, to reduce the selection and spread of life-threating bugs to humans.

Abstract

Colonization of food chain animals such as chickens with extended-spectrum β-lactamases (ESBL) poses a major health threat to human. The current study aimed to determine the phenotypic and genotypic relationship between ESBL-producing E. coli from diseased human and chickens in Egypt. A total of 56 out of 120 chicken farms (46.7%) and 9 human samples (100%) were phenotypically and genotypically identified with at least one ESBL-phenotype/gene. Chicken isolates showed a high proportion of beta lactamase from CTX-M group 9 > TEM > PER families, followed by CTX-M group 1 > SHV > GES > OXA group10 > VEB > OXA group2 families, while human isolates only contained the CTX-M family. A high incidence of ESBL genes from the CTX-M family was recognized in both human and chicken isolates. Furthermore, nucleotide identity showed high similarity between chicken and human isolates. In conclusion, the current study traced phenotypes and genotypes of ESBL-producing E. coli from chickens and human samples in Egypt, reporting degrees of similarity that suggest potential zoonotic transmission. Our data highlighted the significant importance of chicken as a major food source not only in Egypt but all over the world in the spreading of ESBL-producing E. coli to human.

Comparison of antimicrobial resistance and molecular characterization of Escherichia coli isolates from layer breeder farms in Korea

In Korea, 4 big layer companies that possess one grandparent and 3 parent stocks are in charge of 100% of the layer chicken industry. In this study, we investigated the antimicrobial resistance of commensal 578 E. coli isolated from 20 flocks of 4-layer breeder farms (A, B, C, and D), moreover, compared the characteristics of their resistance and virulence genes. Isolates from farms B and D showed significantly higher resistance to the β-lactam antimicrobials (amoxicillin, ampicillin, and 1st-, 2nd-, and 3rd-generation cephalosporins). However, resistance to ciprofloxacin, nalidixic acid, and tetracycline was significantly higher in the isolates from farm A (P < 0.05). Interestingly, the isolates from farm C showed significantly lower resistance to most antimicrobials tested in this study. The isolates from farms B, C, and D showed the high multiple resistance to the 3 antimicrobial classes. Furthermore, the isolates from farm A showed the highest multiple resistance against the 5 classes. Among the 412 β-lactam-resistant isolates, 123 (29.9%) carried bla_TEM-1, but the distribution was significantly different among the farms from 17.5% to 51.4% (P < 0.05). Similarly, the most prevalent tetracycline resistance gene in the isolates from farms B, C, and D was tetA (50.0–77.0%); however, the isolates from farm A showed the highest prevalence in tetB (70.6%). The distribution of quinolone (qnrB, qnrD, and qnrS) and sulfonamide (su12)-resistant genes were also significantly different among the farms but that of chloramphenicol (catA1)- and aminoglycoside (aac [3]-II, and aac [6′]-Ib)-resistant genes possessed no significant difference among the farms. Moreover, the isolates from farm C showed significantly higher prevalence in virulence genes (iroN, ompT, hlyF, and iss) than the other 3 farms (P < 0.05). Furthermore, the phenotypic and genotypic characteristics of E. coli isolates were significantly different among the farms, and improved management protocols are required to control of horizontal and vertical transmission of avian disease, including the dissemination of resistant bacteria in breeder flocks.

Resistance Profiling and Molecular Characterization of Extended-Spectrum/Plasmid-Mediated AmpC β-Lactamase-Producing Escherichia coli Isolated from Healthy Broiler Chickens in South Korea

We aimed to identify and characterize extended-spectrum β-lactamase (ESBL)-and/or plasmid-mediated AmpC β-lactamase (pAmpC)-producing Escherichia coli isolated from healthy broiler chickens slaughtered for human consumption in Korea. A total of 332 E. coli isolates were identified from 339 cloacal swabs in 2019. More than 90% of the isolates were resistant to multiple antimicrobials. ESBL/pAmpC-production was noted in 14% (46/332) of the isolates. Six of the CTX-M-β-lactamase-producing isolates were found to co-harbor at least one plasmid-mediated quinolone resistance gene. We observed the co-existence of blaCMY-2 and mcr-1 genes in the same isolate for the first time in Korea. Phylogenetic analysis demonstrated that the majority of blaCMY-2-carrying isolates belonged to subgroup D. Conjugation confirmed the transferability of blaCTX-M and blaCMY-2 genes, as well as non-β-lactam resistance traits from 60.9% (28/46) of the ESBL/pAmpC-producing isolates to a recipient E. coli J53. The ISECP, IS903, and orf477 elements were detected in the upstream or downstream regions. The blaCTX-M and blaCMY-2 genes mainly belonged to the IncI1, IncHI2, and/or IncFII plasmids. Additionally, the majority of ESBL/pAmpC-producing isolates exhibited heterogeneous PFGE profiles. This study showed that healthy chickens act as reservoirs of ESBL/pAmpC-producing E. coli that can potentially be transmitted to humans.

The occurrence of CTX-M-producing E. coli in the broiler parent stock in Korea

A large number of antimicrobials are used for the treatment of bacterial infections, and the emergence of antimicrobial-resistant Escherichia coli (E. coli) in livestock and the transfer of resistant isolates to humans poses a serious potential risk to public health. In particular, broiler parent stock produce thousands of eggs for commercial broiler chickens and can transfer antimicrobial-resistant bacteria and drug-resistance genes to chicks. This study was conducted to investigate the prevalence and characteristics of third-generation cephalosporin-resistant and extended-spectrum β-lactamases (ESBL)-producing E. coli isolated from the broiler parent stock in Korea. Among 51 cefotaxime-resistant E. coli isolates, 45 (88.2%) isolates were identified as multidrug resistant and 21 isolates showed phenotypic and genotypic characteristics of CTX-M-producing E. coli. The CTX-M genes CTX-M-14, CTX-M-15, CTX-M-1, and CTX-M-1 were detected in 10, 7, 3, and 1 isolates, respectively. ISEcp1 or IS26 + ISEcp1 were identified upstream of all CTX-M-type genes, and orf477 and IS903 were detected downstream of 9 and 10 CTX-M-type genes, respectively. Thirteen (61.9%) of the 21 CTX-M-producing E. coli isolates harbored class 1 integrons with 4 different gene cassette arrangements. Among the plasmid replicons, CTX-M-1 was located on I1, F, and FIB; CTX-M-14 on F and FII; CTX-M-15 on FII, FIA, and FIB; and CTX-M-65 on FIB. This is the first study to investigate the presence and distribution of third-generation cephalosporin-resistant and CTX-M-producing E. coli isolated from the broiler parent stock level in Korea, and the results indicate that comprehensive surveillance and persistent monitoring systems in broiler parent stock farms are necessary to prevent the dissemination of resistant isolates.

Antimicrobial Resistance Pattern of Escherichia coli Isolated from Frozen Chicken Meat in Bangladesh

Escherichia coli is known as one of the most important foodborne pathogens in humans, and contaminated chicken meat is an important source of foodborne infection with this bacterium. The occurrence of extended-spectrum β-lactamase (ESBL)-producing E. coli (ESBL-Ec), in particular, in chicken meat is considered a global health problem. This study aimed to determine the magnitude of E. coli, with special emphasis on ESBL-Ec, along with their phenotypic antimicrobial resistance pattern in frozen chicken meat. The study also focused on the determination of ESBL-encoding genes in E. coli. A total of 113 frozen chicken meat samples were purchased from 40 outlets of nine branded supershops in five megacities in Bangladesh. Isolation and identification of E. coli were done based on cultural and biochemical properties, as well as PCR assay. The resistance pattern was determined by the disc diffusion method. ESBL-encoding genes were determined by multiplex PCR. The results showed that 76.1% of samples were positive for E. coli, of which 86% were ESBL producers. All the isolates were multidrug-resistant (MDR). Resistance to 9-11 and 12-13 antimicrobial classes was observed in 38.4% and 17.4% isolates, respectively, while only 11.6% were resistant to 3-5 classes. Possible extensive drug resistance (pXDR) was found in 2.3% of isolates. High single resistance was observed for oxytetracycline (93%) and amoxicillin (91.9%), followed by ampicillin (89.5%), trimethoprim-sulfamethoxazole, and pefloxacin (88.4%), and tetracycline (84.9%). Most importantly, 89.6% of isolates were resistant to carbapenems. All the isolates were positive for the blaTEM gene. However, the blaSHV and blaCTX-M-2 genes were identified in two ESBL-non producer isolates. None of the isolates carried the blaCTX-M-1 gene. This study provided evidence of the existence of MDR and pXDR ESBL-Ec in frozen chicken meat in Bangladesh, which may pose a risk to human health if the meat is not properly cooked or pickled raw only. This emphasizes the importance of the implementation of good slaughtering and processing practices by the processors.

Antimicrobial resistance monitoring of commensal Enterococcus faecalis in broiler breeders

Enterococcus faecalis (E. faecalis) has rapidly acquired resistance to multiple antimicrobials, and the antimicrobial resistance of E. faecalis from broiler breeders has been implicated in its vertical transmission to their offspring. The objective of this study was to investigate the antimicrobial resistance and genetic diversity of commensal E. faecalis isolated from the broiler breeder farms. Among a total of 229 E. faecalis isolates from 9 broiler breeder farms, the highest resistance rate was observed in tetracycline (78.2%), followed by doxycycline (58.1%) and erythromycin (43.7%), and the prevalence of antimicrobial resistance showed significant differences among the 9 broiler breeder farms (P < 0.05). The tetM gene (77.1%) and ermB gene (85.0%) were detected at the highest levels in 179 TE-and 100 E-resistant isolates, respectively. Twenty-four high-level gentamicin-resistant isolates carried aac(6″)Ie-aph(2″)-la gene, and 9 high-level ciprofloxacin-resistant isolates showed point mutations in both gyrA and parC genes. All high-level gentamicin-resistant or high-level ciprofloxacin-resistant isolates showed one of the two different virulence gene patterns, ace-asa1-efaA-gelE complex or ace-efaA-gelE complex. These results indicate that constant epidemiological monitoring at the breeder level is required to prevent the pyramidal transmission of antimicrobial-resistant E. faecalis.

Emergence of CMY-2-Producing Escherichia coli in Korean Layer Parent Stock

The use of antimicrobials in food animals is the major determinant for the propagation of resistant bacteria in the animal reservoir. Especially, parent stock (PS) produces thousands of eggs for commercial laying hens and can transfer a variety of viral and bacterial agents to chicks. The objective of this study was to investigate the presence and distribution of third-generation cephalosporin-resistant and extended-spectrum β-lactamase (ESBL)- and plasmid-mediated AmpC (pAmpC)-producing Escherichia coli in the PS level of the layer operation system in Korea. A total of 591 E. coli isolates were tested in this study and resistance to the first-generation cephalosporins ranged from 60.0% to 71.1%, whereas the resistance to the second- and third-generation cephalosporins ranged from 18.3% to 28.9% and from 8.3% to 14.5%, respectively. Of the 65 third-generation cephalosporin-resistant E. coli isolates, 51 (78.5%) showed multidrug resistance and 18 (27.7%) exhibited phenotypic and genotypic characteristics of ESBL/pAmpC-producing E. coli. With regard to ESBL/pAmpC gene prevalence, only the CMY-2 gene was identified in all 18 ESBL/pAmpC-producing E. coli and two isolates possessed both the CMY-2 and TEM-1 genes. Pulsed-field gel electrophoresis (PFGE) analysis of the 18 CMY-2-producing E. coli isolates revealed four PFGE patterns from the same PS farm and flock and accorded both CMY-2 genes and antimicrobial resistance pattern. To the best of our knowledge, this is the first study to investigate the prevalence and characteristics of third-generation cephalosporin-resistant and CMY-2-producing E. coli isolated at the layer PS level; our findings support the critical need for a comprehensive surveillance program to monitor the emergence and dissemination of third-generation cephalosporin resistance.