Phenotypic characterization of extended-spectrum-beta-lactamase producing E. coli from healthy individuals, patients, sewage sludge, cattle, chickens and raw meat

Extended-Spectrum β-Lactamases (ESBL): Challenges and Opportunities

The rise of antimicrobial resistance, particularly from extended-spectrum β-lactamase producing Enterobacteriaceae (ESBL-E), poses a significant global health challenge as it frequently causes the failure of empirical antibiotic therapy, leading to morbidity and mortality. The E. coli- and K. pneumoniae-derived CTX-M genotype is one of the major types of ESBL. Mobile genetic elements (MGEs) are involved in spreading ESBL genes among the bacterial population. Due to the rapidly evolving nature of ESBL-E, there is a lack of specific standard examination methods. Carbapenem has been considered the drug of first choice against ESBL-E. However, carbapenem-sparing strategies and alternative treatment options are needed due to the emergence of carbapenem resistance. In South Asian countries, the irrational use of antibiotics might have played a significant role in aggravating the problem of ESBL-induced AMR. Superbugs showing resistance to last-resort antibiotics carbapenem and colistin have been reported in South Asian regions, indicating a future bleak picture if no urgent action is taken. To counteract the crisis, we need rapid diagnostic tools along with efficient treatment options. Detailed studies on ESBL and the implementation of the One Health approach including systematic surveillance across the public and animal health sectors are strongly recommended. This review provides an overview of the background, associated risk factors, transmission, and therapy of ESBL with a focus on the current situation and future threat in the developing countries of the South Asian region and beyond.

Antimicrobial Resistance in E. coli Isolated from Chicken Cecum Samples and Factors Contributing to Antimicrobial Resistance in Nepal

Microorganisms with antimicrobial resistance (AMR) are prevalent among humans and animals, and also found in the environment. Though organisms with AMR can spread to humans via food from animal sources, the burden of AMR in food-producing animals remains largely unknown. Thus, we assessed the resistance pattern among Escherichia coli isolated from chicken cecum samples and explored issues contributing to AMR in animals in the Dhulikhel Municipality of Nepal. We conducted a mixed-methods study, comprising a cross-sectional quantitative component, with collection of chicken cecal samples from slaughter houses/shops. In addition, a descriptive qualitative component was undertaken, with a focus group discussion and key informant interviews among stakeholders involved in animal husbandry. Of the 190 chicken cecum samples collected, 170 (89%) were subjected to culture and drug sensitivity testing, of which E. coli was isolated from 159 (94%) samples. Of the 159 isolates, 113 (71%) had resistance to ≥3 antimicrobial class. Resistance to tetracycline (86%) and ciprofloxacin (66%) were most prevalent. Overuse of antimicrobials, easy availability of antimicrobials, and lack of awareness among farmers about AMR were major issues contributing to AMR. The high prevalence of resistance among E. coli in chicken cecal samples calls for rational use of antimicrobials, educating farmers, and multi-sectoral coordination.

Extended-Spectrum ß-Lactamase-Producing Escherichia coli Among Humans, Beef Cattle, and Abattoir Environments in Nigeria

Introduction

Beef cattle, one of the food-producing animals, are linked to humans through a shared environment and the food chain as a major source of animal protein. Antimicrobial drugs are readily accessible for use in food animal production in Nigeria. Beef cattle and abattoir environments harbor pathogenic bacteria such as Escherichia coli (E. coli) which have developed resistance to antimicrobial agents used for prophylaxis or treatment. This study investigated the zoonotic transmission of extended-spectrum beta-lactamase-producing E. coli (ESBL-EC) among humans, beef cattle, and abattoir environments in Abuja and Lagos, Nigeria.

Materials and Methods

We conducted a cross-sectional study among abattoir workers, beef cattle, and abattoir environments in Abuja and Lagos. Stool, cecal, and environmental samples were collected from apparently healthy workers, slaughtered cattle, and abattoir environments from May to December 2020. Data were collected electronically using open data kit app installed on a mobile phone. Antimicrobial susceptibility patterns were determined using the Kirby–Bauer disk diffusion method against a panel of 16 antimicrobial agents. Phenotypic and genotypic characterizations of the isolates were conducted. Data were analyzed with descriptive statistics.

Results

From 21.7% (n = 97) of 448 samples, ESBL-EC were isolated and further characterized. Prevalence of ESBL-EC was highest in cattle (45.4%; n = 44), abattoir workers (41.2%; n = 40), and abattoir environment (13.4%; n = 13). Whole-genome sequencing of ESBL-EC showed dissemination of blaCTX-M-15 (90.7%; n = 88); blaCTX-M-14 (5.2%; n = 5); and blaCTX-M-55 (2.1%; n = 2) genes. The blaCTX-M-15 coexisted with blaCTX-M-14 and blaTEM-1 genes in 2.1% (n = 2) and 39.2% (n = 38) of the isolates, respectively. The presence of blaCTX-M-14 and blaCTX-M-15 genes was significantly associated with isolates originating from abattoir workers when compared with beef cattle isolates (p = 0.05; p < 0.01). The most prevalent sequence types (ST) were ST10 (n = 11), ST215 (n = 7), ST4684 (n = 7), and ST2178 (n = 6). ESBL-EC strain (ST205/B1) harbored mcr-1.1 and blaCTX-M15 and was isolated from a worker at Lagos abattoir. In 91 ESBL-EC isolates, 219 mobile genetic elements (MGEs) harbored resistance genes out of which β-lactam genes were carried on 64 different MGEs. Isolates showed equal distribution of insertion sequences and miniature inverted repeats although only a few composite transposons were detected (humans n = 12; cattle n = 9; environment n = 4). Two isolates of human and cattle origin (ST46/A) harboring ESBL genes and carried by MGEs were clonally related.

Conclusions

This is the first report of blaCTX-M-55 gene in humans and cattle in Nigeria. This study demonstrates the horizontal transfer of ESBL genes possibly by MGEs and buttresses the importance of genomic surveillance. Healthcare workers should be sensitized that people working closely with cattle or in abattoir environments are a high-risk group for fecal carriage of ESBL-EC when compared with the general population.

Genetic characterization of extended-spectrum β-Lactamase- and carbapenemase-producing Escherichia coli isolated from Egyptian hospitals and environments

Over the past decades, Escherichia coli (E. coli) have acquired extensive resistance to antibiotics; especially β- lactams. This study aimed to investigate the frequency of Extended-spectrum β-lactamase (ESBL) and carbapenemase producers among E. coli isolates and their correlation with serotypes, phylogenetic background, and pathogenicity associated islands. A total of 105 E. coli strains were isolated and subjected to antimicrobial susceptibility testing against β-lactam antibiotics. All isolates showed a high resistance profile. Resistant isolates were tested for ESBL and carbapenemase production. Fifty-three and 18 isolates were positive for ESBL and carbapenemase producers, respectively. ESBL and carbapenemase genes were detected by PCR. TEM gene was the most prevalent gene among all isolates followed by SHV and CTX-M15. In carbapenemase-producers, OXA-48 and IMP were the predominant genes. Enteropathogenic E. coli (EPEC) and Enterohemorrhagic E. coli (EHEC) were the major producers of ESBL and carbapenemase, respectively as indicated by serodiagnosis. They were further assessed for the presence of pathogenicity islands (PAIs) and phylogenetic background. The most predominant DEC PAI and ExPEC PAI were HPI and IICFT073. Most clinically ESBL-producers were group D and B2 while environmentally ones were group B1 and A. On contrary, clinically carbapenemase-producers belonged to group C and D. In conclusion, our study confirms the importance of phylogenetic group D, B2, and C origin for antibiotic resistance in E. coli. Ultimately, our findings support the fact that environmental isolates contribute to the local spread of E. coli pathogenicity in Egypt and these isolates maybe serve as reservoirs for transmission of resistance.

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.

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.

Extended-spectrum ß-lactamase-producing Escherichia coli among humans, chickens and poultry environments in Abuja, Nigeria

BACKGROUND

Globally, chicken is known to be a reservoir for the spread of antimicrobial resistance genes to humans. In Nigeria, antimicrobial drugs are readily accessible for use in poultry production, either for preventive or therapeutic purposes. Extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) are transmissible to humans because of their zoonotic potentials. People working very closely with chickens either on farms or markets are at greater risk. The aim of this study was to investigate the prevalence and zoonotic transmission of ESBL-EC among poultry-workers, chickens, and poultry environments in Abuja, Nigeria.

METHODS

We conducted a cross-sectional study among workers, chickens and poultry environment in selected farms/chicken markets in Abuja. Stool, faecal, and environmental samples were collected from apparently healthy workers, chickens, and farm/market environments from December 2018 to April 2019. Data were collected electronically using an open data kit (ODK) installed on a Smartphone. Antimicrobial resistance was determined using broth micro-dilution methods against a panel of 14 antimicrobial agents. We carried out the phenotypic and genotypic characterization of the isolates. Data were analyzed by computing frequencies, proportions and spearman's correlation (ρ).

RESULTS

Of 429 samples, 26.8% (n = 115) were positive for Escherichia coli (E. coli). Of the 115 E. coli isolates, 32.2% (n = 37) were confirmed ESBL producers by phenotypic characterization. Prevalence of ESBL-EC was highest among both poultry-workers (37.8%; n = 14) and chickens (37.8%; n = 14) followed by the environment (24.3%; n = 9). Both human and chicken isolates showed similar patterns of multidrug resistance to tested antimicrobials with a positive correlation (ρ = 0.91). Among ESBL producers, we observed the dissemination of blaCTX-M (10.8%; n = 4) genes. The coexistence of blaCTX-M-15 and blaTEM-1 genes was observed in 8.1% (n = 3) of the isolates, out of which (66.7%; n = 2) were chicken isolates from the farm, while a single human isolate was from the chicken market.

CONCLUSIONS

ESBL-EC isolates were prevalent amongst apparently healthy individuals, chickens and the poultry farm/market environment in Abuja. It is important to educate healthcare workers that people in proximity with poultry are a high-risk group for faecal carriage of ESBL-EC, hence pose a higher risk to the general population for the spread of antimicrobial resistance.

Prevalence and risk factors for multi-drug resistant Escherichia coli among poultry workers in the Federal Capital Territory, Abuja, Nigeria

Background

Antimicrobial resistance has emerged as a global health threat. Antimicrobial resistant Escherichia coli infections are associated with high morbidity and expenditure when compared with infections caused by susceptible strains. In Nigeria, antimicrobial drugs are readily available over-the-counter with potential for indiscriminate use by poultry farmers and eventual development of drug resistance. The objective of this study was to investigate prevalence and risk factors for multi-drug resistant E. coli among poultry workers (PW) in Abuja, Nigeria.

Materials and methods

A cross-sectional study was conducted among 122 randomly selected apparently healthy poultry workers (poultry-farmers/ sellers) in Municipal and Kuje Area Councils from December 2018 to April 2019. Data was collected on socio-demographics and exposure factors using a structured interviewer-administered questionnaire. E. coli was isolated and identified from stool samples of poultry workers. Antibiotic susceptibility testing was done using Kirby-Bauer disk diffusion method. Multidrug resistance (MDR) was defined as resistance to three or more classes of antimicrobials. Data was analyzed by computing proportions, prevalence odds-ratios (POR) and logistic regression at 5% significance level.

Results

Among PW, there were 121 males (99.2%). Mean age of the male workers was 30.6 ± 9.7years, 54.6% (n = 66) married, 57.9% (n = 70) had secondary education and 62.0% (n = 75) were farm-workers. Prevalence of E. coli was 39.7% (n = 48), highest among farm-workers (POR = 2.7, 95% Confidence Interval [CI] = 1.3–5.7; p = 0.01) compared to poultry-sellers. Of the 48 E. coli isolates, 16.7% (n = 8) were extended spectrum beta lactamase (ESBL) producers and 79.2% (n = 38) were MDR. We detected resistance against Tetracycline: (83.3%, n = 40), Sulfamethoxazole-Trimethoprim: (79.2%, n = 38), Ampicillin: (77.1%, n = 37), Streptomycin: (72.9%, n = 35), Nalidixic acid: (50%, n = 24), Gentamicin: (41.7%, n = 20), Chloramphenicol: (31.3%, n = 15), Cephalothin: (27.1%, n = 13), Nitrofurantoin: (10.4%, n = 5) and Imipenem: (6.3%, n = 3). Absence of lavatory (POR = 2.7, 95% CI = 1.1–6.7); existence of farm/market for >10years (POR = 2.5, 95% CI = 1.1–5.4) and PW’s history of diarrhea in last three months (POR = 2.8, CI = 1.2–6.3) were associated with MDR. Controlling for age, absence of lavatory (adjusted OR [aOR] = 4.31, 95% CI = 1.6–11.9); PW’s history of diarrhea in last three months (aOR = 3.3,95%CI = 1.3–8.5) and work exposure >10years (aOR = 0.3, 95%CI = 0.1–0.9) remained independent risk factors for MDR.

Conclusion

Prevalence of resistant E. coli was highest among farm-workers and associated with older farms/markets, occupational exposure of over 10 years and poor hygienic measures. The management of Municipal and Kuje Area Councils were recommended to provide lavatories for public use in farm-settlements/markets. The importance of hand-hygiene and responsible use of antimicrobials in poultry production was emphasized.

Assessment of extended-spectrum β-lactamase (ESBLs) - producing Escherichia coli from minced meat of cattle and swab samples and hygienic status of meat retailer shops in Jimma town, Southwest Ethiopia

BACKGROUND

The impact of animals sources of food as a possible reservoir for extended-spectrum β-lactamase (ESBL) - Producing E. coli, and the dissemination of such strains into the food production chain need to be assessed. This study was aimed to assess the presence and antimicrobial susceptibility patterns of ESBLs - producing E. coli isolates from minced meat and environmental swab samples at meat retailer shops of Jimma town, Southwest Ethiopia.

METHODOLOGY

A cross-sectional descriptive study was conducted from March to June, 2016. A total of 168 minced meat and swab samples were first enriched by buffered peptone water (BPW) for overnight and streaked onto MacConkey agar. Double disk synergy (DDS) method was used for detection of ESBL-producing strains. A disk of amoxicillin + clavulanic acid (20/10 μg) was placed in the center of Mueller-Hinton agar plate, and cefotaxime (30 μg) and ceftazidime (30 μg) were placed at a distance of 20 mm from the central disk. Checklist was used to assess hygienic status of butcher shops and practices meat handlers.

RESULTS

A total of 35 (20.80%) biochemically confirmed E. coli were obtained from 168 samples. Of these, 21 (23.9%) of them were detected from 88 minced meat and the other 14 (17.5%) from 80 swab samples taken from butcher's hand, knives, chopping board and protective clothing. From 35 E. coli isolates, 7(20%) of them were confirmed as ESBL- producers. Among ESBL- producing strains, 85.7% were resistant for cefotaxime and ceftriaxone and 71.4% for ceftazidime. Among non-ESBLs-producing strains only seven isolates were resistant to third generation cephalosporin. All E. coli isolates were resistant to ampicillin, penicillin and erythromycin, and susceptible to amikacin. Poor hygienic status of butcher shops and unhygienic practice of meat handlers were observed.

CONCLUSION

The detections of ESBLs- producing strains could be contributed for the increment of multi drug resistant isolates. This study also concluded that, unhygienic meat handling and processing practice can contribute for contaminations of meat. Thus, strategies should be planned and implemented to improve the knowledge and practice of butchers about handling and processing of meat.