Species specific PCR based detection of Escherichia coli from Indian foods

Diarrheagenic Escherichia coli with Multidrug Resistance in Cattle from Mexico

Mexico is an important producer/exporter of cattle and cattle products. In the last decade, an increase in antibiotic resistance in E. coli pathotype strains from livestock environments has been reported. This study aimed to determine the prevalence and antibiotic resistance profiles of E. coli pathotype strains from the feces of beef or dairy cattle reared in the states of Aguascalientes (AG, central) and Nuevo Leon (NL, northeastern) in Mexico. One hundred and ten fecal samples were collected (beef cattle-AG = 30; dairy cattle-AG = 20; beef cattle-NL = 30; dairy cattle-NL = 30). From these, E. coli was isolated using selective/differential media and confirmed on chromogenic media. Multiplex PCR was used to identify diarrheagenic E. coli, and the Kirby-Bauer technique was used to determine the antimicrobial susceptibilities. All the animals harbored E. coli, and pathotypes were found in 34 animals from both, beef and dairy cattle, mainly from Aguascalientes. Of the positive samples, 31 harbored a single E. coli pathotype, whereas three samples harbored two different pathotypes; EHEC was the most prevalent, followed by EPEC, ETEC, and EIEC or the combination of two of them in some samples. Most pathotype strains (19/37) were isolated from beef cattle. Neither the animals' productive purpose (beef or dairy cattle) (r = 0.155) nor the geographic regions (Aguascalientes or Nuevo Leon) (r = -0.066) had a strong positive correlation with the number of E. coli pathotype strains. However, animals reared in Aguascalientes had up to 8.5-fold higher risk of harboring E. coli pathotype strains than those reared in Nuevo Leon. All pathotype strains were resistant to erythromycin, tetracycline, and trimethoprim/sulfamethoxazole, and all dairy cattle pathotype strains were further resistant to five β-lactams (χ2, P = 0.017). The existence of these pathotypes and multidrug-resistant pathogens in the food chain is a risk to public health.

Antibiotic prescribing patterns and carriage of antibiotic-resistant Escherichia coli and Enterococcus species in healthy individuals from selected communities in Lusaka and Ndola districts, Zambia

Objectives

This study assessed antibiotic prescribing patterns in primary healthcare facilities and antimicrobial resistance (AMR) profiles of commensal Escherichia coli and enterococci isolated from pregnant women and children under 5 years of age.

Materials and methods

This cross-sectional study was conducted in Lusaka and Ndola districts of Zambia. Prescription pattern data were obtained from hospital pharmacies. Identification and antimicrobial susceptibility profiles of E. coli and enterococci were determined by conventional methods, while confirmation of both pathogens and AMR genes were determined by PCR. Data were analysed using WHONET and SPSS version 25.0.

Results

Most prescribed antibiotics at the primary healthcare facilities belonged to the Access group of the WHO Access, Watch and Reserve (AWaRe) classification. All the primary healthcare facilities adhered to the AWaRe framework of ≥60% prescribed antibiotics belonging to the Access group. However, resistance was highest in the Access group of antibiotics. E. coli resistance to ampicillin ranged from 71% to 77% and to co-trimoxazole from 74% to 80%, while enterococcal resistance to tetracycline was 59%-64%. MDR was highest in E. coli (75%) isolates, while XDR was highest in enterococcal isolates (97%). The identified AMR genes in E. coli included blaCTX-M, sul2 and qnrA, while those of enterococci included erm(B), erm(C) and erm(A).

Conclusions

Resistance was highest in the prescribed WHO Access group of antibiotics. These findings highlight the need to use local susceptibility data to formulate country-specific treatment guidelines in line with WHO AWaRe classification and enforce regulations that prohibit easy access to antibiotics.

A preliminary report on critical antimicrobial resistance in Escherichia coli, Enterococcus faecalis, and Enterococcus faecium strains isolated from healthy dogs in Chile during 2021-2022

Antimicrobial Resistance (AMR) represents one of the main current threats to global public health; where production animals, companion animals, humans, and the environment play a significant role in its dissemination. However, little attention has been given to companion animals as reservoirs and disseminators of relevant antimicrobial resistant bacteria, especially in South American countries such as Chile. For this reason, this research aimed to estimate the prevalence of AMR to different critical antibiotics at a screening level in commensal bacteria such as E. coli and Enterococcus spp., isolated from healthy pet dogs in the Metropolitan Region of Chile, studying their geographical distribution and evaluating associations of phenotypic resistance to different antibiotics. Thus, in E. coli we detected AMR to all critical drugs assessed, including 34.1% to amoxicillin, 20.1% to colistin, 15.7% to enrofloxacin, and 9.2% to cefotaxime. On the other hand, AMR prevalence in E. faecalis was 8.1% for ampicillin and 3.4% for vancomycin; while for E. faecium the AMR prevalence was 19.1% for ampicillin and 10.2% for vancomycin. Additionally, significant differences in prevalence of the different possible AMR were detected according to their geographical distribution, suggesting the existence of various risk factors and stressing the need to establish mitigation measures specific to the differences identified.

Prevalence of multidrug-resistant and extended-spectrum β-lactamase producing Escherichia coli from local and broiler chickens at Cibinong market, West Java, Indonesia

Background and Aim

Antimicrobial resistance (AMR) is becoming a public health concern. Foodborne pathogens are infectious agents that can be transmitted from animals to humans through food and can become resistant due to misuse and overuse of antibiotics, especially in poultry. This study aimed to detect the prevalence of multidrug-resistant and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from local and broiler chickens at the Cibinong market, West Java, Indonesia.

Materials and Methods

A total of 60 cloacal swab samples from 30 local and broiler chickens sold at the Cibinong market in West Java were obtained by random sampling. From these samples, 39 E. coli isolates were obtained after being cultured on eosin methylene blue agar and molecularly identified using polymerase chain reaction (PCR). Six antibiotic disks were used for the antibiotic sensitivity test against E. coli isolates cultured on Mueller-Hinton agar. PCR was performed to detect ESBL genes (blaTEM, blaSHV, and blaCTX-M).

Results

A total of 76.47% (39/51) cloacal swab samples were positive for E. coli. All E. coli isolates were sensitive to imipenem (100%), and 38 isolates were sensitive to cefoxitin (FOX) (97.4%). On average, the isolates were sensitive to amoxicillin-clavulanic acid (AMC) (69.2%) and ceftriaxone (CRO) (89.7%). E. coli isolates were occasionally resistant to enrofloxacin (25.64%), followed by gentamicin (20.51%), CRO (10.25%), AMC (7.69%), and FOX (2.56%). The prevalence of E. coli AMR was 10.25% (4/39). All four multidrug-resistant E. coli isolates (blaTEM and blaCTX-M) were confirmed to have the ESBL gene based on PCR.

Conclusion

The prevalence of multidrug-resistant and ESBL-producing E. coli is still found, proving that there is still inappropriate use of antibiotics and a need for strict supervision of their use, especially around Cibinong market, West Java.

In vivo analysis the effect of antibiotic growth promoters (AGPs), Oxytetracycline di-hydrate and Tylosin phosphate on the intestinal microflora in broiler chicken

Abstract The study was aimed to analyse the effects of antibiotic growth promoters (AGPs), Oxytetracycline di-hydrate and Tylosin phosphate on the intestinal microflora in broiler chicken. The AGPs were provided in different concentrations solely or in combinations for 42 days of rearing. Faecal samples were collected from the intestine (duodenum, jejunum and caeca) of broiler chicken on 14th, 28th and 42nd days of trial. Samples were cultured on different selective medium and bacterial identification was performed by different biochemical and molecular diagnostic tools. Results showed a significant effect of AGPs on the growth of pathogenic microorganisms such as Escherichia coli and Clostridium perfringens in the intestine. Interestingly, an impaired growth was observed for both bacterium showing a significant effect (P<0.05) of AGPs on E. coli and C. perfringens on day 14th, 28th, and 42nd. This effect was observed solely and in combination while using AGPs. Data further showed that the effect was more prominent in combination and with an increase concentration of AGPs. Remarkably, no impairment was seen on the growth of L. reuteri at different sites of intestine and duration (14th, 28th, and 42nd days). The results showed that the use of AGPs in diet has no harmful effect on beneficial bacteria, however, an impaired growth was seen on the harmful bacteria. It is suggested that a combination of AGPs (OXY-1.0+TP-0.5) is economical and have no harmful effect on the broiler chicken. The use of AGPs in a recommended dose and for a specific period of time are safe to use in poultry both as growth promoter and for the prevention of diseases.

Colistin Resistance in Multidrug-Resistant Escherichia coli Isolated from Retail Broiler Meat in Bangladesh

The emergence of colistin resistance in Escherichia coli is a global public health concern. Contaminated food can accelerate the spread of colistin-resistant E. coli to humans. This study aimed to detect and characterize colistin-resistant E. coli from broiler meat in Bangladesh. We analyzed 136 pooled broiler meat samples from 240 carcasses collected from 40 live bird markets in urban and rural areas and 8 metropolitan supermarkets. The mean count of E. coli in broiler meat samples collected from rural retail shops, metropolitan supermarkets, and urban retail shops was 5.3 ± 1.1, 4.1 ± 1.4, and 3.9 ± 0.8 log10 colony-forming unit per gram, respectively. Colistin-resistant E. coli (minimum inhibitory concentration >2 mg/L) was found in 78% (95% confidence interval 70.2-84.1%) of the samples. All colistin-resistant isolates harbored the mcr-1 gene, while the rest of the mcr genes (mcr-2 to mcr-9) were not detected. Most colistin-resistant E. coli isolates (98%) showed coresistance to tetracycline, sulfamethoxazole/trimethoprim followed by ciprofloxacin (95%). Alarmingly, all of the colistin-resistant isolates were found to be multidrug resistant. Phylogenetic analysis showed close similarities of the mcr-1 gene sequences of this study with many strains of Enterobacterales isolated from humans, animals, and the environment. This study detected colistin-resistant E. coli contamination in broiler meat, which can pose a serious public health threat.

Validation of quantitative loop-mediated isothermal amplification assay using a fluorescent distance-based paper device for detection of Escherichia coli in urine

Uropathogenic Escherichia coli (UPEC) causes up to 90% of urinary tract infections (UTI) which is more prevalent among females than males. In urine, patients with symptomatic UTI usually have a high concentration of bacterial infection, ≥ 105 colony-forming units (CFU) per mL, in which the culture method is regularly the gold standard diagnosis. In this study, a simple and inexpensive distance-based paper device (dPAD) combined with the fluorescent closed tube LAMP assay was validated for simultaneously screening and semi-quantifying the infection level of E. coli in 440 urine samples of patients with UTI. The dPAD could measure the LAMP amplicons and semi-quantify the levels of E. coli infection in heavy (≥ 104 CFU/mL), light (≤ 103 CFU/mL) and no infection. The sensitivity and specificity had reliable performances, achieving as high as 100 and 92.7%, respectively. The one step LAMP assay could be performed within 3 h, which was 7.5 times faster than the culture method. To empower early UTI diagnosis and fast treatment, this inexpensive dPAD tool combined with the fluorescent closed tube LAMP assay is simple, reliably fast and practically portable for point-of-care settings, particularly in resource-limited areas, which can be set up in all levels of healthcare facilities.

Predominance of Multidrug Resistant Escherichia coli of Environmental Phylotype in Different Environments of Dhaka, Bangladesh

Considering the ecological diversity of E. coli, the main aim of this study was to determine the prevalence, phylogroup diversity, and antimicrobial susceptibility of E. coli isolated from 383 different clinical and environmental sources. In total, varied prevalence was observed of the 197 confirmed E. coli that were isolated (human-100%, animal-67.5%, prawn-49.23%, soil-30.58%, and water-27.88%). Of these isolates, 70 (36%) were multidrug-resistant (MDR). MDR E. coli was significantly associated with their sources (χ² = 29.853, p = 0.001). Humans (51.67%) and animals (51.85%) carried more MDR E. coli than other environments. The eae gene indicative of recent fecal contamination was not detected in any isolate, indicating that these E. coli isolates could be present in these environments for a long time and became naturalized. Phylogroup B1 (48.22%) was the predominant group, being present in all hosts analyzed and with the commensal E. coli group A (26.9%) representing the second predominant group. According to chi-square analysis, phylogroup B1 was significantly associated with E. coli from humans (p = 0.024), soil (p < 0.001) and prawn samples (p < 0.001). Human samples were significantly associated with phylogroup B1 (p = 0.024), D (p < 0.001), and F (p = 0.016) of E. coli strains, whereas phylogroup A (p < 0.001), C (p < 0.001), and E (p = 0.015) were associated with animal samples. Correspondence analysis results also indicated the association of these phylogroups with their hosts/sources. The findings of this study exhibited a non-random distribution of phylogenetic groups, though the diversity index was highest for human E. coli phylogroups.

High prevalence of extensively drug resistant and extended spectrum beta lactamases (ESBLs) producing uropathogenic Escherichia coli isolated from Faisalabad, Pakistan

Urinary tract infections (UTIs) are predominantly caused by uropathogenic Escherichia coli (E. coli). There is rapid increase in antimicrobial resistance in UTIs, also declared as a serious health threat by World Health Organization (WHO). Present study was designed to investigate the antimicrobial resistance status with specific focus on ESBLs and carbapenemases in local uropathogenic E. coli (UPEC) isolates. E. coli isolates were characterized from patients of all ages visiting diagnostic laboratories for urine examination. Demographic data was also recorded for each patient. Antibiograms were developed to observe antibiotic resistance in UPEC using Kirby Bauer disc diffusion technique. Double Disc Synergy test (DDST) was used for phenotypic ESBL test. ESBLs and carbapenemases genes were detected in UPEC using PCR. The PCR results were confirmed by sequencing. The UPEC isolates under study exhibited 78%, 77%, 74%, 72% and 55% resistance against cefotaxime, amoxicillin, erythromycin, ceftriaxone and cefixime, respectively. Resistance against colistin and meropenem was observed in 64% and 34% isolates, respectively. Phenotypic DDST identified 48% isolates as ESBLs producers. Genotypic characterization identified 70%, 74.4% and 49% prevalence of CTXM-1, TEM-1 and CTXM-15 genes respectively. One isolate was observed exhibiting co-existence of all ESBL genes. TEM-1 + CTXM-1 and TEM-1 + CTXM-1 + CTXM-15 + OXA-1 gene patterns were dominant among ESBLs. For carbapenem-resistance, 14% isolates indicated the presence of KPC whereas GES and VIM was detected in 7% and 3.4% isolates, respectively. In conclusion, our results present a high prevalence of extensively drug resistant UPEC isolates with a considerable percentage of ESBL producers. These findings propose the need of continuous surveillance for antimicrobial resistance and targeted antimicrobial therapy.

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.

Detection of Escherichia coli in Food Samples Using Culture and Polymerase Chain Reaction Methods

Methods for the rapid detection of Escherichia coli and its related toxins are key to minimizing the risk of exposure to foodborne pathogens. The present study aimed to detect E. coli in food specimens using culture and polymerase chain reaction (PCR) techniques. One hundred and fifty samples from different types of food, comprising beef (n=60), chicken (n=72), and fish (n=18), were analyzed for the identification of E. coli by conventional and PCR methods. The results showed that out of 150 food samples, 44 (29.3%) were positive by culture, and 50 (33.3%) were positive by PCR. Significant differences were detected between sample types with culture (p-value < 0.005). When culture was considered the gold standard, the sensitivity of PCR was 100%, while the specificity was 94.34%. The six-hour pre-enrichment and PCR analysis are reliable in fast detection of E. coli in food samples. Hence, the identification of food pathogens using molecular-based methods would become more useful in routine diagnostic laboratories.

Rapid identification of Staphylococcus aureus based on a fluorescence imaging/detection platform that combines loop mediated isothermal amplification assay and the smartphone-based system

Food associated diseases pose significant public health threat in the United States. Health risks associated with food-borne pathogens drive the need for constant monitoring of food products. An efficient method that can diagnose food-borne pathogens rapidly will be invaluable and in high demand. In this study, we showed the feasibility of a novel rapid detection platform based on fluorescence imaging/detection that combines a user-friendly, portable loop mediated isothermal amplification (LAMP) reaction device and a smartphone-based detection system. The proposed platform was used to detect Staphylococcus aureus which is one of the most important food-borne pathogen especially dairy products. The complete protocol is quicker; the reaction is performed under isothermal conditions and completed in 1 h or less. Experimental results show that LAMP assays were ten-fold more sensitive than PCR-based detection. The proposed smartphone detection system was able to detect and quantify LAMP assay samples containing three different concentrations of S. aureus from 10⁹ CFU/mL down to 10³ CFU/mL. The present proof-of-concept study demonstrated that this platform offers a portable, easy to use method for measuring target pathogens with LAMP amplification.

Escherichia coli in different animal feces: phylotypes and virulence genes

In this study, it was aimed to determine the phylogroups of Escherichia coli isolates from horse, cat, dog, sheep, cattle, and chicken feces samples and to investigate some important virulence genes of the isolates. For this purpose, a total of 600 feces samples, 100 from each animal species, were used as material. For the isolation of E.coli, feces samples were directly inoculated on MacConkey agar. The identification of the isolates was performed via phenotypic tests and species-specific multiplex Polymerase Chain Reaction (mPCR) method. PCR methods were used to phylotype E.coli isolates and to investigate virulence genes (bfpA, eaeA, LT, ST, Stx1, and Stx2). Of the total 600 E.coli isolates recovered in this study, 120 (20%), 269 (44.8%), 58 (9.7%), 19 (3.2%), 35 (5.8%), 56 (9.3%), 31 (5.2%), and 12 (2%) were identified as phylogroup A, B1, B2, C, D, E, F, and Escherichia clade I, respectively. While the virulence gene was detected in 149 (24.8%) E.coli isolates, no virulence gene was detected in 451 (75.2%) isolates. According to the analysis results, the most determined virulence gene was Stx1, while the least determined virulence gene was LT. In conclusion, in this study, when both the animal species and the number of E.coli isolates examined are considered, the data obtained are of great importance in epidemiological terms. However, the detection of virulence genes in 13.5% among phylogroup A, B1, and C isolates with commensal characteristics suggest that these isolates may show pathogenic characteristics with the virulence genes they contain.

Prevalence and Antimicrobial Resistance of Escherichia coli in Chicken Meat and Edible Poultry Organs Collected from Retail Shops and Supermarkets of North Western Province in Sri Lanka

Escherichia coli is a commensal bacterium that lives in human and animal intestines. Shiga toxin-producing strains of E. coli STECs are responsible for most food-related E. coli infections. Pathogenic E. coli transmits to human bodies due to the consumption of contaminated, raw, or undercooked food. This study was conducted to identify the prevalence of E. coli contamination in edible poultry meat and meat organs in the North Western Province of Sri Lanka. A total of 250 samples consisting of chicken meat (n = 144) and edible organs (n = 106) were collected from retail shops (n = 181) and supermarkets (n = 69), in both Kurunegala and Puttlam districts. The prevalence of E. coli from 250 chicken meat samples was 66.80% (167/250); E. coli prevalence at retail shops (66.85%) was higher than that at supermarkets (66.67%) and was not statistically significant. E. coli prevalence in chicken meat and edible organs was 65.73% and 69.16%, respectively. Molecular confirmation for the positive samples was done through polymerase chain reaction (PCR) using previously designed primers. An antibiotic susceptibility test was performed according to CLSI using nine antibiotics: ampicillin, amoxicillin, chloramphenicol, ceftazidime, ciprofloxacin, cephalexin, erythromycin, gentamicin, and tetracycline. Most isolates were resistant to erythromycin (80.84%) and amoxicillin (76.05%), while the least resistance was observed for gentamicin (4.79%). This study indicates the potential public health risk associated with chicken sold at retail and supermarket levels in the North Western Province of Sri Lanka.

Antimicrobial Susceptibility and Molecular Characterization of Escherichia coli Recovered from Milk and Related Samples

There is a rising concern about illnesses resulting from milk consumption due to contamination by pathogenic microorganisms including Escherichia coli. This study examined the occurrence and antimicrobial susceptibility of E. coli isolated from cow milk and related samples. Furthermore, partial sequencing was done to ascertain the genetic relatedness and possible cross contamination among the samples. In all, 250 samples, that is, 50 each of raw milk, cow teat, milkers’ hands, milking utensils, and fecal matter of cows, were cultured for the identification of E. coli. E. coli was detected in 101/250 samples (40.4%). Milk and fecal samples recorded the highest percentages of 68.0% and 66.0%, respectively. Forty-two (42) E. coli strains examined for antimicrobial resistance showed an overall 25.5% resistance, 15.0% intermediate resistance, and 59.5% susceptibility. The isolates had a high level of resistance to teicoplanin (100.0%), but were susceptible to chloramphenicol (95.2%) and azithromycin (92.9%). The Multiple Antibiotic Resistance (MAR) index pattern ranged from 0.1 to 0.5, and 40.5% exhibited multiple drug resistance. The E. coli strains formed 11 haplotypes, and a phylogenic tree analysis showed relatedness among the isolates in other African countries. This observation is an indication of cross contamination among the milk and its related samples.

Virulence Profiles and Antibiotic Susceptibility of Escherichia coli Strains from Pet Reptiles

Exotic reptiles are increasingly being bred as pets in many countries around the world, including Poland. However, the close contact between reptiles and their owners provides favourable conditions for the transmission of zoonotic pathogens. In this work, we examined E. coli isolates from 67 captive reptiles regarding their virulence, antibiotic susceptibility, phylogenetic affiliation, and genetic diversity. The incidence of E. coli was highest in snakes (51.6%, 16 isolates/31 samples), and slightly lower in turtles (44.4%, 8/18) and lizards (44.4%, 8/18). Genes encoding virulence factors were confirmed in 50% of isolates and the most common were the traT (37.5%, n = 12), fyuA (21.87%, n = 7), and irp-2 (15.62%, n = 5). The majority (71.87%, n = 23) of E. coli isolates were susceptible to all of the antimicrobial substances used in the study. Streptomycin resistance (21.87%, n = 7) was the most frequent, while resistance to other antimicrobial substances was sporadic. One strain (3.12%) was classified as multidrug-resistant. The presence of resistance genes (aadA, tetA, tetB, tetM, and blaTEM) was confirmed in 12.5% (n = 4) of the isolates. The majority (65.6%, n = 21) of E. coli isolates represented the B1 phylogenetic group. (GTG)₅-PCR fingerprinting showed considerable genetic variation in the pool of tested isolates. The frequency of E. coli in reptiles is much lower than in mammals or birds. Due to the presence of virulence genes, characteristic of both intestinal pathogenic E. coli (IPEC) and extraintestinal pathogenic E. coli (ExPEC), reptilian strains of E. coli have pathogenic potential, and therefore people in contact with these animals should follow good hygiene practices.

Elucidating the resistance repertoire, biofilm production, and phylogenetic characteristics of multidrug-resistant Escherichia coli isolated from community ponds: A study from West Bengal, India

This study details about the phenotypic and molecular characteristics of multidrug-resistant (MDR) Escherichia coli in the fresh community pond water (n = 257) collected from three districts of West Bengal, India. In total, 57 isolates were MDR of which 38 emerged as extended spectrum and 7 as AmpC-type β-lactamase producers in phenotypic assay. Among β-lactamase genes, blaCTXM-1was predominant (87.71%) followed by blaAmpC (77.2%) and blaTEM-1 (22.8%). Six MDR strains carried metallo-β-lactamase (MBL, blaNDM-1) gene. Tissue culture plate assay confirmed strong biofilm (SP) production in four MDR and one non-MDR isolates. In PCR-based replicon typing (PBRT), multiple plasmids of diverse replicon types (Frep, FIB, I1, FIA, K/B, HI1, and Y) were identified. The enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR)-based phylogenetic analysis revealed a high degree of genetic divergence among the MDR isolates. Multiplex PCR-based phylogrouping categorized 11 isolates as virulent (B2/D/F), which carried blaCTXM-1 gene and three had blaNDM-1 gene. Relative transcriptional activity of AcrAB efflux pump was significantly elevated among the SP and MBL producers. The presence of MDR E. coli isolates, particularly those resistant to carbapenem, in pond water used for daily domestic and household work, is a cause of concern as these pathogens may sneak into human food chain causing life-threatening infections. PRACTITIONER POINTS: Multidrug-resistant biofilm producing E. coli isolated from community pond water. A few of them were carbapenem-resistant and belonged to virulent (B2/D) types. Expression of AcrAB efflux pumps was found significantly elevated among biofilm producers and carbapenem-resistant population.

Predominance of genetically diverse ESBL Escherichia coli identified in resistance mapping of Vembanad Lake, the largest fresh-cum-brackishwater lake of India

Antimicrobial resistance (AMR) burden in Escherichia coli along the 90 km stretch of Vembanad Lake, Kerala, India, was assessed. Seventy-seven percent of water samples drawn from 35 different stations of the lake harbored E. coli. Antibiotic susceptibility test performed on 116 E. coli isolates revealed resistance to ≥ one antibiotic with 39 AMR profiles in 81%, multidrug resistance in 30%, and extended spectrum β-lactamase (ESBL) producers in 32%. Of all the 15 antibiotics tested, the probability of isolating cefotaxime-resistant E. coli was the highest (P ≤ 0.05) in the lake. Genetically diverse ESBL types, namely bla_TEM-116, bla_{CTX-M -152}, bla_{CTX-M -27}, bla_{CTX-M -55}, bla_CTX-M-205, and bla_SHV-27, were identified in the lake. This is probably the first report in India for the presence of bla_CTX-M-205 (bla_{CTX-M-group 2}) in the Vembanad Lake. ST11439 and single and double loci variants of ST443 and ST4533 were identified in multilocus sequence typing (MLST). Inc plasmids (B/O, F, W, I1, FIIA, HI1, P-1α, K/B, and N) identified in the lake evidences the resistance transmission potential of the E. coli isolated from the lake. Molecular typing (ERIC-PCR, MLST, and PBRT) delineated diverse E. coli, both between and within the sampling stations. Low multiple antibiotic resistance index (average MAR< 0.2) indicates a lower risk of the lake to the human population, but the occurrence of genetically diverse ESBL E. coli in the Vembanad Lake signals health hazards and necessitates pragmatic control measures.

Fluorescence nucleobase analogue-based strategy with high signal-to-noise ratio for ultrasensitive detection of food poisoning bacteria

We developed a simple and ultrasensitive strategy for the identification of foodborne pathogens utilizing a fluorescent nucleobase analogue [2-aminopurine (2-AP)]-containing split G-quadruplex that binds blocker DNA. Compared to a previous strategy that did not use blocker DNA, this strategy showed a significant increase in the signal-to-noise ratio-by approximately 300%-owing to the displacement of the blocker DNA by the target DNA that induces the formation of an active G-quadruplex structure, thereby leading to a substantial increase in the 2-AP fluorescence signal. The proposed strategy was rationally combined with polymerase chain reaction, which resulted in the successful determination of genomic DNA (within the range of 10-106 copies) derived from the food poisoning bacterium Escherichia coli, with a limit of detection of 5.2 copies and high selectivity. In addition, the practical applicability of this method was demonstrated by analyzing E. coli-spiked lettuce samples.

Prevalence, genotyping and antibiotic resistance of Listeria monocytogenes and Escherichia coli in fresh beef and chicken meats marketed in Zanjan, Iran

Background and Objectives:

The aim of present study was to evaluate the prevalence of Listeria monocytogenes and Escherichia coli, characterization and antimicrobial resistance of their serotypes and genotyping profiles in fresh beef and poultry meats marketed in Zanjan, Iran.

Materials and Methods:

A total of 90 (45 chicken and 45 beef) samples were collected from January to June 2018 focusing on retail meat stores of Zanjan city, Iran. Foodborne pathogen detection and antimicrobial resistance of isolates performed by PCR and disc diffusion methods, respectively. Simplex PCR method was used for screening hly and uidA genes in L. monocytogenes and E. coli isolates, respectively.

Results:

Findings revealed high contamination in beef and chicken meats with E. coli (68.89% and 88.89%, respectively) and L. monocytogenes (53.33% and 46.67%, respectively). The most likelihood of E. coli isolates belonged to E. coli 13479 serotype. All L. monocytogenes isolates from beef and chicken meat samples had high similarity with serotypes L. monocytogenes strain NCTC 10357 and strain MF 4545, respectively. Multi drug resistance (MDR) was seen in both L. monocytogenes and E. coli isolates.

Conclusion:

This study shows an insight of the current status of beef and chicken meat contamination maketed in Zanjan, Iran with E. coli and L. monocytogenes isolates (high contamination rate), their genotypic profile, epidemiological relationship and antimicrobial resistance (AMR) that should be considered as a significant public health concern in Zanjan, Iran.

Distribution and comparison of bacterial communities in HVAC systems of two university buildings: Implications for indoor air quality and public health

The installation of HVAC systems in building is meant to enhance indoor air quality as well as increase comfort to occupants. However, HVAC systems have also become a vehicle of contamination of indoor air with potentially pathogenic microorganisms. DNA was extracted from ten HVAC filter dust samples collected from two buildings and subjected to high throughput sequencing analysis to determine the bacterial community structure. Further, the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) software was used to predict the potential functional capabilities of the bacterial communities. Sequencing analysis led to the identification of five major bacterial phyla, including Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes and Bacteroidetes. At genus level, Mycobacterium, Bacillus, Cupriavidus, Hyphomicrobium and Mesorhizobium were the most dominant. With the exception of the later two bacterial genera, the first three are potential pathogens whose presence in HVAC systems poses a significant public health risk, especially among immunocompromised individuals. Nine pathways associated with antibiotics resistance and bacterial pathogenicity were identified, including polymyxin resistance and peptidoglycan biosynthesis pathways. Further, investigation of the relationship between the detected bacterial meta-communities and predicted potential virulence factors (antibiotic resistance and pathogenic genes) led to the detection of 350 positive associations among 43 core bacteria, 2 pathogenic genes (sitA and uidA) and 14 resistance genes. Overall, the heterogeneous nature of microorganisms found in HVAC systems observed in this study shows that HVAC systems are the origin of airborne infections in indoor environments, and must be periodically cleaned and disinfected to avoid the build-up of pathogens, and the subsequent exposure of human occupants of these pathogens.

High prevalence of mcr-1-encoded colistin resistance in commensal Escherichia coli from broiler chicken in Bangladesh

Colistin is a last-resort antimicrobial used for the treatment of human infections caused by multidrug-resistant Gram-negative bacteria. However, colistin is still widely used in intensive poultry production in Bangladesh. We aimed to investigate the dynamics and genetic diversity of colistin-resistant commensal Escherichia coli from broiler chickens. A total of 1200 E. coli strains were characterized from 20 broiler farms at three-time points along the production period. All strains were screened for mcr-1 to mcr-5 genes by a multiplex PCR, and their genetic diversity was measured by repetitive extragenic palindromic (REP)-PCR fingerprinting. Genomic diversity and characterization were performed by whole genome sequencing (WGS). Twenty-five percent of the commensal E. coli strains harbored mcr-1 genes. Frequency of mcr-1 gene detection correlated positively (odds ratio 1.71; 95% CI 0.96-3.06; p = 0.068) with the use of colistin in poultry flocks. REP-PCR profiles and WGS analysis showed diverse E. coli population carrying multiple antimicrobial resistance genes. Phylogenetic comparison of mcr-1-bearing strains recovered from this study with a global strain collection revealed wide phylogenetic relationship. This study identified a high prevalence of mcr-1 gene among genetically diverse E. coli populations from broiler chickens in Bangladesh suggesting a massive horizontal spread of mcr-1 rather than by clonal expansion.

Molecular Screening of β-glucuronidase and Class 1 Integron of Escherichia coli from Ready-to-Eat Foods in Tiruchirappalli, Tamil Nadu

Ready-to-eat food products procured from different roadside shops in Tiruchirappalli, Tamil Nadu were screened for Escherichia coli. A total of 500 samples from 250 vegetable and 250 meat products were collected from different hotels, restaurants and street food vendors in Tiruchirappalli, Tamilnadu. Out of 500 ready-to-eat food samples, 162 (32.4%) E. coli strains were isolated. The ready-to-eat meat products had higher bacterial count than the vegetable food samples collected due to unhygienic handling, improper storage, inadequate temperature to maintain processed meat and improper cooking. Biochemically identified E. coli colonies were screened for housekeeping gene uidA and 139 (85.8%) E. coli isolates were confirmed to possess β-glucuronidase activity. In addition, antibiotic susceptibility assay was performed using 12 antibiotics. From 139 E. coli strains, 96 (69.1%) isolates showed multidrug resistance. Among them, 16.7% showed 100% resistance to all the antibiotics tested. Whereas, multidrug resistant E. coli isolates showed increased resistance (75.9%) to streptomycin followed by 70-50% level of resistance to ceftriaxone, ampicillin, cefixime, ciprofloxacin, tetracycline, gentamicin, doxycycline, co-trimoxazole, norfloxacin, ofloxacin and chloramphenicol. Furthermore, drug resistant E. coli isolates 56 (58.3%) were detected with the presence of intI1. The source of contamination was found to be water and human handling. Drinking water supply from corporation might have been contaminated with fecal waste source is being discharged into Cauvery river which might disseminate horizontal gene transfer.

A Colorimetric Immunosensor Based on Hemin@MI Nanozyme Composites, with Peroxidase-like Activity for Point-of-care Testing of Pathogenic E. coli O157:H7

Recently, nanozymes have become a topic of particular interest due to their high activity level, stability and biocompatibility. In this study, a visual, sensitive and selective point-of-care immunosensor was established to test the pathogen Escherichia coli O157:H7 (E. coli O157:H7). Hemin and magainin I (MI) hybrid nanocomposites (Hemin@MI) with peroxidase-mimicking activities were synthesized via a "one-pot" method, involving the simple mixing of an antimicrobial peptide (MI) against E. coli O157:H7 and hemin in a copper sulfate sodium phosphate saline buffer. Hemin@MI nanocomposites integrating target recognition and signal amplification were developed as signal probes for the point-of-care colorimetric detection of pathogenic E. coli O157:H7. Hemin@MI nanocomposites exhibit excellent peroxidase activity for the chromogenic reaction of ABTS, which allows for the visual point-of-care testing of E. coli O157:H7 in the range of 10² to 10⁸ CFU/mL, with a limit of detection of 85 CFU/mL. These data suggest this immunosensor provides accessible and portable assessments of pathogenic E. coli O157:H7 in real samples.

Molecular characterization of Shigella species isolated from diarrheal patients in Tehran, Iran: phylogenetic typing and its association with virulence gene profiles and a novel description of Shigella invasion associated locus

The present study aims to employ a multiplex PCR-based method for phylogenetic typing of Shigella and determine the frequency of several virulence genes among Shigella phylogenetic clades and species. Species identification, phylogenetic typing of 44 previously diagnosed Shigella isolates, and frequency of virulence genes and loci, virA, virB, virF, ipaBCD, ial, sen, and set1A were investigated through performing several PCR assays. Distribution of virulence genes among Shigella phylogenetic clades and species was determined by the statistical analysis. The identities of 40 isolates out of 44 were confirmed as Shigella, and these isolates were classified in four phylogenetic clades, S1 (7.5%), S2 (52.5%), S3 (20%), and S5 (20%) and 4 species, S. sonnei (52.5%), S. flexneri (22.5%), S. dysenteriae (20%), and S. boydii (5%). The prevalence of virA, virB, virF, ipaBCD, ial, sen, and set1A was determined as 67.5%, 72.5%, 72.5%, 65%, 75%, 40%, and 5%, respectively. The presence of sen, uidA, or set1A was found to be statistically correlated with either of Shigella phylogenetic clades or species. A significant statistically association was also determined between set1A and Shigella phylogenetic clades. Furthermore, the nucleotide sequence of invasion-associated locus (ial) was determined and mapped on Shigella genome through in silico analysis. The current study shows the distribution of Shigella isolates and its key virulence genes within the five recently described phylogenetic clades for the first time in the Asia. This is also the first description of ial nucleotide sequence and its exact location on Shigella genome after its initial identification.