Prevalence of Virulence Genes and Their Association with Antimicrobial Resistance Among Pathogenic E. coli Isolated from Egyptian Patients with Different Clinical Infections

The role of identified and characterized bacteriophage ZCEC13 in controlling pathogenic and multidrug-resistant Escherichia coli in wastewater: in vitro study

The spread and development of Multi-Drug Resistant (MDR) bacteria in wastewater became beyond control and a global public health concern. The conventional disinfectants used in wastewater treatment methods have been becoming increasingly ineffective against a range of pathogenic and MDR bacteria. Bacteriophages are considered a novel approach to microbial control. Therefore, this study aims to explore the possibility of using phages against pathogenic and MDR Escherichia coli strains isolated from wastewater treatment plants. The wastewater samples were collected from two different treatment plants for E. coli isolation. The antibiotic sensitivity profile and occurrence of virulence and resistant genes were tested in 28 E. coli isolates. Phage ZCEC13 was selected based on its promising activity and host range to undergo identification and characterization. ZCEC13 was evaluated by transmission electron microscopy, genomic sequencing, in vitro lytic activity and tested for its stability under different conditions such as pH, Ultraviolet light exposure, and temperature. The results reported that ZCEC13 belongs to the Caudoviricetes class, with a high antibacterial dynamic. Phage ZCEC13 displayed high stability at different pH values ranging from 2 to 12, good tolerance to temperatures from -4 to 65°C, and high stability at UV exposure for 120 min. Respectively, the findings showed stability of the phage under several conditions and high efficiency in killing MDR bacteria isolated from the treatment plants. Further studies are encouraged to analyse the efficacy of phages as a microbial control agent in wastewater treatment plants.

Unveiling the traits of antibiotic resistance and virulence in Escherichia coli obtained from poultry waste

Antibiotic resistance and virulence factors in avian pathogenic Escherichia coli (APEC) have become significant concerns, contributing to adverse environmental effects. The extensive use of antibiotics in poultry farming has resulted in the emergence of antibiotic-resistant APEC strains. This study prioritizes the molecular screening of APEC to uncover their antibiotic resistance and virulence attributes, with specific attention to their environmental impact. To address the imperative of understanding APEC pathogenesis, our study analyzed 50 poultry waste samples including 10 poultry litter, 15 fecal matter, 15 wastewater, and 10 anatomical waste samples. For the presence of virulence genes, 35 Escherichia coli isolates were subjected to molecular characterization. Amongst these, 27 were APEC strains demonstrating the presence of at least four virulence genes each. Notably, virulence genes such as fimH, ompA, ybjX, waaL, cvaC, hlyF, iss, ompT, and iroN were observed among all the E. coli isolates. Furthermore, eleven of the APEC strains exhibited resistance to tetracycline, ampicillin, sulphonamides, and fluoroquinolones.These findings highlight the role of APEC as a potential source of environmental pollution serving as a reservoir for virulence and resistance genes. Understanding the dynamics of antibiotic resistance and virulence in APEC is essential due to its potential threat to broiler chickens and the broader population through the food chain, intensifying concerns related to environmental pollution. Recognizing the ecological impact of APEC is essential for developing effective strategies to mitigate environmental pollution and safeguard the health of ecosystems and human populations.

Population characteristics of pathogenic Escherichia coli in puerperal metritis of dairy cows in Ningxia region of China: a systemic taxa distribution of virulence factors and drug resistance genes

Escherichia coli (E. coli) is closely associated with the occurrence of puerperal metritis in dairy cows. E. coli carries some the virulence and multi-drug resistant genes, which pose a serious threat to the health of postpartum cows. In this study, E. coli was isolated and identified from the uterine contents of postpartum cows with puerperal metritis in the Ningxia region of China, and its phylogenetic subgroups were determined. Meanwhile, virulence and drug resistance genes carried by E. coli and drug sensitivity were detected, and the characteristics of virulence and drug resistance genes distribution in E. coli phylogroups were further analyzed. The results showed that the isolation rate of E. coli in puerperal metritis samples was 95.2%. E. coli was mainly divided into phylogroups B2 and D, followed by groups A and B1, and was more connected to O157:H7, O169:H4, and ECC-1470 type strains. The virulence genes were mainly dominated by ompF (100%), traT (100%), fimH (97%), papC (96%), csgA (95%), Ang43 (93.9%), and ompC (93%), and the resistance genes were dominated by TEM (99%), tetA (71.7%), aac(3)II (66.7%), and cmlA (53.5%). Additionally, it was observed that the virulence and resistance gene phenotypes could be divided into two subgroups, with subgroup B2 and D having the highest distributions. Drug sensitivity tests also revealed that the E. coli was most sensitive to the fluoroquinolones enrofloxacin, followed by macrolides, aminoglycosides, tetracyclines, β-lactams, peptides and sulfonamides, and least sensitive to lincosamides. These results imply that pathogenic E. coli, which induces puerperal metritis of dairy cows in the Ningxia region of China, primarily belongs to the group B2 and D, contains multiple virulence and drug resistance genes, Moreover, E. coli has evolved resistance to several drugs including penicillin, lincomycin, cotrimoxazole, and streptomycin. It will offer specific guidelines reference for the prevention and treatment of puerperal metritis in dairy cows with E. coli infections in the Ningxia region of China.

Advancements in wound healing: integrating biomolecules, drug delivery carriers, and targeted therapeutics for enhanced tissue repair

Wound healing, a critical biological process vital for tissue restoration, has spurred a global market exceeding $15 billion for wound care products and $12 billion for scar treatment. Chronic wounds lead to delayed or impaired wound healing. Natural bioactive compounds, prized for minimal side effects, stand out as promising candidates for effective wound healing. In response, researchers are turning to nanotechnology, employing the encapsulation of these agents into drug delivery carriers. Drug delivery system will play a crucial role in enabling targeted delivery of therapeutic agents to promote tissue regeneration and address underlying issues such as inflammation, infection, and impaired angiogenesis in chronic wound healing. Drug delivery carriers offer distinct advantages, exhibiting a substantial ratio of surface area to volume and altered physical and chemical properties. These carriers facilitate sustained and controlled release, proving particularly advantageous for the extended process of wound healing, that typically comprise a diverse range of components, integrating both natural and synthetic polymers. Additionally, they often incorporate bioactive molecules. Despite their properties, including poor solubility, rapid degradation, and limited bioavailability, various natural bioactive agents face challenges in clinical applications. With a global research, emphasis on harnessing nanomaterial for wound healing application, this research overview engages advancing drug delivery technologies to augment the effectiveness of tissue regeneration using bioactive molecules. Recent progress in drug delivery has poised to enhance the therapeutic efficacy of natural compounds in wound healing applications.

Correlation between antimicrobial resistance, biofilm formation, and virulence determinants in uropathogenic Escherichia coli from Egyptian hospital

BACKGROUND

Uropathogenic Escherichia coli (UPEC) is the main etiological agent behind community-acquired and hospital-acquired urinary tract infections (UTIs), which are among the most prevalent human infections. The management of UPEC infections is becoming increasingly difficult owing to multi-drug resistance, biofilm formation, and the possession of an extensive virulence arsenal. This study aims to characterize UPEC isolates in Tanta, Egypt, with regard to their antimicrobial resistance, phylogenetic profile, biofilm formation, and virulence, as well as the potential associations among these factors.

METHODS

One hundred UPEC isolates were obtained from UTI patients in Tanta, Egypt. Antimicrobial susceptibility was assessed using the Kirby-Bauer method. Extended-spectrum β-lactamases (ESBLs) production was screened using the double disk synergy test and confirmed with PCR. Biofilm formation was evaluated using the microtiter-plate assay and microscopy-based techniques. The phylogenetic groups of the isolates were determined. The hemolytic activity, motility, siderophore production, and serum resistance of the isolates were also evaluated. The clonal relatedness of the isolates was assessed using ERIC-PCR.

RESULTS

Isolates displayed elevated resistance to cephalosporins (90-43%), sulfamethoxazole-trimethoprim (63%), and ciprofloxacin (53%). Ninety percent of the isolates were multidrug-resistant (MDR)/ extensively drug-resistant (XDR) and 67% produced ESBLs. Notably, there was an inverse correlation between biofilm formation and antimicrobial resistance, and 31%, 29%, 32%, and 8% of the isolates were strong, moderate, weak, and non-biofilm producers, respectively. Beta-hemolysis, motility, siderophore production, and serum resistance were detected in 64%, 84%, 65%, and 11% of the isolates, respectively. Siderophore production was correlated to resistance to multiple antibiotics, while hemolysis was more prevalent in susceptible isolates and associated with stronger biofilms. Phylogroups B2 and D predominated, with lower resistance and stronger biofilms in group B2. ERIC-PCR revealed considerable diversity among the isolates.

CONCLUSION

This research highlights the dissemination of resistance in UPEC in Tanta, Egypt. The evident correlation between biofilm and resistance suggests a resistance cost on bacterial cells; and that isolates with lower resistance may rely on biofilms to enhance their survival. This emphasizes the importance of considering biofilm formation ability during the treatment of UPEC infections to avoid therapeutic failure and/or infection recurrence.

Phage vB_Ec_ZCEC14 to treat antibiotic-resistant Escherichia coli isolated from urinary tract infections

Escherichia coli is a commensal bacterial species in the human gastrointestinal tract; however, it could be pathogenic and cause severe infections in intra and extra-intestinal sites. Uropathogenic E. coli accounts for 80-90% of urinary tract infections that can result in urosepsis and septic shock. Consequently, multidrug-resistant uropathogenic E. coli poses a considerable risk to the healthcare system worldwide. Phage therapy is demonstrated as an optimistic solution to over-the-counter antibiotics that contribute to the global issue of multidrug-resistant bacteria. This study aims to isolate a novel phage that could be implemented to cure urinary tract infections mediated by multidrug-resistant E. coli. Twenty-seven E. coli isolates were collected from patients with urinary tract infections to assess the antibacterial efficacy of phage vB_Ec_ZCEC14. Phage kinetics were encountered against the E. coli strain (EC/4), in addition to evaluating phage stability under various temperatures, pH values, and UV exposure periods. Full genome sequencing and morphological analysis were conducted for further phage characterization, which revealed that phage vB_Ec_ZCEC14 belongs to the family Straboviridae. Phage vB_Ec_ZCEC14 showed thermal tolerance at 80 ℃, pH stability between pH 3 and pH 12, and endurance to UV exposure for 45 min. The phage-host interaction results revealed that phage vB_Ec_ZCEC14 has strong and steady antibacterial action at lower concentrations (MOI 0.1). The study findings strongly indicate that phage vB_Ec_ZCEC14 holds significant promise as a potential therapeutic alternative for treatment of antibiotic-resistant uropathogenic E. coli.

Characterization of uropathogenic E. coli from various geographical locations in India

Objectives

Uropathogenic Escherichia coli (UPEC) is the most common causative agent of urinary tract infection, accounting for more than 80% of cases worldwide. This study presents data on prevalent serotypes, resistance profiles, and colonization-aiding virulence characteristics of UPEC from different geographical regions in India.

Methods

UPEC were serotyped through microtiter plate agglutination. Standard techniques were used to detect various virulence characteristics, i.e., biofilm formation (tissue culture plate method), siderophore production (screened on Chrome Azurol S agar and categorized with Csaky's and Arnow's methods), colicin release (agar overlay technique), gelatin hydrolysis (on gelatinase agar), and cell surface hydrophobicity (salt aggregation method). Antibiotic resistance profiles (against 20 antimicrobial agents) and extended-spectrum beta-lactamase (ESBL) were evaluated according to Clinical and Laboratory Standards Institute guidelines.

Results

UPEC strains exhibited very high drug resistance rates to most of the commonly used antimicrobial agents; the highest resistance rates were observed for ampicillin (63.4%), nalidixic acid (63.4%), and cefotaxime (62.1%). High rates of multi-drug resistance (63.36%), ESBL-production (34.1%), and carbapenem-resistance (25.0%) were detected in UPEC strains from all geographical regions of India. Hydrophobicity (61.2%), biofilm production (62.5%), and siderophore production (67.7%) were the most common virulence characteristics of UPEC isolates. Co-expression of virulence characteristics was common (69.8%) in UPEC strains.

Conclusion

UPEC strains with very high antimicrobial-resistance are in circulation in India, and have diverse serotypes and virulence characteristics.

The Prevalence of Alert Pathogens and Microbial Resistance Mechanisms: A Three-Year Retrospective Study in a General Hospital in Poland

The development of antibiotic resistance mechanisms hinders the treatment process. So far, there is limited data on the problem of bacterial resistance in hospitals in Central and Eastern Europe. Therefore, this study aimed to assess the prevalence of resistance mechanisms and alert pathogens based on reports regarding cultures of samples collected from general hospital patients in Poland in the period 2019-2021. This study examined the prevalence of resistance mechanisms and alert pathogens and the structure of microorganisms, including the type of diagnostic material in the hospital department. The frequency of occurrence and the trends were analysed based on Cochran's Q-test, relative change and the average annual rate of change (AARC). Of all 14,471 cultures, 3875 were positive for bacteria, and 737 were characterised by resistance mechanisms (19.0%). Alert pathogens were identified in 983 cases (24.6%), including pathogens isolated from blood samples. The most commonlyisolated bacteria were Escherichia coli (>20% of positive cultures), Enterococcus faecalis (7%), and Klebsiella pneumoniae (6%) increasing over time; Staphylococcus aureus (13%) was also found, but its proportion was decreasing over time. Extended-spectrum β-lactamase (ESBL) was the most frequent resistance mechanism in Internal Medicine (IM) (p < 0.001) and the Intensive Care Unit (ICU) (p < 0.01), as well as in ICU-COVID; this increased over the study period (AARC ↑34.9%). Methicillin-resistant Staphylococcus aureus (MRSA) (AARC ↓50.82%) and AmpC beta-lactamase (AARC ↓24.77%) prevalence fell over time. Also, the number of alert pathogens was dominant in the IM (p < 0.01) and ICU (p < 0.001). The most common alert pathogen was ESBL-positive E. coli. Gram-negative rods constitute a significant epidemiological problem in hospitals, especially the growing trend of ESBL in IM and ICU, which calls for increased control of sanitary procedures.

Molecular epidemiology and pathogenomics of extended-spectrum beta-lactamase producing- Escherichia coli and - Klebsiella pneumoniae isolates from bulk tank milk in Tennessee, USA

Introduction

The rise in extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in dairy cattle farms poses a risk to human health as they can spread to humans through the food chain, including raw milk. This study was designed to determine the status, antimicrobial resistance, and pathogenic potential of ESBL-producing -E. coli and -Klebsiella spp. isolates from bulk tank milk (BTM).

Methods

Thirty-three BTM samples were collected from 17 dairy farms and screened for ESBL-E. coli and -Klebsiella spp. on CHROMagar ESBL plates. All isolates were confirmed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and subjected to antimicrobial susceptibility testing and whole genome sequencing (WGS).

Results

Ten presumptive ESBL-producing bacteria, eight E. coli, and two K. pneumoniae were isolated. The prevalence of ESBL-E. coli and -K. pneumoniae in BTM was 21.2% and 6.1%, respectively. ESBL-E. coli were detected in 41.2% of the study farms. Seven of the ESBL-E. coli isolates were multidrug resistant (MDR). The two ESBL-producing K. pneumoniae isolates were resistant to ceftriaxone. Seven ESBL-E. coli strains carry the blaCTX-M gene, and five of them co-harbored blaTEM-1. ESBL-E. coli co-harbored blaCTX-M with other resistance genes, including qnrB19, tet(A), aadA1, aph(3'')-Ib, aph(6)-Id), floR, sul2, and chromosomal mutations (gyrA, gyrB, parC, parE, and pmrB). Most E. coli resistance genes were associated with mobile genetic elements, mainly plasmids. Six sequence types (STs) of E. coli were detected. All ESBL-E. coli were predicted to be pathogenic to humans. Four STs (three ST10 and ST69) were high-risk clones of E. coli. Up to 40 virulence markers were detected in all E. coli isolates. One of the K. pneumoniae was ST867; the other was novel strain. K. pneumoniae isolates carried three types of beta-lactamase genes (blaCTX-M, blaTEM-1 and blaSHV). The novel K. pneumoniae ST also carried a novel IncFII(K) plasmid ST.

Conclusion

Detection of high-risk clones of MDR ESBL-E. coli and ESBL-K. pneumoniae in BTM indicates that raw milk could be a reservoir of potentially zoonotic ESBL-E. coli and -K. pneumoniae.

Occurrence of virulence determinants in vibrio cholerae, vibrio mimicus, vibrio alginolyticus, and vibrio parahaemolyticus isolates from important water resources of Eastern Cape, South Africa

BACKGROUND

Virulence determinants are crucial to the risk assessment of pathogens in an environment. This study investigated the presence of eleven key virulence-associated genes in Vibrio cholerae (n = 111) and Vibrio mimicus (n = 22) and eight virulence determinants in Vibrio alginolyticus (n = 65) and Vibrio parahaemolyticus (n = 17) isolated from six important water resources in Eastern Cape, South Africa, using PCR techniques. The multiple virulence gene indexes (MVGI) for sampling sites and isolates as well as hotspots for potential vibriosis outbreaks among sampling sites were determined statistically based on the comparison of MVGI.

RESULT

The PCR assay showed that all the V. cholerae isolates belong to non-O1/non-O139 serogroups. Of the isolates, Vibrio Cholera (84%), V. mimicus (73%), V. alginolyticus (91%) and V. parahaemolyticus (100%) isolates harboured at least one of the virulence-associated genes investigated. The virulence gene combinations detected in isolates varied at sampling site and across sites. Typical virulence-associated determinants of V. cholerae were detected in V. mimicus while that of V. parahaemolyticus were detected in V. alginolyticus. The isolates with the highest MVGI were recovered from three estuaries (Sunday river, Swartkopps river, buffalo river) and a freshwater resource (Lashinton river). The cumulative MVGI for V. cholerae, V. mimicus, V. alginolyticus and V. parahaemolyticus isolates were 0.34, 0.20, 0.45, and 0.40 respectively. The targeted Vibrio spp. in increasing order of the public health risk posed in our study areas based on the MVGI is V. alginolyticus > V. parahaemolyticus > V. cholerae > V. mimicus. Five (sites SR, PA5, PA6, EL4 and EL6) out of the seventeen sampling sites were detected as the hotspots for potential cholera-like infection and vibriosis outbreaks.

CONCLUSIONS

Our findings suggest that humans having contact with water resources in our study areas are exposed to potential public health risks owing to the detection of virulent determinants in human pathogenic Vibrio spp. recovered from the water resources. The study affirms the relevancy of environmental Vibrio species to the epidemiology of vibriosis, cholera and cholera-like infections. Hence we suggest a monitoring program for human pathogenic Vibrio spp. in the environment most especially surface water that humans have contact with regularly.

Incidence and Virulence Factor Profiling of Vibrio Species: A Study on Hospital and Community Wastewater Effluents

This study aimed to determine the incidence and virulence factor profiling of Vibrio species from hospital wastewater (HWW) and community wastewater effluents. Wastewater samples from selected sites were collected, processed, and analysed presumptively by the culture dependent methods and molecular techniques. A total of 270 isolates were confirmed as Vibrio genus delineating into V. cholerae (27%), V. parahaemolyticus (9.1%), V. vulnificus (4.1%), and V. fluvialis (3%). The remainder (>50%) may account for other Vibrio species not identified in the study. The four Vibrio species were isolated from secondary hospital wastewater effluent (SHWE), while V. cholerae was the sole specie isolated from Limbede community wastewater effluent (LCWE) and none of the four Vibrio species was recovered from tertiary hospital wastewater effluent (THWE). However, several virulence genes were identified among V. cholerae isolates from SHWE: ToxR (88%), hylA (81%), tcpA (64%), VPI (58%), ctx (44%), and ompU (34%). Virulence genes factors among V. cholerae isolates from LCWE were: ToxR (78%), ctx (67%), tcpA (44%), and hylA (44%). Two different genes (vfh and hupO) were identified in all confirmed V. fluvialis isolates. Among V. vulnificus, vcgA (50%) and vcgB (67%) were detected. In V. parahaemolyticus, tdh (56%) and tlh (100%) were also identified. This finding reveals that the studied aquatic niches pose serious potential health risk with Vibrio species harbouring virulence signatures. The distribution of virulence genes is valuable for ecological site quality, as well as epidemiological marker in the control and management of diseases caused by Vibrio species. Regular monitoring of HWW and communal wastewater effluent would allow relevant establishments to forecast, detect, and mitigate any public health threats in advance.

Whole genome-based genetic insights of blaNDM producing clinical E. coli isolates in hospital settings of Pakistan

Carbapenem resistance among Enterobacterales has become a global health concern. Clinical Escherichia coli isolates producing the metallo β-lactamase NDM have been isolated from two hospitals in Faisalabad, Pakistan. These E. coli strains were characterized by MALDI-TOF, PCR, antimicrobial susceptibility testing, XbaI and S1 nuclease pulsed-field gel electrophoresis (PFGE), conjugation assay, DNA hybridization, whole genome sequencing, bioinformatic analysis, and Galleria mellonella experiments. Thirty-four blaNDM producing E. coli strains were identified among 52 nonduplicate carbapenem-resistant strains. More than 90% of the isolates were found to be multidrug resistant by antimicrobial susceptibility testing. S1 PFGE confirmed the presence of blaNDM gene on plasmids ranging from 40 kbps to 250 kbps, and conjugation assays demonstrated transfer frequencies of blaNDM harboring plasmids ranging from 1.59 × 10-1 to 6.46 × 10-8 per donor. Whole genome sequencing analysis revealed blaNDM-5 as the prominent NDM subtype with the highest prevalence of blaOXA-1, blaCTX-M-15, aadA2, aac(6')-Ib-cr, and tet(A) associated resistant determinants. E. coli sequence types: ST405, ST361, and ST167 were prominent, and plasmid Inc types: FII, FIA, FIB, FIC, X3, R, and Y, were observed among all isolates. The genetic environment of blaNDM region on IncF plasmids included partial ISAba125, the bleomycin ble gene, and a class I integron. The virulence genes terC, traT, gad, fyuA, irp2, capU, and sitA were frequently observed, and G. mellonella experiments showed that virulence correlated with the number of virulence determinants. A strong infection control management in the hospital is necessary to check the emergence of carbapenem resistance in Gram-negative bacteria.IMPORTANCEWe describe a detailed analysis of highly resistant clinical E. coli isolates from two tertiary care centers in Pakistan including carbapenem resistance as well as common co-resistance mechanisms. South Asia has a huge problem with highly resistant E. coli. However, we find that though these isolates are very difficult to treat they are of low virulence. Thus the Western world has an increasing problem with virulent E. coli that are mostly of low antibiotic resistance, whereas, South Asia has an increasing problem with highly resistant E. coli that are of low virulence potential. These observations allow us to start to devise methodologies to limit both virulence and resistance and combat problems in developing nations as well as the Western world.

Co-existence of blaIMP, blaNDM-1, and blaSHV, genes of Pseudomonas aeruginosa isolated from Quetta: Antimicrobial resistance and clinical significance

Objective

Molecular detection and co-presence of carbapenem-resistant genes in the isolates of Pseudomonas aeruginosa are less commonly reported from Quetta. In the present study, we determined to highlight the antibiotic sensitivity profile and genetic mechanism of carbapenem resistance.

Methods

The cross-sectional study was conducted from May to September 2018 at the Hi-tech laboratory, Centre for Advance Studies in Vaccinology and Biotechnology, University of Baluchistan, Quetta. Biochemical and molecular methods were ascertained for the recognition of the isolates and minimum inhibitory concentration was performed using E-test and broth microdilution methods. The molecular basis of carbapenemase activity was determined by identifying carbapenemase genes in the isolates.

Results

Of the (n=23) P. aeruginosa isolated from pus aspirates obtained from surgical/burn units, we have detected blaIMP (n=7/8) 87.5%, blaNDM-1 (n=5/8) 62.5%, and blaSHV (n=4/8) 50%. The co-existence of multiple antibiotic-resistant genes, blaIMP, blaNDM-1 and blaSHV was found in (n=2/8) 25% isolates. These isolates displayed resistance against a range of antimicrobials from β-lactams, tetracyclines, cephalosporins, quinolones, monobactams, aminoglycosides, sulphonamides, phosphoric acid, macrolides, and polypeptide groups, suggesting extensive-drug resistance.

Conclusion

The emergence of MBL and ESBL producers is an alarming threat in the region. It is of great importance to determine the resistance mechanism of bacterial bugs. The lack of new antimicrobials particularly against gram-negative bacteria is quite alarming worldwide.

Contamination Levels and Phenotypic and Genomic Characterization of Antimicrobial Resistance in Escherichia coli Isolated from Fresh Salad Vegetables in the United Arab Emirates

Contaminated fresh produce has been identified as a vehicle for human foodborne illness. The present study investigated the counts, antimicrobial resistance profile, and genome-based characterization of Escherichia coli in 11 different types of fresh salad vegetable products (n = 400) sampled from retailers in Abu Dhabi and Dubai in the United Arab Emirates. E. coli was detected in 30% of the tested fresh salad vegetable items, with 26.5% of the samples having an unsatisfactory level (≥100 CFU/g) of E. coli, notably arugula and spinach. The study also assessed the effect of the variability in sample conditions on E. coli counts and found, based on negative binominal regression analysis, that samples from local produce had a significantly higher (p-value < 0.001) E. coli count than imported samples. The analysis also indicated that fresh salad vegetables from the soil-less farming system (e.g., hydroponic and aeroponic) had significantly (p-value < 0.001) fewer E. coli than those from traditional produce farming. The study also examined the antimicrobial resistance in E. coli (n = 145) recovered from fresh salad vegetables and found that isolates exhibited the highest phenotypic resistance toward ampicillin (20.68%), tetracycline (20%), and trimethoprim-sulfamethoxazole (10.35%). A total of 20 (13.79%) of the 145 E. coli isolates exhibited a multidrug-resistant phenotype, all from locally sourced leafy salad vegetables. The study further characterized 18 of the 20 multidrug-resistant E. coli isolates using whole-genome sequencing and found that the isolates had varying numbers of virulence-related genes, ranging from 8 to 25 per isolate. The frequently observed genes likely involved in extra-intestinal infection were CsgA, FimH, iss, and afaA. The β-lactamases gene bla_CTX-M-15 was prevalent in 50% (9/18) of the E. coli isolates identified from leafy salad vegetable samples. The study highlights the potential risk of foodborne illness and the likely spread of antimicrobial resistance and resistance genes associated with consuming leafy salad vegetables and emphasizes the importance of proper food safety practices, including proper storage and handling of fresh produce.

Antibacterial effect of vitamin C against uropathogenic E. coli in vitro and in vivo

BACKGROUND

Resistance to antibiotics has increased steadily over time, thus there is a pressing need for safer alternatives to antibiotics. Current study aims to evaluate the influence of vitamin C as an antibacterial and anti-biofilm agent against uropathogenic E. coli (UPEC) strains. The expression of beta-lactamases and biofilm encoding genes among E. coli isolates before and after treating the isolates with sub MIC of vitamin C was analyzed by Real-time PCR. The in vivo assessment of the antibacterial and anti-biofilm effects of vitamin C against uropathogenic E. coli strains was done using a urinary tract infection (UTI) rat model.

RESULTS

The effective concentration of vitamin C that could inhibit the growth of most study isolates (70%) was 1.25 mg/ml. Vitamin C showed a synergistic effect with most of the studied antibiotics; no antagonistic effect was detected at all. Vitamin C showed an excellent anti-biofilm effect against studied isolates, where 43 biofilm-producing isolates were converted to non-biofilm at a concentration of 0.312 mg/ml. The expression levels of most studied genes were down-regulated after treatment of E. coli isolates with vitamin C. In vivo assessment of vitamin C in treating UTIs showed that vitamin C has a rapid curative effect as the comparable antibiotic. Administration of both vitamin C and nitrofurantoin at a lower dose for treatment of UTI in rats had a better effect.

CONCLUSION

Vitamin C as an antibacterial and anti-biofilm agent either alone or in combination with antibiotics could markedly improve UTI in experimental rats.

Occurrence of High-Risk Clonal Lineages ST58, ST69, ST224, and ST410 among Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Healthy Free-Range Chickens (Gallus gallus domesticus) in a Rural Region in Tunisia

Antimicrobial-resistant Escherichia coli isolates have emerged in various ecologic compartments and evolved to spread globally. We sought to (1.) investigate the occurrence of ESBL-producing E. coli (ESBL-Ec) in feces from free-range chickens in a rural region and (2.) characterize the genetic background of antimicrobial resistance and the genetic relatedness of collected isolates. Ninety-five feces swabs from free-range chickens associated with two households (House 1/House 2) in a rural region in northern Tunisia were collected. Samples were screened to recover ESBL-Ec, and collected isolates were characterized for phenotype/genotype of antimicrobial resistance, integrons, and molecular typing (pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST)). Overall, 47 ESBL-Ec were identified, with the following genes detected: 35 bla_CTX-M-1, 5 bla_CTX-M-55, 5 bla_CTX-M-15, 1 bla_SHV-2, and 1 bla_SHV-12. Resistance to fluoroquinolones, tetracycline, sulfonamides, and colistin was encoded by aac(6')-Ib-cr (n = 21), qnrB (n = 1), and qnrS (n = 2); tetA (n = 17)/tetB (n = 26); sul1 (n = 29)/sul2 (n = 18); and mcr-2 (n = 2) genes, respectively. PFGE and MLST identified genetic homogeneity of isolates in House 1; however, isolates from House 2 were heterogeneous. Notably, among nine identified sequence types, ST58, ST69, ST224, and ST410 belong to pandemic high-risk clonal lineages associated with extrapathogenic E. coli. Minor clones belonging to ST410 and ST471 were shared by chickens from both households. The virulence genes fyuA, fimH, papGIII, and iutA were detected in 35, 47, 17, and 23 isolates, respectively. Findings indicate a high occurrence of ESBL-Ec in free-range chickens and highlight the occurrence of pandemic zoonotic clones.

The emergence of plasmid-encoded oxacillinase and carbapenemase among uropathogenic Escherichia coli (UPEC) isolated from hospitalized patients in the North of Iran

Carbapenemase enzyme production is responsible for resistance to carbapenem among Gram-negative bacteria. This study aimed to detect common carbapenemase and oxacilinase genes among uropathogenic E. coli (UPEC) isolated from hospitalized patients in Rasht, north of Iran. In the present study, from 2000 urine samples, 263 UPEC strains were isolated from inpatients with urinary tract infections (UTI) in 2020. The Kirby-Bauer disk diffusion susceptibility test was used to determine the sensitivity or resistance of isolates to antimicrobial compounds. The double-disk test confirmed extended-spectrum β lactamase (ESBL) production phenotypically, and the presence and distribution of genes encoding carbapenemase and oxacilinase were investigated using polymerase chain reaction (PCR). Based on the findings, 13/263 isolates (8 ESBL and five non-ESBL) showed a non-susceptible phenotype to at least one of the studied carbapenem group antibiotics, and 121 (46%) isolates were ESBL-producers. PCR for oxacilinase and carbapenemase genes was done on all 126 isolates, including ESBL-positive and carbapenem-resistant strains, in which 10 (7.9%) and 25 (19.8%) isolates harbored OXA-1 and IMP genes, respectively. Also, OXA-2, OXA-10, OXA-48, VIM, and NDM genes were not found in any studied isolates. IMP and OXA-1 genes among carbapenemase-producing isolates indicate the possible spread of antibiotic-resistant strains. Hence, identification and control of ESBL and carbapenemase-producing strains, although with almost low frequency due to plasmid genes encoding carbapenemase, is essential for infection control.

Study of Virulence Genes, Antimicrobial Resistance, and Genetic Relatedness of Foodborne Salmonella Isolates from Tunisia

ABSTRACT

Nontyphoidal Salmonella strains are among the major foodborne pathogens with emerging multidrug-resistant phenotypes. In this study, antimicrobial susceptibility testing of a collection of Salmonella isolates (n = 54) recovered from poultry and bivalve molluscs was performed. The study also investigated profiling of virulence and resistance genes as well as phylogenetic relationships through pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting. Results revealed the presence of multiple virulence genes among Salmonella isolates. Salmonella intestinal infection A (siiA), Salmonella outer protein (sopB and sopE), putative 4-hydroxybutyrate coenzyme A transferase (cat2), Salmonella atypical fimbria C (safC), and Salmonella Enteritidis fimbria B (sefB) were present in most (83.32 to 100%) of the isolates, whereas the remaining tested genes (Salmonella plasmid virulence [spvC and spvB]), and the sopE gene, were exclusively detected within the serotype Enteritidis. The highest resistance rates were observed for oxacillin (94.4%), ampicillin (37%), and nalidixic acid (27.7%), followed by cefotaxime and amoxicillin-clavulanic acid (14.8%), trimethoprim-sulfamethoxazole (9.3%), and ciprofloxacin (5.5%). The results indicate that the Salmonella Enteritidis serotype possessed the widest range of virulence determinants and increasing levels of resistance. Such high-risk clones should be particularly controlled in Tunisia. Overall, increased resistance and virulence confer a selective advantage for the evolution of these bacteria and represent an alarming problem for global public health. The genetic study via PFGE and ERIC-PCR showed the high diversity of the clonal origins of these bacteria and the sources of contamination and revealed the great capacity of Salmonella to diversify within food-producing animals.

HIGHLIGHTS

Intimin (eae) and virulence membrane protein pagC genes are associated with biofilm formation and multidrug resistance in Escherichia coli and Salmonella enterica isolates from calves with diarrhea

Objectives

This study aimed to evaluate the association of the intimin (eae) and pagC genes with biofilm formation and multidrug resistance (MDR) phenotype in Escherichia coli and Salmonella enterica collected from calves with diarrhea.

Results

Fecal samples (n: 150) were collected from calves with diarrhea. Of 150 fecal samples, 122 (81.3%) were culture positive and 115/122 (94.2%) were Gram-negative bacteria. Among them, E. coli (n = 64/115, 55.6%) was the most common isolate followed by S. enterica (n = 41/115, 35.6%). Also, 10 (8.6%) isolates were other Enterobacteriaceae bacteria including Klebsiella and Proteus species. Eighty-nine isolates (77.4%) from calf diarrhea, including 52 (81.3%) E. coli and 37 (90.2%) S. enterica were MDR. The eae and pagC genes were detected in 33 (51.5%) E. coli and 28 (68.3%) S. enterica isolates, respectively. There was a strong association between these genes and biofilm formation and MDR phenotype (P-value = 0.000). All E. coli isolates carrying the eae gene were biofilm producers and MDR. Also, all pagC-positive S. enterica isolates were MDR and 25 (89.3%) isolates of them produced biofilm.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-022-06218-6.

Phage Therapy: A Different Approach to Fight Bacterial Infections

Phage therapy is one of the alternatives to treat infections caused by both antibiotic-sensitive and antibiotic-resistant bacteria, with no or low toxicity to patients. It was started a century ago, although rapidly growing bacterial antimicrobial resistance, resulting in high levels of morbidity, mortality, and financial cost, has initiated the revival of phage therapy. It involves the use of live lytic, bioengineered, phage-encoded biological products, in combination with chemical antibiotics to treat bacterial infections. Importantly, phages will be removed from the body within seven days of clearing an infection. They target specific bacterial strains and cause minimal disruption to the microbial balance in humans. Phages for medication must be screened for the absence of resistant genes, virulent genes, cytotoxicity, and their interaction with the host tissue and organs. Since they are immunogenic, applying a high phage titer for therapy exposes them and activates the host immune system. To date, no serious side effects have been reported with human phage therapy. In this review, we describe phage–phagocyte interaction, bacterial resistance to phages, how phages conquer bacterial resistance, the role of genetic engineering and other technologies in phage therapy, and the therapeutic application of modified phages and phage-encoded products. We also highlight the comparison of antibiotics and lytic phage therapy, the pros and cons of phage therapy, determinants of human phage therapy trials, phage quality and safety requirements, phage storage and handling, and current challenges in phage therapy.

Molecular Characterization of Extended Spectrum β-Lactamase (ESBL) and Virulence Gene-Factors in Uropathogenic Escherichia coli (UPEC) in Children in Duhok City, Kurdistan Region, Iraq

Background: The presence of extended-spectrum β-lactamase (ESBL)-producing bacteria among uropathogens is significantly increasing in children all over the world. Thus, this research was conducted to investigate the prevalence of E. coli and their antimicrobial susceptibility pattern, and both genes of ESBL-producing E. coli resistant and virulence factor in UTIs patients among children in Duhok Province, Kurdistan, Iraq. Method: a total of 67 E. coli were identified from 260 urine samples of pediatric patients diagnosed with UTIs aged (0−15 years) which were collected from Heevi Pediatric Teaching Hospital, from August 2021 to the end of February 2022. Result: a high proportion of UPEC infections at ages <5 years and the rates among girls (88%) were significantly higher than those among the boys. A wide variety of E. coli are resistant to most antibiotics, such as Amoxicillin, Ampicillin and Tetracycline, and 64% of them were positive for ESBL. Interestingly, the presence of both the ESBL marker genes (blaTEM, and blaCTX-M) as well as both virulence marker genes (pai and hly) were detected in above 90% of E. coli. Conclusion: the data illustrate an alarming increase in UPEC with ESBL production and the emergence of multidrug-resistant drugs in the early age of children. The public health sectors should further monitor the guidelines of using antibiotics in Kurdistan, Iraq.

Antimicrobial Resistance, Virulence Factor-Encoding Genes, and Biofilm-Forming Ability of Community-Associated Uropathogenic Escherichia coli in Western Saudi Arabia

To explore the prevalence of multidrug-resistant community-associated uropathogenic Escherichia coli (UPEC) and their virulence factors in Western Saudi Arabia. A total of 1,000 urine samples were examined for the presence of E. coli by selective plating on MacConkey, CLED, and sheep blood agar. Antimicrobial susceptibility patterns were determined using Vitek^® 2 Compact (MIC) and the disc diffusion method with Mueller-Hinton agar. Genes encoding virulence factors (kpsMTII, traT, sat, csgA, vat, and iutA) were detected by PCR. The overall prevalence of UTI-associated E. coli was low, and a higher prevalence was detected in samples of female origin. Many of the isolates exhibited resistance to norfloxacin, and 60% of the isolates showed resistance to ampicillin. No resistance to imipenem, meropenem, or ertapenem was detected. In general, half of the isolates showed multiple resistance patterns. UPEC exhibited a weak ability to form biofilms, where no correlation was observed between multidrug resistance and biofilm-forming ability. All uropathogenic E. coli isolates carried the kpsMTII, iutA, traT, and csgA genes, whereas the low number of the isolates harbored the sat and vat genes. The diversity of virulence factors harbored by community-associated UPEC may render them more virulent and further explain the recurrence/relapse cases among community-associated UITs. To the best of our knowledge, this study constitutes the first exploration of virulence, biofilm-forming ability, and its association with multidrug resistance among UPEC isolates in Saudi Arabia. Further investigations are needed to elucidate the epidemiology of community-associated UPEC in Saudi Arabia.

Antibiotic Resistance and Biofilm Development of Escherichia coli on Different Surfaces

The goal of this research is on antibiotic resistance and biofilm formation of Escherichia coli on different surfaces. 37 E.coli isolates were obtained from K.A.P. Viswanatham Government Medical College, Tiruchirappalli, Tamil Nadu, India. Biochemical assays were used to re-confirm all the isolates. Ampicillin, Cefepime, Cefotaxime, Co-trimoxazole, Tetracycline and Levofloxacin showed substantial levels of resistance. Meropenem, Tigecycline, and Colistin showed the least amount of resistance. 75.6% of the E.coli strains were multidrug resistant (MDR). Biofilm formation of E.coli was higher in TSBG than in TSB in all (polystyrene, polypropylene, glass and stainless steel) surfaces. It is evident that the presence of glucose or any sugar substrate promotes biofilm development, resulting in notable antibiotic resistance. This situation is hazardous to human health.

Correlation of phenotypic and genotypic virulence markers, antimicrobial susceptibility pattern, and outcome of Pseudomonas aeruginosa sepsis infection

INTRODUCTION

Pseudomonas aeruginosa (PA) possesses several virulence genes that enable them to evade the immune system and to cause injury in the host tissue. However, the number of studies that characterized the virulence genes profile in PA sepsis is limited.

AIM

The main objective of this study was to identify and characterize virulence genes in PA causing sepsis, as well as investigate the relationship between virulence genes, antimicrobial susceptibility patterns, and infection outcomes.

METHODOLOGY

A prospective study, conducted between October 2020-October 2021, isolates were recovered from blood samples and identified using standard microbiological procedures. Phenotypic techniques were used to screen for capsule, siderophore production, biofilm formation, serum resistance, hemolysin production, and protease. Molecular techniques were performed to screen for alginate D (alg D), exoenzyme S (Exo S), exotoxin A (tox A), phospholipase H (plc H), phospholipase N (plc N), and elastase B (las B). Kirby-Bauer disc diffusion method was used to determine the antimicrobial susceptibility pattern of isolates, which was then interpreted according to the CLSI 2021 guidelines.

RESULTS

Out of the n = 215 Gram-negative bacteria recovered from sepsis patients during our study, n = 20 were Pseudomonas aeruginosa. PA isolates were susceptible to all antibiotics tested except for 3 of the isolates that were resistant to gentamycin, 2 to imipenem, and 1 to ceftazidime, cefepime, meropenem, tobramycin, and amikacin. The most prevalent virulence genes present were capsule (100%), siderophore production (100%), alg D (100%), Las B (100%), and Tox A (100%).

CONCLUSION

Our study found that PA causing sepsis harbours a high level of virulence genes. However, the high presence of virulence factors was not statistically associated with antimicrobial susceptibility, as most isolates in our study were susceptible to the antibiotics tested.

Genomic Characterization of International High-Risk Clone ST410 Escherichia coli Co-Harboring ESBL-Encoding Genes and blaNDM-5 on IncFIA/IncFIB/IncFII/IncQ1 Multireplicon Plasmid and Carrying a Chromosome-Borne blaCMY-2 from Egypt

The accelerated dispersion of multidrug-resistant (MDR) Escherichia coli due to the production of extended-spectrum β-lactamases (ESBLs) or AmpC enzymes has been noted in Egypt, presenting a serious treatment challenge. In this study, we investigate the prevalence of ESBLs and AmpC enzymes among 48 E. coli isolates collected from patients with urinary tract infections admitted to a teaching hospital in Alexandria. Phenotypic and genotypic methods of detection are conducted. Isolates producing both enzymes are tested for the mobilization of their genes by a broth mating experiment. Whole genome sequencing (WGS) is performed for isolate EC13655. The results indicate that 80% of the isolates are MDR, among which 52% and 13% were ESBL and AmpC producers, respectively. Conjugation experiments fail to show the mobilization of blaCMY-2 in EC13655, which was chosen for WGS. In silico analysis reveals that the isolate belongs to a ST410-H24Rx high-risk clone. It coharbors the ESBL-encoding genes blaCTX-M-15, blaTEM-1, and blaOXA-1 on an IncFIA/IncFIB/IncFII/IncQ1 multireplicon plasmid. The chromosomal location of blaCMY-2 is detected with a flanking upstream copy of ISEcp1. This chromosomal integration of blaCMY-2 establishes the stable maintenance of the gene and thus, necessitates an imperative local surveillance to reduce further spread of such strains in different clinical settings.

Multidrug resistant Escherichia coli from fresh produce sold by street vendors in South African informal settlements

The aim of this study was to assess the prevalence of commensal and pathogenic Escherichia coli on informally sold fresh produce in South Africa, who harbour and express antimicrobial resistance genes and therefore pose indirect risks to public health. The majority (85.71%) of E. coli isolates from spinach, apples, carrots, cabbage and tomatoes, were multidrug resistant (MDR). Resistance to Aminoglycoside (94.81%), Cephalosporin (93.51%), Penicillin (93.51%) and Chloramphenicol (87.01%) antibiotic classes were most prevalent. Antibiotic resistance genes detected included bla_TEM (89.29%), tetA (82.14%), tetB (53.57%), tetL (46.43%), sulI (41.07%), sulII (51.79%), aadA1a (58.93%) and strAB (51.79%). A single isolate was found to harbour eae virulence factor. Moreover, E. coli isolates were grouped into the intra-intestinal infectious phylogenetic group E (28.57%), the rare group C (26.79%), the generalist group B1 (21.43%) and the human commensal group A (16.07%). Presence of MDR E. coli represents a transmission route and significant human health risk.

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.

Virulence determinant and antimicrobial resistance traits of Emerging MDR Shiga toxigenic E. coli in diarrheic dogs

Shiga-toxigenic Escherichia coli (STEC) is incriminated in severe hemorrhagic enteritis in dogs, which is considered a veterinary and public health alarm. To investigate the prevalence, antimicrobial resistance patterns, virulence determinants, and distribution of antimicrobial resistance genes in STEC strains isolated from dogs: 80 fecal samples were obtained from diseased dogs suffering from hemorrhagic diarrhea from pet animal clinics in Ismailia governorate, Egypt. The obtained samples were examined bacteriologically. Moreover, the retrieved isolates were tested for serogrouping, Congo-red binding, antimicrobial resistance, and PCR-based determination of virulence and antimicrobial resistance genes. The prevalence of E. coli in the examined diseased dogs was 23.75% (19/80). The serogrouping of the recovered isolates revealed that 84.2% of the tested isolates were distributed into three serogroups: O146 (36.8%), O111 (31.5%), and O26 (15.7%). Meanwhile, three isolates were untypable (15.8%). Moreover, all the tested E. coli serovars were positive for CR-binding. PCR revealed that the prevalence of stx1, eaeA, hlyA, and stx2 virulence genes was 100%, 100%, 100%, and 47.3%, respectively. Our findings revealed that 31.5% of the recovered isolates showed MDR to five antimicrobial classes and harbored bla_TEM, bla_CTX-M, tetA, tetB, and sul1 genes. Alarmingly, three isolates were carbapenem-resistant. Two strains harbored the bla_KPC gene, while one strain carried the bla_NDM-1 gene. Concisely, as far as we know, this is the first study that reported the existence of MDR-STEC in dogs in Egypt. The stx1 gene is the most predominant Shiga toxin gene that accompanied the STEC isolated from hemorrhagic enteritis in dogs. The emerging MDR-STEC in dogs commonly harbors bla_TEM, bla_CTX-M, sul1, tetA, tetB, and qnrA resistance genes. Meropenem, levofloxacin, and tigecycline exhibited talented antimicrobial activity against MDR-STEC isolated from dogs.

Characterization of virulence determinants and phylogenetic background of multiple and extensively drug resistant Escherichia coli isolated from different clinical sources in Egypt

Abstract

Escherichia coli is a multifaceted microbe since some are commensals, normally inhabiting the gut of both humans and animals while others are pathogenic responsible for a wide range of intestinal and extra-intestinal infections. It is one of the leading causes of septicemia, neonatal meningitis, urinary tract infections (UTIs), cystitis, pyelonephritis, and traveler’s diarrhea. The present study aims to survey the distribution and unravel the association of phylotypes, virulence determinants, and antimicrobial resistance of E. coli isolated from different clinical sources in Mansoura hospitals, Egypt. One hundred and fifty E. coli isolates were collected from different clinical sources. Antimicrobial resistance profile, virulence determinants, and virulence encoding genes were detected. Moreover, phylogenetic and molecular typing using ERIC-PCR analysis was performed. Our results have revealed that phylogroup B2 (26.67%) with the greatest content in virulence traits was the most prevalent phylogenetic group. Different virulence profiles and varying incidence of virulence determinants were detected among tested isolates. High rates of resistance to different categories of antimicrobial agents, dramatic increase of MDR (92.67%), and emergence of XDR (4%) were detected. ERIC-PCR analysis revealed great diversity among tested isolates. There was no clustering of isolates according to resistance, virulence patterns, or phylotypes. Our research has demonstrated significant phylogenetic diversity of E. coli isolated from different clinical sources in Mansoura hospitals, Dakahlia governorate, Egypt. E. coli isolates are equipped with various virulence factors which contribute to their pathogenesis in human. The elevated rates of antimicrobial resistance and emergence of MDR and XDR mirror the trend detected globally in recent years.

Key points

• Clinical E. coli isolates exhibited substantial molecular and phylogenetic diversity.

• Elevated rates of antimicrobial resistance and emergence of XDR in pathogenic E. coli.

• B2 Phylogroup with the highest VS was the most prevalent among pathogenic E. coli.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11740-x.

K1 Antigen Is Associated with Different AST Profile in Escherichia coli: A One-Month-Long Pilot Study

Escherichia coli is responsible for diseases of varying severity. The “K” antigen designates the capsular polysaccharides on the bacterial surface, which are mostly similar to those of highly pathogenic bacteria. The K1 antigen is often found in pathogenic E. coli. Aim: While the published studies on the AST profile of K1-positive E. coli have focused on pregnant women or newborns, this study aimed to characterize the AST profile of K1-positive E. coli independently of the clinical sample of isolation. Over a 4-week-long period, all patients hospitalized/consulting at the Poitiers University Hospital presenting a determined AST on E. coli were prospectively included to define their K1-status (Pastorex Meningitis) and to collect the clinical (age/sex) or biological metadata (AST/MIC). Among the 296 included samples, no differential representation was observed between K1 results regarding sample nature. K1-negative results were associated with multiple antibiotic-resistance (12.3% vs. 33.0%; p < 0.01). AST phenotypes differed between these groups, with a higher proportion of K1-negativity among resistant strains, especially on β-lactams (ureidopenicillin, 25.8% vs. 14.9%; and ampicillin/inhibitor, 50.0% vs. 26.8%; p < 0.05) or quinolone (19.8% vs. 7.0%) and sulfamethoxazole-trimethoprim (30.2% vs. 12.3%) (p < 0.01). This study analyzed E. coli ASTs in clinical samples of all types, regarding their K1-antigen status.

Co-Existence of Certain ESBLs, MBLs and Plasmid Mediated Quinolone Resistance Genes among MDR E. coli Isolated from Different Clinical Specimens in Egypt

The emergence of multi-drug resistant (MDR) strains and even pan drug resistant (PDR) strains is alarming. In this study, we studied the resistance pattern of E. coli pathogens recovered from patients with different infections in different hospitals in Minia, Egypt and the co-existence of different resistance determinants. E. coli was the most prevalent among patients suffering from urinary tract infections (62%), while they were the least isolated from eye infections (10%). High prevalence of MDR isolates was found (73%) associated with high ESBLs and MBLs production (89.4% and 64.8%, respectively). bla_TEM (80%) and bla_NDM (43%) were the most frequent ESBL and MBL, respectively. None of the isolates harbored bla_KPC and bla_OXA-48 carbapenemase like genes. Also, the fluoroquinolone modifying enzyme gene aac-(6′)-Ib-cr was detected in 25.2% of the isolates. More than one gene was found in 81% of the isolates. Azithromycin was one of the most effective antibiotics against MDR E. coli pathogens. The high MAR index of the isolates and the high prevalence of resistance genes, indicates an important public health concern and high-risk communities where antibiotics are abused.

Genomic-based characterization of Enterococcus spp.: an emerging pathogen isolated from human gut

BACKGROUND

Enterococci are ubiquitous microorganisms having diverse ecological niches but most prominently in gastrointestinal tract of humans and animals. Production of enterocins makes them a good probiotic candidate. However, their role as probiotics has become ambiguous in the last few years because of the presence of virulence factors and antibiotic resistance genes. These virulence traits are known to be transferred genetically, which makes them opportunistic pathogens in the gastrointestinal tract leading to serious concerns about their being used as probiotics. In the present study, Enterococcusspp. isolated from the human gut were subjected to Whole-Genome Sequencing (WGS) to determine the presence of resistance and virulence genes.

METHODS AND RESULTS

Four human origins Enterococcus spp. including Enterococcus faecalis, Enterococcus casseliflavus, and two Enterococcus gallinarum were isolated from human fecal samples and further cultured on blood agar. Sanger sequencing was done using Applied Biosystems 3730xl DNA Analyzer. These strains were further subjected to WGS using oxford nanopore technology MinION. Raw data were analyzed using the free online tool epi2me. The Comprehensive Antibiotic Resistance Database (CARD) and RAST (Rapid Annotation using Subsystem Technology) software were used to look for the presence of antibiotic resistance genes in these strains. Resistance determinants for clinically important antibiotics (vancomycin) and functional virulence factor genes were detected. G-view server was used for comparative genomics of all strains.

CONCLUSION

The genomic sequencing of Enterococcus suggested that E. faecalis, E. casseliflavus, and E. gallinarum strains are opportunistic pathogens, having antibiotic resistance genes. All isolates had vancomycin resistance genes, which were expressed phenotypically. Genes related to bacteriocin resistance were also present in E. casseliflavus and E. gallinarum.

Antibiotic Susceptibility, Virulome, and Clinical Outcomes in European Infants with Bloodstream Infections Caused by Enterobacterales

Mortality in neonates with Gram-negative bloodstream infections has remained unacceptably high. Very few data are available on the impact of resistance profiles, virulence factors, appropriateness of empirical treatment and clinical characteristics on patients’ mortality. A survival analysis to investigate 28-day mortality probability and predictors was performed including (I) infants <90 days (II) with an available Enterobacterales blood isolate with (III) clinical, treatment and 28-day outcome data. Eighty-seven patients were included. Overall, 299 virulence genes were identified among all the pathogens. Escherichia coli had significantly more virulence genes identified compared with other species. A strong positive correlation between the number of resistance and virulence genes carried by each isolate was found. The cumulative probability of death obtained by the Kaplan-Meier survival analysis was 19.5%. In the descriptive analysis, early age at onset, gestational age at onset, culture positive for E. coli and number of classes of virulence genes carried by each isolate were significantly associated with mortality. By Cox multivariate regression, none of the investigated variables was significant. This pilot study has demonstrated the feasibility of investigating the association between neonatal sepsis mortality and the causative Enterobacterales isolates virulome. This relationship needs further exploration in larger studies, ideally including host immunopathological response, in order to develop a tailor-made therapeutic strategy.

Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States

Fluoroquinolones and cephalosporins are critically important antimicrobial classes for both human and veterinary medicine. We previously found a drastic increase in enrofloxacin resistance in clinical Escherichia coli isolates collected from diseased pigs from the United States over 10 years (2006 to 2016). However, the genetic determinants responsible for this increase have yet to be determined. The aim of the present study was to identify and characterize the genetic basis of resistance against fluoroquinolones (enrofloxacin) and extended-spectrum cephalosporins (ceftiofur) in swine E. coli isolates using whole-genome sequencing (WGS). bla_CMY-2 (carried by IncA/C2, IncI1, and IncI2 plasmids), bla_CTX-M (carried by IncF, IncHI2, and IncN plasmids), and bla_SHV-12 (carried by IncHI2 plasmids) genes were present in 87 (82.1%), 19 (17.9%), and 3 (2.83%) of the 106 ceftiofur-resistant isolates, respectively. Of the 110 enrofloxacin-resistant isolates, 90 (81.8%) had chromosomal mutations in gyrA, gyrB, parA, and parC genes. Plasmid-mediated quinolone resistance genes [qnrB77, qnrB2, qnrS1, qnrS2, and aac-(6)-lb′-cr] borne on ColE, IncQ2, IncN, IncF, and IncHI2 plasmids were present in 24 (21.8%) of the enrofloxacin-resistant isolates. Virulent IncF plasmids present in swine E. coli isolates were highly similar to epidemic plasmids identified globally. High-risk E. coli clones, such as ST744, ST457, ST131, ST69, ST10, ST73, ST410, ST12, ST127, ST167, ST58, ST88, ST617, ST23, etc., were also found in the U.S. swine population. Additionally, the colistin resistance gene (mcr-9) was present in several isolates. This study adds valuable information regarding resistance to critical antimicrobials with implications for both animal and human health.

IMPORTANCE Understanding the genetic mechanisms conferring resistance is critical to design informed control and preventive measures, particularly when involving critically important antimicrobial classes such as extended-spectrum cephalosporins and fluoroquinolones. The genetic determinants of extended-spectrum cephalosporin and fluoroquinolone resistance were highly diverse, with multiple plasmids, insertion sequences, and genes playing key roles in mediating resistance in swine Escherichia coli. Plasmids assembled in this study are known to be disseminated globally in both human and animal populations and environmental samples, and E. coli in pigs might be part of a global reservoir of key antimicrobial resistance (AMR) elements. Virulent plasmids found in this study have been shown to confer fitness advantages to pathogenic E. coli strains. The presence of international, high-risk zoonotic clones provides worrisome evidence that resistance in swine isolates may have indirect public health implications, and the swine population as a reservoir for these high-risk clones should be continuously monitored.

Relationship between Virulence and Resistance among Gram-Negative Bacteria

Bacteria present in the human body are innocuous, providing beneficial functions, some of which are necessary for correct body function. However, other bacteria are able to colonize, invade, and cause damage to different tissues, and these are categorised as pathogens. These pathogenic bacteria possess several factors that enable them to be more virulent and cause infection. Bacteria have a great capacity to adapt to different niches and environmental conditions (presence of antibiotics, iron depletion, etc.). Antibiotic pressure has favoured the emergence and spread of antibiotic-resistant bacteria worldwide. Several studies have reported the presence of a relationship (both positive and negative, and both direct and indirect) between antimicrobial resistance and virulence among bacterial pathogens. This review studies the relationship among the most important Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) taking into account two points of view: (i) the effect the acquisition of resistance has on virulence, and (ii) co-selection of resistance and virulence. The relationship between resistance and virulence among bacteria depends on the bacterial species, the specific mechanisms of resistance and virulence, the ecological niche, and the host.