Occurrence of Multi-Drug-Resistant Escherichia coli in Chickens, Humans, Rodents and Household Soil in Karatu, Northern Tanzania

Isolation and characterization of cefotaxime resistant Escherichia coli from household floors in rural Bangladesh

Antimicrobial resistance (AMR) is a rising health concern worldwide. As an indicator organism, E. coli, specifically extended-spectrum β-lactamase (ESBL) producing E. coli, can be used to detect AMR in the environment and estimate the risk of transmitting resistance among humans, animals and the environment. This study focused on detecting cefotaxime resistant E. coli in floor swab samples from 49 households in rural villages in Bangladesh. Following isolation of cefotaxime resistant E. coli, DNA extracted from isolates was subjected to molecular characterization for virulence and resistance genes, determination of resistance to multiple classes of antibiotics to define multidrug resistant (MDR) and extensively drug resistant (XDR) strains, and the biofilm forming capacity of the isolates. Among 49 households, floor swabs from 35 (71 %) households tested positive for cefotaxime resistant E. coli. Notably, all of the 91 representative isolates were ESBL producers, with the majority (84.6 %) containing the bla CTX-M gene, followed by the bla TEM and bla SHV genes detected in 22.0 % and 6.6 % of the isolates, respectively. All isolates were MDR, and one isolate was XDR. In terms of pathogenic strains, 8.8 % of the isolates were diarrheagenic and 5.5 % were extraintestinal pathogenic E. coli (ExPEC). At 25 °C, 45 % of the isolates formed strong biofilm, whereas 43 % and 12 % formed moderate and weak biofilm, respectively. On the other hand, at 37 °C, 1.1 %, 4.4 % and 93.4 % of the isolates were strong, moderate and weak biofilm formers, respectively, and 1.1 % showed no biofilm formation. The study emphasizes the importance of screening and characterizing cefotaxime resistant E. coli from household floors in a developing country setting to understand AMR exposure associated with floors.

Antibiotic susceptibility and genomic analysis of ciprofloxacin-resistant and ESBLs-producing Escherichia coli in vegetables and their irrigation water and growing soil

The rise of antibiotic resistance in Escherichia coli has become a major global public health concern. While there is extensive research on antibiotic-resistant E. coli from human and animal sources, studies on vegetables and their environments are limited. This study investigated the prevalence and characteristics of ciprofloxacin-resistant (CIPR) E. coli in 13 types of edible raw vegetables, along with their irrigation water and soil in Shaanxi, China. Of 349 samples collected (157 vegetables, 59 water, and 133 soil), a total of 48 positive samples were detected, with one CIPRE. coli strain isolated from each sample being selected for further analyses. A striking observation was its high prevalence in irrigation water at 44.1 %, markedly exceeding that in vegetables (12.0 %) and soil (4.5 %). The susceptibility of Forty-eight CIPRE. coli isolates was evaluated using the disc diffusion method for 18 different antibiotics, all these isolates were not only resistant to the tested fluoroquinolones antibiotics (levofloxacin, nalidixic acid), but also displayed a multi-drug resistance (MDR) pattern. Twenty-eight (58.3 %) of 48 CIPRE. coli isolates exhibited extended spectrum β-lactamases (ESBLs) (CIPR-ESBLs) producing phenotype. Subsequently, whole-genome sequencing was performed on these 28 isolates. We identified 12 serotypes and STs each, with O101: H9 (35.7 %, 10/28) and ST10 (21.4 %, 6/28) being the most common. Further classification placed these isolates into five phylogenetic groups: A (57.1 %, 16/28), B1 (32.1 %, 9/28), D (3.6 %, 1/28), B2 (3.6 %,1/28), and F (3.6 %,1/28). Notelly, Identical ST types, serotypes and phylogroups were found in certain CIPR-ESBLs-producing E. coli from both vegetables and adjacent irrigation water. Genomic analysis of the 28 CIPR-ESBLs-producing E. coli isolates unveiled 73 resistance genes, associated with 13 amino acid mutations in resistance-determining regions (QRDRs) and resistance to 12 types of antibiotics. Each isolate was confirmed to carry both ESBLs and fluoroquinolone resistance genes, with the Ser83Ala mutation in GyrA (96.4 %, 27/28) being the most prevalent. A detailed analysis of Mobile Genetic Elements (MGEs) revealed that IncFIB and IncFII plasmid subtypes were most prevalent in 60.7 % and 67.9 % of isolates, respectively, with 75 % containing over 10 insertion sequences (IS) each. Furthermore, we observed that certain ESBL and PMQR genes were located on plasmids or in proximity to insertion sequences. In conclusion, our research highlights the widespread presence of CIPRE. coli in irrigation water and thoroughly examines the genetic characteristics of CIPR-ESBLs-producing E. coli strains, underlining the need for ongoing monitoring and management to reduce multidrug-resistant bacteria in vegetables and their environment.

Investigation of 29 Antimicrobial Compounds in Soil Using Newly Developed UHPLC-MS/MS Method

While the prudent and reasonable use of veterinary antimicrobial agents in food-producing animals is necessary, researchers over the decades have shown that these antimicrobial agents can spread into the environment through livestock manure and wastewater. The analysis of the occurrence of antimicrobial compounds in soil samples is of a great importance to determine potential impacts on human and animal health and the environment. In this study, an affordable, rugged and simple analytical method has been developed for the determination of twenty-nine antimicrobial compounds from five different classes (tetracyclines, fluoro(quinolones), macrolides, sulfonamides and diaminopirimidines). Liquid-liquid extraction (LLE) with extract filtration combined with ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) was the best strategy for the simultaneous determination of all analytes. The developed method was validated according to the Commission Implementing Regulation (EU) 2021/808. The limit of detections (LODs) ranged from 0.5 to 2.0 µg/kg, while the limit of quantitation (LOQ) was established at 1.0 to 20.0 µg/kg. The developed method was successfully applied for the determination of antimicrobial residues in one hundred and eighteen soil samples obtained from four European countries (Austria, Czech Republic, Estonia and Portugal). Doxycycline in the concentration levels of 9.07 µg/kg-20.6 µg/kg was detected in eight of the analysed samples. Samples were collected from areas where natural fertilizers (swine or cow manure) were applied. Our method can be efficiently used to monitor anti-microbial compounds in soil samples.

A systematic review and meta-analysis on prevalence and antimicrobial resistance profile of Escherichia coli isolated from water in africa (2000-2021)

Water is essential for the survival of humans, animals and plants. Numerous research has been conducted on the prevalence and antibiotic resistance of Escherichia coli (E. coli) in water from various African countries, however, there is lack of comprehensive analysis of published literature. We conducted a systematic review and meta-analysis following the PRISMA guidelines where articles published in English language between January 2000 and March 2022 were searched from ScienceDirect, PubMed, Google Scholar, Scopus, African Journal Online (AJO), and Africa Index Medicus (AIM). Comprehensive Meta-Analysis (CMA) Ver 3.0 software was used to analyze the data. The pooled prevalence estimate (PPE) with 95% confidence interval was calculated using the random-effects model (CI). The overall PPE and antimicrobial resistance trends of E. coli isolated from water was screened from 4009 isolates which were isolated from 2586 samples. We extracted data from 17 studies including drinking water (n = 6), rivers (n = 5), wastewaters (n = 4) and wastewater/river (n = 1) which are all covering 27 countries in Africa with 3438 isolates. The PPE of E. coli in water was 71.7% (0.717; 95% CI: 0.562-0.833). The highest PPE antibiotic resistance was against penicillin followed by erythromycin, and ampicilin with resistance rates of 93.4%, 92.3%, and 69.4%, respectively. This systematic review provides critical evidence of E. coli consolidated prevalence and antibiotic resistance profiles, as well as regions where future studies and enhanced reporting could be beneficial in the African continent.

Determination of antimicrobial resistance patterns of Escherichia coli isolates from farm workers in broiler poultry production and assessment of antibiotic resistance awareness levels among poultry farmers in Lusaka, Zambia

The challenges posed by antibiotic-resistant pathogens have continued to increase worldwide, particularly in resource-limited countries. Human-livestock interactions are implicated in the complex AMR causal web. A cross-sectional study was conducted in four districts of Lusaka Province, Zambia to determine the antibiotic resistance patterns, ESBL production of E. coli isolated from stool samples of broiler poultry farm workers, and to assess poultry farmers' antibiotic resistance awareness. Sixty-six human stool samples were collected and processed for E. coli isolation, antibiotic resistance testing, and screened for ESBL production. In addition, 80 farmers were assessed for their level of awareness on antibiotic resistance. A total of 58 single E. coli isolates were obtained which showed high (87.9%) resistance to tetracycline, trimethoprim/sulfamethoxazole (48.3%), and ampicillin (46.8%); followed by nalidixic acid (19.0%), ciprofloxacin (12.1%), cefotaxime (8.6%) and chloramphenicol (5.2%). The prevalence of AMR E. coli was 67.2%, and 29.3% were MDR. Two (3.4%) isolates were identified to be ESBL producers, harboring the CTX-M gene. The study results also showed that broiler farmers were aware and knowledgeable of antibiotic resistance, although knowledge about its impact on human health was low. This study demonstrated the presence of resistant and ESBL producing E. coli among poultry farm workers.

Human Colonization with Antibiotic-Resistant Bacteria from Nonoccupational Exposure to Domesticated Animals in Low- and Middle-Income Countries: A Critical Review

Data on community-acquired antibiotic-resistant bacterial infections are particularly sparse in low- and middle-income countries (LMICs). Limited surveillance and oversight of antibiotic use in food-producing animals, inadequate access to safe drinking water, and insufficient sanitation and hygiene infrastructure in LMICs could exacerbate the risk of zoonotic antibiotic resistance transmission. This critical review compiles evidence of zoonotic exchange of antibiotic-resistant bacteria (ARB) or antibiotic resistance genes (ARGs) within households and backyard farms in LMICs, as well as assesses transmission mechanisms, risk factors, and environmental transmission pathways. Overall, substantial evidence exists for exchange of antibiotic resistance between domesticated animals and in-contact humans. Whole bacteria transmission and horizontal gene transfer between humans and animals were demonstrated within and between households and backyard farms. Further, we identified water, soil, and animal food products as environmental transmission pathways for exchange of ARB and ARGs between animals and humans, although directionality of transmission is poorly understood. Herein we propose study designs, methods, and topical considerations for priority incorporation into future One Health research to inform effective interventions and policies to disrupt zoonotic antibiotic resistance exchange in low-income communities.

Multi-Drug Resistant Pathogenic Escherichia coli Isolated from Wild Birds, Chicken, and the Environment in Malaysia

Transmission of pathogenic microorganisms in the last decades has been considered a significant health hazard and pathogenic E. coli, particularly antibiotic-resistant strains, have long been identified as a zoonotic problem. This study aimed to investigate multidrug resistant pathogenic E. coli isolates from wild birds, chickens, and environment in selected Orang Asli and Malay villages in Peninsular Malaysia. The bacteriological culture-based technique, disc diffusion method, and multiplex Polymerase Chain Reaction (mPCR) assay was used to determine the occurrence of pathogenic E. coli strains in the several samples in the study. E. coli isolates showed a variety of multi-drug resistant (MDR) antibiotypes and Enteropathogenic E. coli (EPEC) and Enteroinvasive E. coli (EIEC) were the most predominantly identified pathogenic E. coli strains. The findings of this study demonstrated the significance of animal reservoirs and the environment as sources of pathogenic E. coli, resistant bacteria, and resistance genes. Hence, there is a need for adoption of a practical surveillance approach on MDR pathogens to control foodborne contamination.

Determination of Sulphonamides and Tetracycline Residues in Liver Tissues of Broiler Chicken Sold in Kinondoni and Ilala Municipalities, Dar es Salaam, Tanzania

In Tanzania, the increased demand for animal-derived foods, particularly eggs, meat, and milk, has resulted in the intensification of farming systems with the use of antimicrobials, particularly sulphonamides and tetracyclines. According to the FAO/WHO Codex Alimentarius commission, concentrations of antimicrobial residues in food exceeding the acceptable daily intake (ADI) and maximum residual limit (MRL) pose a health risk to consumers. This cross-sectional study determined the concentrations of sulphonamide and tetracycline residues in the liver tissues of commercial broiler chicken sold in Dar es Salaam, Tanzania, to find out whether the amounts of residues were within the legally permitted and acceptable limits in food. We conveniently sampled eighty-four liver tissue samples from broiler chicken sold in two out of six large markets in Dar es Salaam. The amounts of tetracycline and sulphonamide residues were determined using an ELISA kit (Shenzhen Lvshiyuan Biotechnology Company, Shenzhen, China). The results showed that all 100% (n = 84) samples contained tetracycline residues and 21.4% (n = 18) samples contained sulphonamide residues, while 21.4% (n = 18) contained both sulphonamide and tetracycline residues. The concentrations of sulphonamide residues were within the maximum residual limit (MRL). However, 90.5% (n = 76) of the samples had tetracycline levels that exceeded the acceptable daily intake (ADI) range 0–3 µg/kg and 13.1% (n = 11) of the samples had tetracycline levels that exceeded the maximum residue limit of 300 µg/kg. The observed presence of antibiotic residues in the poultry tissues poses a health risk to consumers, and may lead to antimicrobial resistance micro-organisms, which may spread to humans and animals via the environment. Vigorous surveillance and observation of the withdrawal periods should be advocated to ensure that the food from animals is safe with regard to the residues of veterinary medicines.

Antimicrobial Resistance Pattern of Escherichia coli Isolates from Small Scale Dairy Cattle in Dar es Salaam, Tanzania

Simple Summary

Dearth of information on antimicrobial resistance (AMR) in small-scale dairy cattle in Dar es Salaam, the commercial city of Tanzania, prompted us to conduct this study. The objective was to determine the different levels of resistance phenotypical patterns among Escherichia coli (E. coli) isolates from rectal swabs of apparently healthy cattle. Antimicrobial resistance occurs when microorganisms develop the ability to tolerate antimicrobial concentrations to which they were initially susceptible. It is a phenomenon of global concern, which is on the rise due to antimicrobial use in food-producing animals. In dairy farms, cattle carry high levels of AMR Escherichia coli (E. coli), and may act as a potential reservoir. The study revealed that resistance to ampicillin, cefotaxime, tetracycline and trimethoprim/sulfamethoxazole was the most frequent. Resistance to nalidixic acid, ciprofloxacin, chloramphenicol, and gentamycin was also observed among the E. coli isolates, but with lower percentages. E. coli resistant to third generation cephalosporins was also detected. The results of the current study give an insight into the status of antimicrobial resistance and multidrug resistance in small-scale dairy cattle in Dar es Salaam, Tanzania. The findings call for further research, prudent antimicrobial use, and surveillance initiatives.

Abstract

In Tanzania, information on antimicrobial resistance in small-scale dairy cattle is scarce. This cross-sectional study was conducted to determine the different levels and pattern of antimicrobial resistance (AMR), in 121 Escherichia coli isolated from rectal swab of 201 apparently healthy small-scale dairy cattle in Dar es Salaam, Tanzania. Isolation and identification of E. coli were carried out using enrichment media, selective media, and biochemical tests. Antimicrobial susceptibility testing was carried out using the Kirby–Bauer disk diffusion method on Mueller-Hinton agar (Merck), according to the recommendations of Clinical and Laboratory Standards Institute (CLSI). Resistance was tested against ampicillin, gentamicin, chloramphenicol, trimethoprim-sulfamethoxazole, tetracycline, nalidixic acid, ciprofloxacin and cefotaxime. Resistance to almost all antimicrobial agents was observed. The agents to which resistance was demonstrated most frequently were ampicillin (96.7%), cefotaxime (95.0%), tetracycline (50.4%), trimethoprim-sulfamethoxazole (42.1%) and nalidixic acid (33.1%). In this case, 20 extended-spectrum beta-lactamases (ESBLs) producing E. coli were identified. 74.4% (90/121) of the isolates were Multidrug resistant (MDR), ranging from a combination of three to 8 different classes. The most frequently observed phenotypes were AMP-SXT-CTX with a prevalence of 12.4%, followed by the combination AMP-CTX with 10.7% and TE-AMP-CTX and NA + TE + AMP + CTX with 8.3% each. The high prevalence and wide range of AMR calls for prudent antimicrobial use.

Tetracycline-Resistant Genes in Escherichia coli from Clinical and Nonclinical Sources in Rivers State, Nigeria

Background

Monitoring the occurrence of tetracycline resistance and its determinants in both clinical and nonclinical settings is essential in understanding the role played by continuous usage of this drug in animal husbandry and the withdrawal of this drug from clinical practice. Limited information is available on this from our locale. This study, therefore, set out to explore the occurrence of specific tetracycline-resistant genes in Escherichia coli from clinical and nonclinical sources in Rivers State, Nigeria.

Methods

Two hundred clinical and nonclinical samples were analyzed for the presence of E. coli using standard phenotypic and genotypic tests. Susceptibility testing was carried out using the Kirby–Bauer disc diffusion method, and specific tetracycline-resistant genes (tetA, tetB, tetG, and tetM) were assayed.

Results

Results showed that stool samples had the highest occurrence of E. coli (39, 78%), and soil had the lowest (13, 26%). Tetracycline resistance was observed in 80.7% of total isolates. The tetA genes were the most commonly occurring (n = 80, 89.9%) detected in confirmed E. coli isolates, and tetG, the least commonly occurring (n = 16,18%) of isolates. The combined presence of tetA-tetM was the highest (n = 14, 15.7%), followed by tetA-tetB (n = 13, 14.8%).

Conclusion

The present study reports on the occurrence and distribution of four tetracycline-resistant determinants in E. coli from clinical and nonclinical sources in Rivers State, Nigeria. The high-level occurrence of the most commonly occurring tetracycline gene even in nonclinical isolates could be indicative of a potential reservoir of this resistance. And, this could limit the reintroduction of tetracycline even in combination therapy.

Molecular Epidemiology of Antibiotic Resistance Genes and Virulence Factors in Multidrug-Resistant Escherichia coli Isolated from Rodents, Humans, Chicken, and Household Soils in Karatu, Northern Tanzania

The interaction of rodents with humans and chicken in the household environment can facilitate transmission of multidrug-resistant (MDR) Escherichia coli (E. coli), causing infections that are difficult to treat. We investigated the presence of genes encoded for carbapenem, extended spectrum beta-lactamases (ESBL), tetracycline and quinolones resistance, and virulence among 50 MDR E. coli isolated from human (n = 14), chicken (n = 12), rodent (n = 10), and soil (n = 14) samples using multiplex polymerase chain reaction (PCR). Overall, the antimicrobial resistance genes (ARGs) detected were: blaTEM 23/50 (46%), blaCTX-M 13/50 (26%), tetA 23/50 (46%), tetB 7/50 (14%), qnrA 12/50 (24%), qnrB 4/50 (8%), blaOXA-48 6/50 (12%), and blaKPC 3/50 (6%), while blaIMP, blaVIM, and blaNDM-1 were not found. The virulence genes (VGs) found were: ompA 36/50 (72%), traT 13/50 (26%), east 9/50 (18%), bfp 5/50 (10%), eae 1/50 (2%), and stx-1 2/50 (4%), while hlyA and cnf genes were not detected. Resistance (blaTEM, blaCTX-M, blaSHV, tetA, tetB, and qnrA) and virulence (traT) genes were found in all sample sources while stx-1 and eae were only found in chicken and rodent isolates, respectively. Tetracycline resistance phenotypes correlated with genotypes tetA (r = 0.94), tetB (r = 0.90), blaKPC (r = 0.90; blaOXA-48 (r = 0.89), and qnrA (r = 0.96). ESBL resistance was correlated with genotypes blaKPC (r = 0.93), blaOXA-48 (r = 0.90), and qnrA (r = 0.96) resistance. Positive correlations were observed between resistance and virulence genes: qnrB and bfp (r = 0.63) also blaTEM, and traT (r = 0.51). Principal component analysis (PCA) indicated that tetA, tetB, blaTEM, blaCTX-M, qnrA, and qnrB genes contributed to tetracycline, cefotaxime, and quinolone resistance, respectively. While traT stx-1, bfp, ompA, east, and eae genes contributed to virulence of MDR E. coli isolates. The PCA ellipses show that isolates from rodents had more ARGs and virulence genes compared to those isolated from chicken, soil, and humans.

Molecular Detection of Integrons, Colistin and β-lactamase Resistant Genes in Salmonella enterica Serovars Enteritidis and Typhimurium Isolated from Chickens and Rats Inhabiting Poultry Farms

The rapid growth of multidrug-resistant Salmonella is a global public health concern. The aim of this study was to detect integrons, colistin and β-lactamase resistance genes in Salmonella enteritidis and typhimurium. A total of 63 isolates of S. enteritidis (n = 18) and S. typhimurium (n = 45) from fecal samples of layers and rats at chicken farms were screened for antibiotic resistant genes. Conventional PCR was performed for the detection of integrons (classes 1, 2, and 3), colistin (mcr-1-5) and β-lactamase (bla_CTX-M, bla_CTX-M-1, bla_CTX-M-2, bla_CTX-M-9, bla_CTX-M-15, bla_TEM, bla_SHV, and bla_OXA) resistant genes. Of these isolates, 77% and 27% of S. typhimurium and S. enteritidis harboured the mcr-4 encoded gene for colistin, respectively. The prevalence of class 1 integrons for S. typhimurium and S. enteritidis was 100% for each serovar, while for class 2 integrons of S. typhimurium and S. enteritidis it was 49% and 33% respectively, while class 3 integron genes was not detected. Our study also detected high levels of β-lactamase encoding genes (bla gene), namely bla_CTX-M, bla_CTX-M-1, bla_CTX-M-9 and bla_TEM from both S. typhimurium and S. enteritidis. This, to our knowledge, is the first report of mcr-4 resistance gene detection in Salmonella serovars in South Africa. This study also highlights the importance of controlling rats at poultry farms in order to reduce the risk of transmission of antibiotic resistance to chickens and eventually to humans.