Coli Prevalence Research Articles

Prevalence of Uropathogenic E. Coli, Antimicrobial Susceptibility Profiles and Carriage of Extended-Spectrum Beta-Lactamases Genes at Mama Lucy Hospital, Kenya

Purpose: Urinary tract infection (UTI) is a common bacterial infection affecting millions worldwide. Escherichia coli (E. coli) is the most prevalent causative agent of UTIs. This study aimed to determine the prevalence, antimicrobial susceptibility profiles and carriage of ESβL resistance genes among uropathogenic E. coli recovered from adults at Mama Lucy Hospital. Methodology: A cross-sectional study was conducted. A purposive method was used to obtain 347 urine samples from patients who presented with symptoms suggestive of UTI and were cultured for E. coli using cysteine lactose electrolyte-deficient agar and eosin methylene blue agar. The collected urine samples were also subjected to dipstick analysis and microscopy. Questionnaires were used to collect sociodemographic data and possible risk factors for urinary tract infections. The recovered isolates were identified using conventional biochemical tests. Antimicrobial susceptibility profiles were determined using the Kirby diffusion disc method. The occurrence of ESβLs, including TEM, OXA, SHV, and CTX-M, was determined by polymerase chain reaction (PCR). Findings: The overall prevalence rate of UTIs was 23.7%, whereas the E. coli prevalence rate was 13.3%. The isolates presented high levels of resistance to trimethoprim-sulfamethoxazole (81.3%), amoxicillin-clavulanic acid (66.7%), ciprofloxacin (62.5%), tetracycline (60.4%), ceftriaxone (54.2%), and cefoxitin (54.2%), whereas they were more susceptible to meropenem (14.6%), chloramphenicol (12.5%), and nitrofurantoin (8.3%). A total of 25 of the 46 E. coli isolates were screened for ESβL genes. TEM was the most common gene21/25 (84%), SHV12/25 (48%), OXA 7/25 (28%), and CTX-M 18/25 (66.1%), which indicates a high frequency of β-lactamase gene production among UTIs causing E. coli. Unique Contribution to Theory, Practice and Policy: Based on these findings, current treatment guidelines should be revised to prevent increasing antimicrobial resistance through continuous surveillance, screening for extended-spectrum beta-lactamase genes, routine culture and antibiotic sensitivity testing. Additionally, the prevalence of UTIs should be continuously monitored to monitor trends that form a basis for preventive and treatment guidelines, such as policy development and prudent use of antibiotics, to reduce the increasing UTI burden in the population.

Prevalence and factors associated with multidrug resistant Escherichia coli carriage on chicken farms in west Nile region in Uganda: A cross-sectional survey.

Infections with multi-drug-resistant (MDR) pathogens in food-animals threaten public health and food security. However, the epidemiology and factors associated with MDR Escherichia coli (MDR E. coli) on Ugandan farms are not well known. This study investigated the prevalence, resistance patterns and factors associated with MDR E. coli carriage on chicken farms. Escherichia coli was isolated from each of the 158 chicken farms sampled. The disc diffusion method for susceptibility testing was performed. Clinical breakpoints were interpreted according to Clinical and Laboratory Standards Institute guidelines. MDR was defined as resistance to three or more classes of antibiotics. MDR E. coli prevalence on chicken farms was 62.7% (95% CI: 55.0-70.3). High resistance was observed against ampicillin 79.8% (95% CI: 72.7-85.4), tetracycline 72.8% (95% CI: 65.2-79.2), cotrimoxazole 55.7% (95% CI: 47.8-63.3), and ciprofloxacin 38% (95% CI: 30.7-45.9). Male farm managers (Adjusted prevalence ratio [APR] = 0.72, CI: 0.55-0.93), attainence of at least secondary education (APR = 0.64, CI: 0.46-0.88) and administration of recommended antibiotic doses (APR = 0.76, CI: 0.59-0.96) posed a lower risk of MDR E. coli carriage while farms without footbaths posed a heighten risk (APR = 1.48, CI: 1.16-1.88). MDR E. coli carriage was highly prevalent on chicken farms in Uganda. This study underscores the urgent need for antimicrobial stewardship and improved infection prevention strategies on chicken farms.

Distribution and Antimicrobial Susceptibility Profile of Extended Spectrum Beta-Lactamase Producing-Escherichia coli from Ruminants in Maiduguri, Nigeria: Public Health Implications

Extended spectrum beta-lactamase (ESBL) producing Escherichia coli (E. coli) is resistant to many antibiotics, including cephalosporins and penicillin. The emergence of ESBL-E. coli poses a threat to the entire animal and human community, not just individuals with direct exposure to ruminants but also to the environment. The study evaluated the isolation rate and antimicrobial susceptibility profile of ESBL-producing E. coli from 128 ruminants in the University of Maiduguri campus. E. coli was isolated from 32 (25%) of the rectal swabs collected from cattle, goats, and sheep. ESBL-producing E. coli was more common in young animals 8(30.8%) than in adult animals 12 (11.8%). More than 80% of the isolates were resistant to all of the beta-lactam antibiotics used in the study. The study suggests that the high prevalence of ESBL-producing E. coli in ruminants may be associated with the unregulated use of beta-lactam antibiotics in veterinary practice and animal husbandry. We recommend public health awareness about the dangers of antimicrobial resistance. Also, continued monitoring of BL-E. coli prevalence in both animals and humans is crucial to track trends and guide interventions. Promoting the judicious use of antibiotics in both human and veterinary medicine is essential to reduce selective pressure for resistance development. Improved hygiene practices at farms, slaughterhouses, and food processing facilities can minimize contamination and human exposure.

268 Assessment of antimicrobial exposure on generic Escherichia coli and Enterococcus spp. concentration, prevalence, and resistance to antimicrobials in beef cattle raised with or without antimicrobials

Abstract To investigate the effects of antimicrobial exposure, Angus steers [n = 288; initial body weight (BW) = 314 and 300 kg) were sorted into 1 of 2 treatments over 2 consecutive years: steers raised without antimicrobials (NAT) and conventionally raised steers exposed to antimicrobials (CONV). Pens within treatment were adjacent and separated via empty pens from the other treatment. Before cattle arrival, pens were renovated, and soil was replaced from an area not subjected to livestock production. Monensin and tylosin were included in CONV steer diets targeting 250 and 85 mg/steer daily, respectively. On d 123, CONV steers received a metaphylactic antimicrobial; NAT steers received a sterile saline injection. From d 0 to 168, diet and rectal fecal samples were collected longitudinally at 5 timepoints to determine E. coli and Enterococcus spp. concentration, prevalence, and resistance patterns. The MIXED procedure of SAS was used with fixed effects of treatment, day, and treatment × day interaction, and random effect of pen nested within a treatment × year interaction. Feed E. coli and Enterococcus spp. concentrations were greater in NAT diets than CONV diets (P < 0.01). Erythromycin (8ERYR; 128ERYR), tetracycline (TETR), trimethoprim-sulfamethoxazole (COTR), and cefotaxime (CTXR) resistant E. coli concentrations and prevalence were greater in NAT diets than CONV diets (P < 0.02). Fecal E. coli concentrations tended to be greater in NAT steers than CON steers (P = 0.07). A treatment × day tendency was detected for 8ERYRE. coli concentrations (P = 0.06), with NAT steers tending to have greater concentrations on d 64 and 130. Conversely, CONV steers had greater 128ERYRE. coli concentrations on d 130 and 168 than NAT steers (P < 0.01). Fecal TETRE. coli concentrations were greater in CONV steers than NAT steers (P = 0.03). Fecal COTR and CTXRE. coli prevalence had a treatment × day interaction (P < 0.01), with CONV steers having greater prevalence at the beginning of the finishing phase (d 0). Conversely, NAT steers had greater COTR (d 123 and 130) and CTXR (d 130 and 168) E. coli prevalence towards the end of the finishing phase than CONV steers. Fecal Enterococcus spp. concentrations did not differ between treatments (P = 0.11). A treatment × day interaction was detected for 8ERYR and 128ERYREnterococcus spp. concentrations (P < 0.05), with CONV steers having greater concentrations on d 64, 130, and 168 than NAT steers. Overall, these data suggest that antimicrobial exposure does not inherently increase E. coli and Enterococcus spp. concentrations. Treatment differences observed for ERYREnterococcus spp. concentrations are likely a result of tylosin exposure whereas differences in 128ERYR and TETRE. coli concentrations are likely an effect of metaphylactic administration. USDA is an equal opportunity employer.

ESBL-producing Escherichia coli prevalence and sharing across seabirds of central Chile

Antimicrobial resistance (AMR) is a major global public threat, now largely reported in natural environments. Seabirds are carriers of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli), but different foraging and breeding behaviour could impact ESBL-E. coli circulation. We compared the prevalence and genetic determinants of ESBL-E. coli from resident Kelp gulls (Larus dominicanus, Ld), migratory Franklin's gulls (Larus pipixcan, Lp), and endemic Peruvian pelicans (Pelecanus thagus, Pt) from the Humboldt Current Ecosystem (HCE) of central Chile. From 2020 to 2022, we collected 699 fresh faecal samples (Ld = 449, Lp = 116, Pt = 134), and isolated 271 ESBL-E. coli (39 %). Whole-genome-sequencing (WGS) was performed on 85 E. coli selected isolates to identify their Sequence Type (ST), AMR genes, virulence genes, mobile genetic elements (MGE), and to assess potential interspecies transmission. ESBL-genes were detected in the remaining ESBL-E. coli isolates by PCR. ESBL-E. coli prevalence in Ld (46 % [CI: 42–51 %]) and Pt (34 % [CI: 27–43 %]) was higher than in Lp (15 % [CI: 9–22 %]). WGS revealed 41 ESBL-E. coli STs including pandemic clones ST10, ST58, ST131 and ST410. The blaCTX-M-1 and blaCTX-M-15 genes were the most prevalent among ESBL genes, and were mostly associated with MGE IncI1-I(Alpha) and ISEc9. We also report the pAmpC blaCMY-2 gene associated to MGE Inc1-I(Alpha) and IS640 in two E. coli from a Ld and a Lp. Eight ESBL-E. coli of the same ST were shared by at least two seabird species, including ST10 (Ld and Pt); ST88, ST410 and ST617 (Pt and Lp); ST38, ST58, ST131, and SST1722 (three species). Single nucleotide polymorphism (SNP) phylogenetic analyses of ST38, ST617 and ST1722 showed a low difference of SNPs between STs found in different seabird species, suggesting ESBL-E. coli clonal exchanges. Our results highlight ESBL-E. coli dissemination across seabirds of the HCE, including species that unusually forage on human waste like pelicans.

Implementation of the WHO Tricycle protocol for surveillance of extended-spectrum β-lactamase producing Escherichia coli in humans, chickens, and the environment in Madagascar: a prospective genomic epidemiology study

Antimicrobial resistance (AMR) is a major public health threat, affecting not only people but also animals and the environment. The One Health dimension of AMR is well known; however, data are lacking on the circulation of resistance-conferring genes, particularly in low-income countries. In 2017, WHO proposed a protocol called Tricycle, focusing on extended-spectrum β-lactamase (ESBL)-Escherichia coli surveillance in the three sectors (humans, animals, and the environment). We implemented Tricycle in Madagascar to assess ESBL-E coli prevalence and describe intrasector and intersector circulation of ESBL-E coli and plasmids. In this prospective study, we collected blood culture data from hospitalised patients with a suspected bloodstream infection processed from May 1, 2018, to April 30, 2019, and rectal swabs from healthy pregnant women from July 30, 2018, to April 27, 2019, both from three hospitals in Antananarivo, Madagascar; and caeca from farm chickens and surface waters from the Ikopa river, wastewater, and slaughterhouse effluents in the Antananarivo area, Madagascar, from April 9, 2018, to April 30, 2019. All samples were tested for ESBL-E coli. The genomes of all isolates were sequenced using a short-read method on NextSeq 500 and NovaSeq 6000 platforms (Illumina, San Diego, CA, USA) and those carrying plasmid replicons using an additional long-read method on a MinION platform (Oxford Nanopore Technologies, Oxford, UK). We characterised genomes of isolated strains (sequence type, resistance and virulence gene content, and plasmid replicons). We then compared isolates using the variant calling method (single-nucleotide polymorphism). Data from 1056 blood cultures were collected and 289 pregnant women, 246 chickens, and 28 surface waters were sampled. Of the blood cultures, 18 contained E coli, of which seven (39%) were ESBL. ESBL-E coli was present in samples from 86 (30%) of 289 pregnant women, 140 (57%) of 246 chickens, and 28 (100%) of 28 surface water samples. The wet season (November to April) was associated with higher rates of carriage in humans (odds ratio 3·08[1·81-5·27]) and chickens (2·79 [1·65-4·81]). Sequencing of 277 non-duplicated isolates (82 from pregnant women, 118from chickens, and 77 from environmental samples) showed high genetic diversity (90 sequence types identified) with sector-specific genomic features. Single nucleotide polymorphism (SNP) analysis revealed that 169(61%) of 277 isolates grouped into 44 clusters (two or more isolates) of closely related isolates (<40 SNPs), of which 24 clusters contained isolates from two sectors and five contained isolates from all three sectors. ESBL genes were all blaCTX-M variants (215 [78%] of 277 being blaCTX-M-15) and were located on a plasmid in 113 (41%) of 277isolates. These ESBL-carrying plasmids were mainly IncF (63 [55%] of 114; one strain carried two plasmids) and IncY (42 [37%] of 114). The F31/36:A4:B1 (n=13) and F-:A-:B53 (n=8) pMLST subtypes, and the IncY plasmids, which were all highly conserved, were observed in isolates of differing genetic backgrounds from all sectors and were transferable invitro by conjugation. Despite sector-specific population structures, both ESBL-E coli strains and plasmids are circulating among humans, chickens, and the environment in Antananarivo, Madagascar. The Tricycle protocol can be implemented in a low-income country and represents a powerful tool for investigating dissemination of AMR from a One Health perspective. Fondation Mérieux and INSERM, Université Paris Cité.

Characteristics of antimicrobial resistance in Escherichia coli isolated from retail meat products in North Carolina.

Escherichia coli is commonly used as an indicator for antimicrobial resistance (AMR) in food, animal, environment, and human surveillance systems. Our study aimed to characterize AMR in E. coli isolated from retail meat purchased from grocery stores in North Carolina, USA as part of the National Antimicrobial Resistance Monitoring System (NARMS). Retail chicken (breast, n = 96; giblets, n = 24), turkey (n = 96), and pork (n = 96) products were purchased monthly from different counties in North Carolina during 2022. Label claims on packages regarding antibiotic use were recorded at collection. E. coli was isolated from meat samples using culture-based methods and isolates were characterized for antimicrobial resistance using whole genome sequencing. Multi-locus sequence typing, phylogroups, and a single nucleotide polymorphism (SNP)-based maximum-likelihood phylogenic tree was generated. Data were analyzed statistically to determine differences between antibiotic use claims and meat type. Of 312 retail meat samples, 138 (44.2%) were positive for E. coli, with turkey (78/138; 56.5%) demonstrating the highest prevalence. Prevalence was lower in chicken (41/138; 29.7%) and pork (19/138;13.8%). Quality sequence data was available from 84.8% (117/138) of the E. coli isolates, which included 72 (61.5%) from turkey, 27 (23.1%) from chicken breast, and 18 (15.4%) from pork. Genes associated with AMR were detected in 77.8% (91/117) of the isolates and 35.9% (42/117) were defined as multidrug resistant (MDR: being resistant to ≥3 distinct classes of antimicrobials). Commonly observed AMR genes included tetB (35%), tetA (24.8%), aph(3'')-lb (24.8%), and blaTEM-1 (20.5%), the majority of which originated from turkey isolates. Antibiotics use claims had no statistical effect on MDR E. coli isolates from the different meat types (X2 = 2.21, p = 0.33). MDR was observed in isolates from meat products with labels indicating "no claims" (n = 29; 69%), "no antibiotics ever" (n = 9; 21.4%), and "organic" (n = 4; 9.5%). Thirty-four different replicon types were observed. AMR genes were carried on plasmids in 17 E. coli isolates, of which 15 (88.2%) were from turkey and two (11.8%) from chicken. Known sequence types (STs) were described for 81 E. coli isolates, with ST117 (8.5%), ST297 (5.1%), and ST58 (3.4%) being the most prevalent across retail meat types. The most prevalent phylogroups were B1 (29.1%) and A (28.2%). Five clonal patterns were detected among isolates. E. coli prevalence and the presence of AMR and MDR were highest in turkey retail meat. The lack of an association between MDR E. coli in retail meat and antibiotic use claim, including those with no indication of antimicrobial use, suggests that additional research is required to understand the origin of resistance. The presence of ST117, an emerging human pathogen, warrants further surveillance. The isolates were distinctly diverse suggesting an instability in population dynamics.

Assessment of Salmonella Species and Escherichia Coli Prevalence, as well as Antimicrobial Profiles, in Sliced Pineapple Vended within Abakaliki Metropolis

The prevalent practice of vending sliced pineapple and various fruits on the streets of Nigeria due to cost constraints among buyers has raised concerns regarding potential contaminations and subsequent health risks to consumers. This study procured sixty samples of sliced, ready-to-eat pineapple from street vendors in Abakaliki Metropolis, analyzing them for Salmonella and E. coli contamination using microbiological and biochemical techniques. The isolates underwent antibiotic sensitivity screening via the disc diffusion method. The findings revealed a 20% prevalence of Salmonella species and a striking 70% prevalence of Escherichia coli in the sliced pineapple fruits. Further investigation into antibiotic susceptibility exhibited a concerning pattern of high multidrug resistance among the isolated organisms. Salmonella species showcased resistance percentages ranging from 50% to 100% against ceftriaxone, nitrofurantoin, meropenem, pefloxacin, chloramphenicol, ofloxacin, and amoxicillin. In comparison, Escherichia coli exhibited resistance values varying between 28.6% and 100% against the same antibiotics. This study emphasizes that the prevalent practice of slicing and vending fruits on the streets significantly contributes to the dissemination of multi-drug resistant pathogens. Urgent intervention and discouragement of this practice by pertinent authorities are imperative to mitigate the escalating health risks associated with such contaminated fruit vending practices. Keywords: Street vended fruits, sliced pineapple fruits, fruit contamination, multi-drug resistance, Samonella species, E. coli.

Occurrence and antimicrobial susceptibility patterns of Escherichia coli and Escherichia coli O157 isolated from cow milk and milk products, Ethiopia

Escherichia coli is a major foodborne pathogen worldwide. This study was conducted to assess the prevalence, risk factors, and antimicrobial susceptibility of E. coli and E. coli O157 in milk and milk products and hygienic practices in West Shoa, Oromia, Ethiopia. Five hundred fifty-six milk samples comprising 421 udder milk, 57 bulk tank milk, and 78 milk products were investigated. Moreover, a questionnaire was administered to 145 participants to assess hygienic practices. A standard microbiological procedure was used to detect E. coli and E. coli O157. The Kirby Bauer disc diffusion method was used to test the antimicrobial susceptibility of the isolates. Petri film plates were used to enumerate the coliform in raw bulk tank milk. Farm and animal-level E coli prevalence were estimated and association with risk factors was assessed. Escherichia coli was detected in 33.8% (95% confidence interval (CI) 29.9–37.9%) of the samples, of which only one isolate (0.2%) was E. coli O157. Escherichia coli contamination was higher in bulk tank samples (47.4%; 95% CI 34.0–61.0%) than in udder milk (34.7%; CI 30.1–39.4%), cottage cheese (27.0%; 95% CI 14.6–43.9%), and yoghurt 10.5% (95% CI 2.9–24.8%). For the animal-level E. coli contamination, only the study area was identified as a risk factor. Risk factors such as types of milk containers, udder washing practices, hygiene, and management systems were associated with both farm-level and milk products E. coli contamination. Most (59.0%) of the farmers practice udder washing only before milking and the remaining did not practice udder washing at all. The mean coliform count in raw bulk tank milk was higher than the international standard (4.09 log10 CFU/ml). All the 42 E. coli isolates tested were multidrug resistant. The occurrence of E. coli is high, while that of E. coli O157 is too low. The milk-handling practices are poor in the study areas. The high prevalence of E. coli, as well as the high coliform count and higher multi-drug resistance may pose risk to public health and food safety. Therefore, proper hygienic practices throughout the milk chain as well as rational drug use are advised.

Dynamics of Extended-spectrum Beta-lactamase–producing, Third-generation Cephalosporin-resistant and Tetracycline-resistant Escherichia coli in Feedlot Cattle With or Without Tylosin Administration

The impact of in-feed use of tylosin in feedlot cattle on Gram-negative foodborne bacteria is unknown. We evaluated the effect of continuous in-feed tylosin use on the concentration and prevalence of tetracycline-resistant (TETr)-, third-generation cephalosporin-resistant (3GCr)-, and extended-spectrum β-lactamase–producing (ESBLs) E. coli in feedlot cattle. A cohort of weaned calves (10 animals/group) were randomized to receive a feed ration with or without tylosin. Fecal samples, regularly collected over the entire feeding period, and pen surface and feed samples, collected at the end of the feeding period, were cultured on selective media. Enumeration and binary outcomes were analyzed by mixed effects linear regression or logistic regression, respectively, using treatment and days on feed as fixed factors, and animal ID as a random variable. Tylosin supplementation did not affect the fecal concentrations of TETrE. coli or fecal prevalence of 3GCrE. coli. However, cattle in the tylosin group were 1.5 times more likely (Odds ratio = 1.5: 95% confidence interval: 1.1–2.0) to harbor ESBLs E. coli than the control cattle. Regardless of tylosin treatment, fecal concentrations of TETrE. coli and the prevalence of 3GCr- and ESBLs-E. coli increased over time. Tylosin-supplemented feed did not affect the prevalence of TETrE. coli; 3GCr and ESBLs-E. coli were not detected from the feed samples. Most of the 3GCr- and ESBLs-E. coli isolates carried the blaCTX-M-15 gene, widely detected among ESBLs-E. coli human isolates. In summary, although in-feed tylosin use in feedlot cattle did not select for TETr- and 3GCr-E. coli, it increased the likelihood of detecting ESBL-producing E. coli. Furthermore, the study indicated that the feedlot production setting gradually increases the levels of E. coli resistant to the critically and/or important antibiotics for public health, indicating an increased risk of their dissemination beyond the feedlot environment.

Isolation, Identification and Characterization of Poultry Associated Bacterial Pathogens

In order to meet consumer demand, the global poultry business is constantly expanding; hence it is crucial to ensure the bio-safety of the poultry farms. In poultry farms, the main sources of bacterial development, increased antibiotic resistance, and environmental dispersion may be poultry feed, litter, and water. The focus of this research is on the identification and characterization of bacterial pathogens found in commercial poultry farms, drinking water samples, feed samples, and litter samples. The 100 samples were gathered from chicken farms in different districts of Tamil Nadu and transported to the lab for additional examination. Serial dilution was used to analyse the samples, which were then examined for colony morphology, microscopic features, and the biochemical traits of the bacteria Escherichia coli, Pseudomonas spp., Proteus spp., Salmonella spp., Shigella spp., Bacillus spp., staphylococcus spp., and Streptococcus spp. The disc diffusion method was used to evaluate bacterial isolates against various antibiotic drugs. The results of this research indicate that the main sources of bacterial infections are chicken feed, drinking water samples and poultry litter. Salmonella, Pseudomonas, and E. coli prevalence rates were 94%, 80%, and 75%, respectively. Chloramphenicol and Tetracycline both had overall antibiotic resistance rates of 65.65% and 59.23%, respectively. Public health is alarmingly threatened by the presence of these harmful microorganisms in poultry habitats. To reduce the chance of transmitting the bacterial diseases linked to poultry, strict hygiene procedures must be put in place. The use of antibiotics in chicken for promoting growth and illness prevention needs to be properly regulated and executed.

Triplex qPCR assay for Campylobacter jejuni and Campylobacter coli monitoring in wastewater

Campylobacter spp. is one of the most frequent pathogens of bacterial gastroenteritis recorded worldwide. Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli) are the two major disease-associated species, accounting for >95 % of infections, and thus have been selected for disease surveillance. Monitoring temporal variations in pathogen concentration and diversity excreted from community wastewater allows the early detection of outbreaks. Multiplex real-time/quantitative PCR (qPCR) enables multi-target quantification of pathogens in various types of samples including wastewater. Also, an internal amplification control (IAC) is required for each sample when adopting PCR-based methods for pathogen detection and quantification in wastewater to exclude the inhibition of the wastewater matrix. To achieve reliable quantification of C. jejuni and C. coli towards wastewater samples, this study developed and optimized a triplex qPCR assay by combining three qPCR primer-probe sets targeting Campylobacter jejuni subsp. jejuni, Campylobacter coli, and Campylobacter sputorum biovar sputorum (C. sputorum), respectively. This triplex qPCR assay not only can directly and simultaneously detect the concentration of C. jejuni and C. coli in wastewater but also can achieve the PCR inhibition control using C. sputorum primer-probe set. This is the first developed triplex qPCR assay with IAC for C. jejuni and C. coli, to be used in the wastewater-based epidemiology (WBE) applications. The optimized triplex qPCR assay enables the detection limit of the assay (ALOD100%) and wastewater (PLOD80%) as 10 gene copy/μL and 2 log10 cells/mL (2 gene copies/μL of extracted DNA), respectively. The application of this triplex qPCR to 52 real raw wastewater samples from 13 wastewater treatment plants demonstrated its potential as a high-throughput and economically viable tool for the long-term monitoring of C. jejuni and C. coli prevalence in communities and the surrounding environments. This study provided an accessible methodology and a solid foundation for WBE-based monitoring of Campylobacter spp. relevant diseases and paved the road for future WBE back-estimation of C. jejuni and C. coli prevalence.

Biosecurity and Hygiene Procedures in Pig Farms: Effects of a Tailor-Made Approach as Monitored by Environmental Samples.

In livestock, the importance of hygiene management is gaining importance within the context of biosecurity. The aim of this study was to monitor the implementation of biosecurity and hygiene procedures in 20 swine herds over a 12-month period, as driven by tailor-made plans, including training on-farm. The measure of adenosine triphosphate (ATP) environmental contents was used as an output biomarker. The presence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) and extended-spectrum β-lactamase producing Escherichia coli (ESBL-E. coli) was also investigated as sentinels of antibiotic resistance. A significant biosecurity improvement (p = 0.006) and a reduction in the ATP content in the sanitised environment (p = 0.039) were observed. A cluster including 6/20 farms greatly improved both biosecurity and ATP contents, while the remaining 14/20 farms ameliorated them only slightly. Even if the ESBL-E. coli prevalence (30.0%) after the hygiene procedures significantly decreased, the prevalence of LA-MRSA (22.5%) was unaffected. Despite the promising results supporting the adoption of tailor-made biosecurity plans and the measure of environmental ATP as an output biomarker, the high LA-MRSA prevalence still detected at the end of the study underlines the importance of improving even more biosecurity and farm hygiene in a one-health approach aimed to preserve also the pig workers health.

Occurrence and antimicrobial resistance pattern of E. coli O157:H7 isolated from foods of Bovine origin in Dessie and Kombolcha towns, Ethiopia.

E. coli are frequently isolated food-borne pathogens from meat, milk, and their products. Moreover, there has been a significant rise in the antimicrobial resistance patterns of E. coli O157:H7 to commonly used antibiotics. A cross-sectional study was conducted from October 2019 to July 2021 to estimate prevalence and identify associated factors of E. coli and E. coli O157:H7 and to determine antibiotic resistance pattern of E. coli O157:H7 from foods of bovine origin in Dessie and Kombolcha towns. A total of 384 samples were collected. Systematic and simple random sampling techniques were employed for sampling carcasses and milking cows, respectively. E. coli and E. coli O157:H7 were detected according to recommended bacteriological protocols. E. coli O157:H7 strains were evaluated for in vitro antimicrobial susceptibility using agar disk diffusion method. Both descriptive and inferential statistical techniques were applied to analyze the data. Overall prevalence rates of E. coli and E. coli O157:H7 were 54.7% and 6.5%, respectively. Highest prevalence rates of E. coli (79.6%) and E. coli O157:H7 (16.7%) were obtained from carcass swabs and milk tank samples, respectively. Unlike E. coli O157:H7, a statistically significant difference in the E. coli prevalence (P<0.05) was observed among the different sample types. Multidrug resistance was observed among all isolates of E. coli O157:H7. All E. coli O157:H7 isolates (100.0%) were susceptible to Ampicillin, Sulfamethoxazole-trimethoprim, and Norfloxacin. On the contrary, all of the isolates (100%) were resistant to Penicillin G, Vancomycin, and Oxacillin. The current study indicated that different foods of bovine origin in the study area were unsafe for human consumption. Hence, good hygienic production methods should be employed to ensure the safety of foods of bovine origin.

Antibiotic-resistant pathogenic bacterial isolates from patients attending the outpatient department of university of Cape Coast hospital, Ghana: A retrospective study between 2013-2015.

Uropathogenic Escherichia coli (E. coli) is an important urinary tract infection (UTI) that has been associated with both complicated and uncomplicated disease conditions. The global emergence of multiple drug-resistant (MDR) and extended-spectrum β-lactamase (ESBL) is of public health concern as the resistance limits the current treatment options. The objective of this study was to analyze the antibiotic-resistant patterns among the uropathogenic E. coli isolates at the University of Cape Coast (UCC) hospital between 2013 and 2015 as baseline data to understand the current antibiotic resistance situation within UCC and its environs. A retrospective cross-sectional study of bacteria isolates at UCC hospital from January 2013 to December 2015 were analyzed. A standard biochemical and antibiotic susceptibility tests were performed using Kirby-Bauer NCCLs modified disc diffusion technique. The network of interaction between pathogenic isolates and antibiotic resistance was performed using Cytoscape software. Statistical significance was tested using ANOVA and one-sample Wilcoxon test. The overall E. coli prevalence was 15.76% (32/203); females had the highest infection of 17.33% (26/150) compared to male subjects who had 11.32% (6/53) out of all the pathogenic infections. The E. coli prevalence among the age categories were 2/21 (9.52%), 27/154 (17.53%) and 4/21 (19.05%) among ≤20 years, 21-40 years and 41-60 years respectively. The isolated resistant pathogens exhibited different antibiotic resistance patterns. An interaction network of nodes connecting to other nodes indicating positive correlations between the pathogens and antibiotic resistance was established. Escherichia coli, Citrobacter spp, Klebsiella spp among other isolated pathogens formed higher centrality in the network of interaction with antibiotic resistance. The individual E. coli isolates showed a significant difference in the mean ± SD (95% CI) pattern of antibiotic resistance, 2.409±1.205 (1.828-2.990), χ2 = 36.68, p<0.0001. In conclusion, the study reports the interaction of E. coli isolates at UCC hospital and its antibiotic-resistant status between 2013 and 2015. This data forms the baseline information for assessing the current antibiotic status in UCC and its environs.

Factors influencing the detection of antibacterial-resistant Escherichia coli in faecal samples from individual cattle.

To investigate whether on-farm antibacterial usage (ABU), environmental antibacterial-resistant (ABR) Escherichia coli prevalence, sampling and sample handling methodologies are associated with ABR E. coli positivity in individual faecal samples from dairy heifers. Three hundred and sixty-four heifers from 37 farms were sampled via rectal or faecal pat sampling. Samples were stored at -80°C for variable periods before microbiological analysis. Data analysis was done through a multilevel, multivariable logistic regression approach. Individual rectal samples had increased odds of positivity for amoxicillin-, cefalexin- and tetracycline-resistant E. coli. Sample storage for 6-12months was associated with decreased odds of finding amoxicillin- and tetracycline-resistant E. coli. On-farm ABU had little influence, and environmental ABR E. coli prevalence had no significant influence on the odds of sample-level positivity for ABR E. coli. Sampling methodology and sample handling have a greater association than on-farm factors with the detection of ABR E. coli in individual faecal samples from dairy heifers. Sampling and storage methodologies should be considered carefully at the point of designing ABR surveillance studies in livestock and their environments and, where possible, these methodologies should be standardized between and within future studies.

Effect of aromatic oils on the expression of some virulence-associated and antimicrobial resistance genes of Escherichia coli isolated from broilers.

Objectives:This study aimed to prove the effects of Escherichia coli isolates isolated from diseased broilers to form biofilms, describe their antimicrobial sensetivity, and determine the effect of allicin and cinnamon essential oils on the expression of some genes (fimH, int1, and luxS) through quantitative polymerase chain reaction (q-PCR).Materials and Methods:140 samples were obtained from diseased broilers in Beni-Suef Governorate, Egypt. These samples were examined by conventional bacteriology methods to detect the causative agent. The antimicrobial susceptibility of the isolated bacteria was assessed using the disc diffusion method, The ability of yeast extract-casamino acids Congo Red Agar to generate phenotypic biofilms was next tested. The presence of resistance and virulence genes in some multidrug resistant isolates was genotypically investigated. The antibacterial effects of allicin and cinnamon oil were evaluated against the growth of multidrug-resistant E. coli. Finally, q-PCR was utilized to assess changes in some genes’ expression.Results:Escherichia coli was isolated from 61 samples (43.6%). An antimicrobial susceptibility test revealed that multidrug-resistance (MDR) (could resist more than three antimicrobial classes) E. coli prevalence was 100%. 40.8% of isolates phenotypically produce biofilms. The detection of resistance and virulence genes by PCR showed that all tested isolates carry aadB, fimH, int1, qnrS, and luxS genes, while only 40% harbor iss genes. q-PCR showed that after treatment with allicin and cinnamon oils, gene expression went down.Conclusion:This investigation highlights that E. coli showed resistance against most of the tested antimicrobials; all isolates were MDR. The study showed wide dissemination of virulence and resistance genes among E. coli. Allicin and cinnamon oils have antimicrobial activities and could be used as alternatives to synthetic antimicrobial agents.

The Darkest Place Is under the Candlestick-Healthy Urogenital Tract as a Source of Worldwide Disseminated Extraintestinal Pathogenic Escherichia coli Lineages.

Since the discovery of the urinary microbiome, including the identification of Escherichia coli in healthy hosts, its involvement in UTI development has been a subject of high interest. We explored the population diversity and antimicrobial resistance of E. coli (n = 22) in the urogenital microbiome of ten asymptomatic women (representing 50% of the sample tested). We evaluated their genomic relationship with extraintestinal pathogenic E. coli (ExPEC) strains from healthy and diseased hosts, including the ST131 lineage. E. coli prevalence was higher in vaginal samples than in urine samples, and occasionally different lineages were observed in the same individual. Furthermore, B2 was the most frequent phylogenetic group, with the most strains classified as ExPEC. Resistance to antibiotics of therapeutic relevance (e.g., amoxicillin-clavulanate conferred by blaTEM-30) was observed in ExPEC widespread lineages sequence types (ST) 127, ST131, and ST73 and ST95 clonal complexes. Phylogenomics of ST131 and other ExPEC lineages revealed close relatedness with strains from gastrointestinal tract and diseased host. These findings demonstrate that healthy urogenital microbiome is a source of potentially pathogenic and antibiotic resistant E. coli strains, including those causing UTI, e.g., ST131. Importantly, diverse E. coli lineages can be observed per individual and urogenital sample type which is relevant for future studies screening for this uropathogen.

Prevalence, Risk Factors, and Genetic Characterization of Extended-Spectrum Beta-Lactamase Escherichia coli Isolated From Healthy Pregnant Women in Madagascar.

Antimicrobial resistance is a major public health concern worldwide affecting humans, animals and the environment. However, data is lacking especially in developing countries. Thus, the World Health Organization developed a One-Health surveillance project called Tricycle focusing on the prevalence of ESBL-producing Escherichia coli in humans, animals, and the environment. Here we present the first results of the human community component of Tricycle in Madagascar. From July 2018 to April 2019, rectal swabs from 492 pregnant women from Antananarivo, Mahajanga, Ambatondrazaka, and Toamasina were tested for ESBL-E. coli carriage. Demographic, sociological and environmental risk factors were investigated, and E. coli isolates were characterized (antibiotic susceptibility, resistance and virulence genes, plasmids, and genomic diversity). ESBL-E. coli prevalence carriage in pregnant women was 34% varying from 12% (Toamasina) to 65% (Ambatondrazaka). The main risk factor associated with ESBL-E. coli carriage was the rainy season (OR = 2.9, 95% CI 1.3–5.6, p = 0.009). Whole genome sequencing was performed on 168 isolates from 144 participants. blaCTX–M–15 was the most frequent ESBL gene (86%). One isolate was resistant to carbapenems and carried the blaNDM–5 gene. Most isolates belonged to commensalism associated phylogenetic groups A, B1, and C (90%) and marginally to extra-intestinal virulence associated phylogenetic groups B2, D and F (10%). Multi locus sequence typing showed 67 different sequence types gathered in 17 clonal complexes (STc), the most frequent being STc10/phylogroup A (35%), followed distantly by the emerging STc155/phylogroup B1 (7%), STc38/phylogroup D (4%) and STc131/phylogroup B2 (3%). While a wide diversity of clones has been observed, SNP analysis revealed several genetically close isolates (n = 34/168) which suggests human-to-human transmissions. IncY plasmids were found with an unusual prevalence (23%), all carrying a blaCTX–M–15. Most of them (85%) showed substantial homology (≥85%) suggesting a dissemination of IncY ESBL plasmids in Madagascar. This large-scale study reveals a high prevalence of ESBL-E. coli among pregnant women in four cities in Madagascar associated with warmth and rainfall. It shows the great diversity of E. coli disseminating throughout the country but also transmission of specific clones and spread of plasmids. This highlights the urgent need of public-health interventions to control antibiotic resistance in the country.

Prevalence and Risk Factors for ESBL/AmpC-E. coli in Pre-Weaned Dairy Calves on Dairy Farms in Germany.

The objectives of this study were to ascertain the fecal ESBL/AmpC-E. coli prevalence and to detect risk factors for their occurrence in young pre-weaned calves and their dams on large dairy farms in Germany. From 2018–2019 we investigated 2816 individual fecal samples from pre-weaned dairy calves and their dams, representing seventy-two farms (mean = 667 milking cows) from eight German federal states. To assess possible risk factors associated with ESBL/AmpC-E. coli prevalence in calves and dams, a questionnaire was performed, collecting management data. We observed an ESBL/AmpC-E. coli prevalence of 63.5% (95% CI: 57.4–69.5) among the sampled calves and 18.0% (95% CI: 12.5–23.5) among the dams. On all farms, at least one positive sample was obtained. To date, this is the highest ESBL/AmpC-E. coli prevalence observed in dairy herds in Europe. Feeding with waste milk was identified as a significant risk factor for a high prevalence of ESBL/AmpC-E. coli in calves. Many calves at large dairies in Germany are fed with waste milk due to the large amounts generated as a result of antibiotic dry-off routines and mastitis treatment with antibiotics. Other notable risk factors for high ESBL/AmpC-E. coli in calves were the general fitness/health of dams and calves, and the quality of farm hygiene. Taken together, these findings suggest that new or improved approaches to animal health management, for example, antibiotic dry cow management (selective dry cow therapy) and mastitis treatment (high self-recovery), as well as farm hygiene, should be researched and implemented.