Significant association between genes encoding virulence factors with antibiotic resistance and phylogenetic groups in community acquired uropathogenic Escherichia coli isolates

Third-Generation Cephalosporin-Resistant Uropathogenic Escherichia coli From Community- and Hospital-Acquired Infections Show High Level of Antibiotic Resistance and Specific Virulence Traits

Escherichia coli is a leading cause of both community-acquired and nosocomial infections. In particular, E. coli is responsible for 90% of all uncomplicated urinary tract infections (UTIs) and 65% of complicated UTIs. Among complicated UTIs, those caused by third-generation cephalosporin (3GC)-resistant E. coli strains, expressing extended-spectrum beta-lactamases (ESBLs), are on the rise. These strains show often a multidrug-resistant (MDR) phenotype, limiting the therapeutic options and the increasing incidence of MDR E. coli in Algeria is concerning. This study aims to compare the antibiotic resistance rates and profiles as well as the virulence traits between 3CG-resistant E. coli isolates, collected from Algerian inpatients (IPs) and outpatients (OPs). Our analyses include phenotypic and genotypic resistance factor detection, strains classification by genotyping and phylogrouping, as well as genotypic and phenotypic virulence factor evaluation. Among 42 E. coli isolates, 76.20% caused UTIs. ESBL producers (n = 35) carried all the bla CTX-M, while bla TEM was found in 69.04% of isolates. All isolates were MDR, and no significant differences in type and rate of antibiotic resistance were observed between IP- and OP-isolates. OP-isolates demonstrated greater virulence, exhibiting higher motility and biofilm production, compared to IP-isolates. Moreover, pathogenic Phylogroup B2 was prevalent among OP-isolates, while IP-isolates belonged predominantly to Phylogroup A. Our data suggest a uniform spreading of antibiotic-resistant genes within hospitals and communities. However, hospital environment selects for less virulent strains with increasing level of resistance; differently, communities host more virulent strains. This study highlights the urgent need to implement the surveillance of 3CG-resistant E. coli and to adopt the One Health approach to monitor the antimicrobial resistance (AMR) in the country.

Listeria monocytogenes and Listeriosis: The Global Enigma

Listeria monocytogenes is an intracellular, Gram-positive, non-spore-forming, non-encapsulated, facultative anaerobic, rod-shaped, and psychrotrophic food-borne pathogen that causes the infection, listeriosis, thus it attracts great attention following listeriosis outbreaks, which are often associated with high mortality rates. The prevalence of listeriosis is quite low globally; however, the most recent and deadliest outbreak occurred in South Africa, during which 216 persons lost their lives. L. monocytogenes is endowed with the potential to multiply through a wide range of harsh environmental conditions, forming biofilms on varying surfaces in the food industry, as well as having persistent and antibiotic-resistant cells, which pose a major threat and burden to the ready-to-eat food industry. A more frustrating characteristic of this bacterium is its strain divergence, alongside an increased level of antibiotic resistance registered among the strains of L. monocytogenes recovered from food, humans, and environmental sources, especially to those antibiotics involved in the treatment of human listeriosis. Antibiotic resistance exerted by and among pathogenic food-borne microbes is an ongoing public health menace that continues to be an issue. Against this background, a thorough search into different databases using various search engines was performed, which led to the gathering of salient information that was organised, chronologically, based on Listeria monocytogenes and listeriosis. Altogether, the findings elaborated in this study present up-to date knowledge on different aspects of this pathogen which will improve our understanding of the mystery associated with it and the ways to prevent and control its dissemination through ready-to-eat foods. In addition, constant monitoring of the antibiotic resistance profiles of strains of L. monocytogenes from varying sources detected changes, giving an update on the trend in antibiotic resistance. Overall, monitoring of bacterial contamination serves as the key aspect in the control of the food safety output in the food industry.

Influence of bacterial morphotype on urine culture and molecular epidemiological differences in Escherichia coli harboring bacterial morphotype-induced urinary tract infections

Bacteria that adhere to epithelial cells, form intracellular bacterial communities (IBCs), or transition to filamentous forms are referred to as morphotype-positive bacteria. Escherichia coli (E. coli) with this morphotype plays a critical role in urinary tract infections (UTIs), yet its impact on urine culture outcomes and molecular epidemiological characteristics remains unclear. In this retrospective study, we assessed the effect of bacterial morphotype on urine culture results and investigated the molecular differences between E. coli strains with and without this morphotype, using PCR and whole genome sequencing (WGS). We observed that E. coli with the morphotype-positive phenotype frequently appeared in urine sediments, leading to fewer colony-forming units (CFUs) in culture and contributing to false-negative results. However, vortexing the urine samples significantly increased CFUs, improving culture sensitivity. Additionally, E. coli with the positive morphotype carried more adhesion-related virulence genes (VGs), with the majority belonging to phylogenetic group B2. Whole genome sequencing further revealed a broader array of virulence genes in these strains. Our findings demonstrate that vortexing is an effective method to enhance urine culture positivity by releasing intracellular bacteria, and that morphotype-positive E. coli harbors a diverse set of virulence factors, indicating their potential high pathogenicity. These results highlight the importance of detecting bacterial morphotypes in urine samples for accurate UTI diagnosis and emphasize the need for increased attention to these highly virulent strains.

IMPORTANCE

Uropathogenic Escherichia coli (UPEC) is widely acknowledged as the primary pathogen responsible for urinary tract infections (UTIs). Following adherence to the epithelium, UPEC undergoes periodic morphological changes, such as filamentation, which not only contribute to immune evasion but also lead to false-negative results. This study focuses on three transient stages of UPEC morphological changes: adherence to the epithelium, formation of intracellular bacterial communities (IBCs), and the presence of filamentous UPEC. Any one of these characteristics is acceptable to classify UPEC strains as morphotype-positive UPEC. This study reported the prevalence of UPEC with the bacterial morphotype and established a direct relationship between urine culture and bacterial morphotype. The molecular epidemiological distinctions were both revealed. These findings provide further evidence of the necessary for bacterial morphotype detection, and greater attention should be given to E. coli harboring this bacterial morphotype.

Understanding the Burden and Management of Urinary Tract Infections in Women

Urinary tract infections (UTIs) represent a prevalent health concern among the female population, with anatomical and physiological determinants such as a shorter urethra and its proximity to the rectum augmenting vulnerability. The presence of Escherichia coli and various other pathogens plays a significant role in the etiology of these infections, which can be aggravated by sexual intercourse and disturbances to the vaginal microbiome. The physiological alterations associated with pregnancy further elevate the likelihood of UTIs, with untreated cases potentially leading to severe complications such as pyelonephritis, preterm labor, and stillbirth. Furthermore, postmenopausal women encounter an augmented risk of UTIs attributable to estrogen deficiency and vaginal atrophy, as well as conditions including pelvic organ prolapse (POP) and urinary incontinence (UI), which hinder optimal bladder functionality. The aforementioned factors, in conjunction with the rising prevalence of cesarean deliveries and catheterization, complicate the management of UTIs. While precise diagnosis is paramount, it remains a formidable challenge, notwithstanding advancements in molecular diagnostic techniques. Management strategies encompass antibiotic-sparing therapies; however, the increasing incidence of multidrug resistance represents an alarming trend. Diverse guidelines from various medical specialties endeavor to standardize treatment approaches, yet significant inconsistencies continue to exist. This study systematically appraises the extant guidelines, evaluating the quality of evidence while identifying areas of agreement and discord to supply practitioners with effective strategies for UTI management.

Genomic and Drug Resistance Profile of Bovine Multidrug-Resistant Escherichia coli Isolated in Kazakhstan

While studying the prevalence and profile of antibiotic resistance among E. coli isolated from the feces of calves with signs of colibacillosis, a strain with a wide spectrum of drug resistance was isolated. Whole-genome sequencing, followed by bioinformatic processing and the annotation of genes of this strain, showed that the genome has a total length of 4,803,482 bp and contains 4986 genes, including 122 RNA genes. A total of 31% of the genes are functionally significant and represent 26 functional groups. Additionally, 55 antibiotic resistance genes were revealed. A phenotypic drug-resistance study was performed according to CASFM and CLSI guidelines, which showed that the investigated strain was resistant to eight antibacterial drugs of different classes, including colistin. This is the first report on the AMR profile of an E. coli isolate obtained from a sick calf with evidence of escherichiosis in Kazakhstan. The provided information on the genome will be valuable in studying the evolution and development of antibiotic-resistant forms of E. coli and increase our knowledge of pathogenicity. It may also be a source for future comparative studies of the virulence and drug resistance of E. coli isolates.

Antimicrobial resistance in wild game mammals: a glimpse into the contamination of wild habitats in a systematic review and meta-analysis

BACKGROUND

Wild game meat has over the years gained popularity across the globe as it is considered a food source with high protein content, low fat content, and a balanced composition of fatty acids and minerals, which are requirements for a healthy diet. Despite this popularity, there is a concern over its safety as many species of wildlife are reservoirs of zoonotic diseases including those of bacterial origin, more so antibiotic-resistant bacteria.

METHODS

This study aimed to describe the prevalence of antibiotic-resistant bacteria in mammalian wild game, following the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines.

RESULTS

The overall pooled prevalence of antibiotic resistance was established at 59.8% while the prevalence of multidrug resistance (MDR) was 17.2%. Resistance was reported in 32 wild game species and the meta-analysis revealed the highest prevalence of antibiotic resistance in Yersinia spp. (95.5%; CI: 76.8 - 100%) followed by Enterococcus spp. (71%; CI: 44.1 - 92%), Salmonella spp. (69.9%; CI: 44.3 - 90.0%), Staphylococcus spp. (69.3%; CI: 40.3 - 92.3%), and Escherichia coli (39.5%; CI: 23.9 - 56.4%). Most notably, resistance to highest priority, critically important antimicrobials, was recorded in all genera of bacteria studied. Additionally, a significantly higher prevalence of antibiotic resistance was observed in studies conducted in remote settings than those in the vicinity of anthropogenic activities, pointing to extensive contamination of wild habitats.

CONCLUSION

This review shows the presence of antibiotic resistance and the carriage of antimicrobial resistance (AMR) genes by bacteria isolated from mammalian wild game species. This is a cause for concern if critical steps to prevent transmission to humans from meat and meat products are not applied in the wild game meat production chain. The extensive occurrence of antibiotic resistance in the wild calls for expansion and adaptation of future AMR surveillance plans to include areas with various anthropogenic pressures including in sylvatic habitats.

Molecular Assessment Using the MASTDISCS® Combi D72C Set for the Phenotypic Detection of Extended-Spectrum Beta-Lactamases, AmpC Beta-Lactamases, and Carbapenemase Enzymes in Escherichia coli and Klebsiella pneumoniae

Beta-lactam resistance poses a global issue and a considerable challenge to effective antimicrobial therapy. The study aimed to ascertain the phenotypic and genotype traits of carbapenemase, extended-spectrum beta (β)-lactamases (ESBL), and AmpC β-lactamase-producing isolates collected from hospitals. A range of clinical samples consisted of 63 Escherichia coli (E. coli) and 30 Klebsiella pneumoniae (K. pneumoniae) isolates. Phenotypic characterization was carried out utilizing the MASTDISCS® Combi ESBL, AmpC, and carbapenemase detection set-D72C (Mast Group Ltd, Bootle, United Kingdom). Molecular assays were used to detect carbapenemase, ESBL, and AmpC genes. Both E. coli and K. pneumoniae clinical isolates exhibited noticeably enhanced resistance to β-lactam antibiotics. MASTDISCS® Combi D72C phenotype detection tests revealed that 57 (90.6%) E. coli and 30 (100%) K. pneumoniae isolates produced ESBL and AmpC enzymes, with evidence of carbapenemase activity. The majority of isolates had at least one β-lactamase-related gene. Based on molecular findings, the majority of ESBL-producing isolates in both pathogens had 17 (56.6%) of the blaCTX-M gene in K. pneumoniae and 16 (53.3%) of the blaSHV gene in both pathogens. The AmpC-associated genes, both blaCMY1, and blaCMY2, were exposed in five (16.6%) K. pneumoniae isolates and nine (30%) and 10 (33.3%) among E. coli, respectively. In terms of the carbapenemase gene, blaOXA was the most prevalent gene, appearing in 20 (66.6%) of the two pathogens.This study demonstrated that K. pneumoniae and E. coli that produceβ-lactamases have emergedas pathogens linked to infections in healthcare settings. Accurate identification of β-lactamase-producing bacterial pathogens is essential for patient treatment. We observed co-expression of AmpC, carbapenemase, and ESBL genes in most isolates, indicating a need to implement modern plans against these pathogens.

Emergence of extensively-drug-resistant hypervirulent Acinetobacter baumannii isolated from patients with bacteraemia: bacterial phenotype and virulence analysis

OBJECTIVES

Individuals infected with extensively-drug-resistant (XDR) Acinetobacter baumannii are difficult to cure and have a high mortality rate. This study compared the genomic and phenotypic differences between XDR and non-multi-drug-resistant (MDR) A. baumannii, and further characterized hypervirulent XDR A. baumannii.

METHODS

In total, 1403 acinetobacter isolates were collected from patients with bacteraemia between 1997 and 2015. Antimicrobial susceptibility tests were performed to categorize isolates into non-MDR, MDR and XDR groups. The presence of selected virulence-associated genes was determined by polymerase chain reaction. Bacterial phenotypes, including iron acquisition, biofilm formation, capsule production, and virulence to larvae and mice, were determined.

RESULTS

Multi-locus sequence typing revealed a high prevalence of sequence type (ST) 2 (81.6%) and ST129 (18.4%) among 49 XDR isolates, and the STs of 18 non-MDR isolates were more diverse. Virulence-associated phenotypic assays showed that XDR isolates had higher iron acquisition ability, greater capsule production, and virulence to Galleria mellonella larvae. However, their ability to form biofilm was lower compared with that of non-MDR isolates. XDR isolates were more likely to have virulence genes (tonB, hemO, abaI and ptk), while non-MDR isolates were more likely to have pld and ompA genes. Twenty-one XDR isolates that had a <20% larvae survival rate after 7 days post-infection were defined as hypervirulent XDR isolates. Among them, isolates 1677 (ST129) and 929-1 (ST2) caused the death of all infected mice within 2 days.

CONCLUSION

Some subpopulations of highly-drug-resistant ST2 isolates exhibit high virulence. As such, it is of utmost importance to continue monitoring the spread of hypervirulent XDR A. baumannii isolates.

Characterization of microbiome, resistome, mobilome, and virulome in anoxic and oxic wastewater treatment processes in Slovakia and Taiwan

This study presents a comprehensive analysis of samples from urban wastewater treatment plants using anoxic/oxic processes in Slovakia and Taiwan, focusing on microbiome, resistome, mobilome, and virulome, which were analyzed using a shotgun metagenomic approach. Distinct characteristics were observed; in Taiwan, a higher abundance and diversity of antibiotic resistance genes were found in both influent and effluent samples, while there was a higher prevalence of mobile genetic elements and virulence factor genes in Slovakia. Variations were noted in microbial community structures; influent samples in Taiwan were reflected from fecal and hospital sources, and those in Slovakia were derived from environmental elements. At the genus level, the samples from Taiwan's sewage treatment plants were dominated by Cloacibacterium and Bacteroides, while Acinetobacter was predominant in samples from Slovakia. Despite similar antibiotic usage patterns, distinct wastewater characteristics and operational disparities influenced microbiome, resistome, mobilome, and virulome compositions, with limited reduction of most resistance genes by the studied anoxic/oxic processes. These findings underscore the importance of region-specific insights into microbial communities for understanding the dynamics of antimicrobial resistance and pathogenicity in urban wastewater treatment systems. Such insights may lay the groundwork for optimizing treatment processes and reducing the dissemination of antibiotic resistance and pathogenicity genes for safeguarding public health.

Evolutionary principles for modifying pathogen virulence

Current methods for combatting infectious diseases are largely limited to the prevention of infection, enhancing host immunity (via vaccination), and administration of small molecules to slow the growth of or kill pathogens (e.g. antimicrobials). Beyond efforts to deter the rise of antimicrobial resistance, little consideration is given to pathogen evolution. Natural selection will favor different levels of virulence under different circumstances. Experimental studies and a wealth of theoretical work have identified many likely evolutionary determinants of virulence. Some of these, such as transmission dynamics, are amenable to modification by clinicians and public health practitioners. In this article, we provide a conceptual overview of virulence, followed by an analysis of modifiable evolutionary determinants of virulence including vaccinations, antibiotics, and transmission dynamics. Finally, we discuss both the importance and limitations of taking an evolutionary approach to reducing pathogen virulence.

Phylogenetic diversity and virulence gene characteristics of Escherichia coli from pork and patients with urinary tract infections in Thailand

Extraintestinal pathogenic Escherichia coli (ExPEC), especially uropathogenic E. coli (UPEC) are responsible for urinary tract infections (UTIs), while diarrheagenic E. coli (DEC) cause foodborne illnesses. These pathogenic E. coli are a serious threat to human health and a public concern worldwide. However, the evidence on pork E. coli (PEC) harboring UPEC virulence-associated genes is currently limited. Therefore, this study aimed to determine the phylogroups, virulence genes, and their association between PEC and UPEC from UTI patients. In this study, 330 E. coli were obtained from archived stock culture isolated from pork (PEC; n = 165) and urine of patients with UTIs (UPEC; n = 165) during 2014-2022. Phylogroups, UPEC- and diarrheagenic E. coli (DEC) associated virulence genes were assessed using PCR assays. The results showed that phylogroups A (50.3%), and B1 (32.1%) were commonly found among PEC whereas phylogroups B2 (41.8%), and C (25.5%) were commonly detected in the UPEC. PEC and UPEC carried similar virulence-associated genes with different percentages. The most frequent UPEC virulence-associated gene among UPEC, and PEC strains was fimH, (93.3%, and 92.1%), followed by iucC (55.2%, and 12.7%), papC (21.8%, and 4.2%), afaC (22.4%, and 0%), hlyCA (17%, and 0.6%), cnf (16.4%, and 0.6%), and sfa/focDE (8.5%, and 4.8%). Additionally, 6 of 27 UPEC virulence-associated gene patterns were found in both PEC and UPEC strains regardless of phylogroups. Furthermore, the DEC virulence-associated genes were found in only 3 strains, one from PEC harboring eae, and two from UPEC carried fimH-bfpA or afaC-CVD432 indicating hybrid strains. Cluster analysis showed a relationship between PEC and UPEC strains and demonstrated that PEC harboring UPEC virulence-associated genes in pork may be associated with UPEC in humans. Food safety and hygiene practices during pork production chain are important procedures for minimizing cross-contamination of these strains that could be transmitted to the consumers.

Molecular typing and virulence characteristics of Escherichia coli strains isolated from hospital and community acquired urinary tract infections

BACKGROUND

The main causes of hospital- and community-acquired urinary tract infections (UTIs) are a group of Escherichia coli (E. coli) strains with multiple virulence factors known as uropathogenic E. coli.

METHODS AND RESULTS

One hundred E. coli isolates from the urine specimens of hospital- and community-acquired UTI patients were characterized based on their virulence factors and genetic relatedness using PCR and RAPD‒PCR, respectively. Among all, the traT (71%), sitA (64%), ompT (54%), malX (49%), ibeA (44%), tsh (39%), hlyD (18%) and cnf1 (12%) genes had the highest to lowest frequencies, respectively. There was no significant difference between the frequency of tested virulence genes in E. coli isolates from inpatients and outpatients. The frequency of the hlyD gene was significantly greater in E. coli isolates from patients hospitalized in gynecology, dermatology and intensive care unit (ICU) wards than in those from other wards. Eight virulence gene patterns were common among the isolates of inpatients in different wards of the same hospital, of which five patterns belonged to the isolates of inpatients in the same ward. More E. coli isolates with similar virulence gene patterns and greater genetic similarity were found in female patients than in male patients. The analysis of the RAPD‒PCR dendrograms revealed more genetic similarities among the E. coli isolates from inpatients than among those from outpatients.

CONCLUSION

Our findings indicate the presence of a wide variety of virulence factors in E. coli isolates and the possibility of spreading the same clones in different wards of the hospital.

Resistant Escherichia coli isolated from wild mammals from two rescue and rehabilitation centers in Costa Rica: characterization and public health relevance

This study aimed to characterize the antimicrobial resistance (AMR) and virulence profiles of 67 Escherichia coli isolates obtained from faecal samples of 77 wild mammals from 19 different species, admitted in two rescue and rehabilitation centers in Costa Rica. It was possible to classify 48% (n = 32) of the isolates as multidrug-resistant, and while the highest resistance levels were found towards commonly prescribed antimicrobials, resistance to fluoroquinolones and third generation cephalosporins were also observed. Isolates obtained from samples of rehabilitated animals or animals treated with antibiotics were found to have significantly higher AMR levels, with the former also having a significant association with a multidrug-resistance profile. Additionally, the isolates displayed the capacity to produce α-haemolysins (n = 64, 96%), biofilms (n = 51, 76%) and protease (n = 21, 31%). Our results showed that AMR might be a widespread phenomenon within Costa Rican wildlife and that both free-ranging and rehabilitated wild mammals are potential carriers of bacteria with important resistance and virulence profiles. These results highlight the need to study potential sources of resistance determinants to wildlife, and to determine if wild animals can disseminate resistant bacteria in the environment, potentially posing a significant threat to public health and hindering the implementation of a "One Health" approach.

Enterobacterales Biofilm-Specific Genes and Antimicrobial and Anti-Inflammatory Biomarkers in the Blood of Patients with Ischemic Heart Disease

BACKGROUND

Ischemic heart disease (IHD) is the most prevalent type of cardiovascular disease. The main cause of IHD is atherosclerosis, which is a multifactorial inflammatory disease of blood vessels. Studies show that bacteria might have a significant impact on the pathogenesis of atherosclerosis and plaque rupture. This study aimed to evaluate the complexity of interactions between bacteria and the human body concerning metabolites and bacterial genes in patients with ischemic heart disease.

METHODS

Bacterial 16S rDNA and wcaF, papC, and sdhC genes were detected in whole blood using a real-time PCR methodology. An enzyme-linked immunosorbent assay was used to measure the concentration of the LL-37 protein. An analysis of ARA in blood plasma was performed.

RESULTS

Bacterial 16S rDNA was detected in 31% of the study patients, and the genes wcaF and sdhC in 20%. Enterobacterales genes were detected more frequently in patients younger than 65 years than in patients aged 65 years and older (p = 0.018) and in patients with type 2 diabetes (p = 0.048). Concentrations of the human antimicrobial peptide LL-37 and 12S-HETE concentrations were determined to be higher if patients had 16S rDNA and biofilm-specific genes.

CONCLUSIONS

The results of this study enhance the understanding that Enterobacterales bacteria may participate in the pathogenesis of atherosclerosis and IHD. Bacterial DNA and host metabolites in higher concentrations appear to be detected.

Characteristics of MDR E. coli strains isolated from Pet Dogs with clinic diarrhea: A pool of antibiotic resistance genes and virulence-associated genes

The increasing number of multi-drug resistant (MDR) bacteria in companion animals poses a threat to both pet treatment and public health. To investigate the characteristics of MDR Escherichia coli (E. coli) from dogs, we detected the antimicrobial resistance (AMR) of 135 E. coli isolates from diarrheal pet dogs by disc diffusion method (K-B method), and screened antibiotic resistance genes (ARGs), virulence-associated genes (VAGs), and population structure (phylogenetic groups and MLST) by polymerase chain reaction (PCR) for 74 MDR strains, then further analyzed the association between AMRs and ARGs or VAGs. Our results showed that 135 isolates exhibited high resistance to AMP (71.11%, 96/135), TET (62.22%, 84/135), and SXT (59.26%, 80/135). Additionally, 54.81% (74/135) of the isolates were identified as MDR E. coli. In 74 MDR strains, a total of 12 ARGs in 6 categories and 14 VAGs in 4 categories were observed, of which tetA (95.95%, 71/74) and fimC (100%, 74/74) were the most prevalent. Further analysis of associations between ARGs and AMRs or VAGs in MDR strains revealed 23 significant positive associated pairs were observed between ARGs and AMRs, while only 5 associated pairs were observed between ARGs and VAGs (3 positive associated pairs and 2 negative associated pairs). Results of population structure analysis showed that B2 and D groups were the prevalent phylogroups (90.54%, 67/74), and 74 MDR strains belonged to 42 STs (6 clonal complexes and 23 singletons), of which ST10 was the dominant lineage. Our findings indicated that MDR E. coli from pet dogs carry a high diversity of ARGs and VAGs, and were mostly belong to B2/D groups and ST10. Measures should be taken to prevent the transmission of MDR E. coli between companion animals and humans, as the fecal shedding of MDR E. coli from pet dogs may pose a threat to humans.

Comparative study of virulence potential, phylogenetic origin, CRISPR-Cas regions and drug resistance of Escherichia coli isolates from urine and other clinical materials

INTRODUCTION

Urinary tract infections (UTI), among which the main etiological factor is uropathogenic Escherichia coli (UPEC, E. coli), remain an important issue for clinicians. The aim of the study was to demonstrate clear differences in the pathogenic properties of urine-derived E. coli compared to other extraintestinal E. coli clinical isolates (derived from: blood, lower respiratory tracts, sputum, reproductive tract, body fluids, perianal pus, other pus, wound, postoperative wound and other sources).

METHODS

The collection of 784 E. coli isolates was collected from various materials of hospitalized patients. They were analyzed in terms of virulence-associated genes (papC, sfaD/sfaE, cnf1, usp., fimG/H, hlyA), belonging to phylogenetic groups and the presence of CRISPR-Cas regions using PCR. In addition, the epidemiological data and the antibiotic resistance profiles provided by the hospital's microbiology department were included for statistical analyses.

RESULTS

Urine-derived E. coli showed significantly greater virulence potential compared to other isolates, but they were generally unremarkable in terms of drug resistance. The isolates most often belonged to phylogenetic group B2. Drug resistance was negatively correlated with CRISPR 2 presence and high average virulence score, but positively correlated with CRISPR 4 presence. To the best of our knowledge, we are the first to report significant differences in sputum-derived isolates-they revealed the lowest virulence potential and, at the same time, the highest drug resistance.

DISCUSSION

In conclusion, we demonstrated significant differences of urinary-derived E. coli compared to other clinical E. coli isolates. We would like to suggest excluding penicillins from use in E. coli infection at this time and monitoring strains with a high pathogenicity potential.

Quinolone resistance and biofilm formation capability of uropathogenic Escherichia coli isolates from an Iranian inpatients' population

BACKGROUND

Uropathogenic Escherichia coli (UPEC) is a major pathogen of the urinary tract infection (UTI), and biofilm formation is crucial as it facilitates the colonization in the urinary tract. We aimed to investigate the antibiotic susceptibility pattern, biofilm formation capability, distribution of quinolone resistance genes, and phylogenetic groups among UPEC isolates from an Iranian inpatients' community.

METHODS AND RESULTS

A collection of 126 UPEC obtained from hospitalized patients with symptomatic UTI at 3 teaching hospitals during 2016 were included. Antibiogram of all isolates against quinolone and fluoroquinolones was performed using the disk diffusion method. Phylogenetic groups and qnr A, B, and S genes were assessed by PCR. Susceptibility pattern showed that more than 50% and 81% of the isolates were resistant to fluoroquinolones and quinolones, correspondingly. The frequency of qnrS and qnrB genes was 22% and 13.5%, correspondingly. Our result indicated no significant association between the presence of fluoroquinolone genes and antibiotic resistance to them. The frequent common phylogroup was B2 (84.1%), followed by D (10.3%), A (3.2%) and B1 (2.4%) groups. Indeed, 80.2% of the isolates were biofilm producers, so that 42.1%, 16.7% and 21.4% of them were classified as weak, moderate and strong producers, respectively.

CONCLUSIONS

Our results showed considerable fluoroquinolone and quinolone resistance among UPEC along with a remarkable rate of biofilm-producing isolates from symptomatic hospitalized patients, making them a serious health concern in the region. This survey highlights the need for awareness on quinolone resistance and careful prescription of them by physicians.

Antibiotic resistance and virulence genes profiling of Vibrio cholerae and Vibrio mimicus isolates from some seafood collected at the aquatic environment and wet markets in Eastern Cape Province, South Africa

The current study determines the density of Vibrio spp. and isolates V. cholerae and Vibrio mimicus from fish-anatomical-sites, prawn, crab and mussel samples recovered from fish markets, freshwater and brackish water. Virulence and antibiotic resistance profiling of isolates were carried out using standard molecular and microbiology techniques. Vibrio spp. was detected in more than 90% of samples [134/144] and its density was significantly more in fish than in other samples. Vibrio. cholerae and V. mimicus were isolated in at least one sample of each sample type with higher isolation frequency in fish samples. All the V. cholerae isolates belong to non-O1/non-O139 serogroup. One or more V. cholerae isolates exhibited intermediate or resistance against each of the eighteen panels of antibiotics used but 100% of the V. mimicus were susceptible to amikacin, gentamycin and chloramphenicol. Vibrio cholerae exhibited relatively high resistance against polymyxin, ampicillin and amoxicillin/clavulanate while V. mimicus isolates exhibited relatively high resistance against nitrofurantoin, ampicillin and polymixin. The multiple-antibiotic-resistance-index [MARI] for isolates ranges between 0 and 0.67 and 48% of the isolates have MARI that is >0.2 while 55% of the isolates exhibit MultiDrug Resistance Phenotypes. The percentage detection of acc, ant, drf18, sul1, mcr-1, blasvh, blaoxa, blatem, blaoxa48, gyrA, gyrB and parC resistance-associated genes were 2%, 9%, 14%, 7%, 2%, 25%, 7%, 2%, 2%, 32%, 25% and 27% respectively while that for virulence-associated genes in increasing other was ace [2%], tcp [11%], vpi [16%], ompU [34%], toxR [43%], rtxC [70%], rtxA [73%] and hyla [77%]. The study confirmed the potential of environmental non-O1/non-O139 V. cholerae and V. mimicus to cause cholera-like infection and other vibriosis which could be difficult to manage with commonly recommended antibiotics. Thus, regular monitoring of the environment to create necessary awareness for this kind of pathogens is important in the interest of public health.

Genomic analysis of multidrug-resistant Escherichia coli strains carrying the mcr-1 gene recovered from pigs in Lima-Peru

Antibiotic resistance is a current problem that significantly impacts overall health. The dissemination of antibiotic resistance genes (ARGs) to urban areas primarily occurs through ARG-carrying bacteria present in the gut microbiota of animals raised in intensive farming settings, such as pig production. Hence, this study aimed to isolate and analyzed 87 Escherichia coli strains from pig fecal samples obtained from intensive farms in Lima Department. The isolates were subjected to Kirby-Bauer-Disk Diffusion Test and PCR for mcr-1 gene identification. Disk-diffusion assay revealed a high level of resistance among these isolates to oxytetracycline, ampicillin, cephalothin, chloramphenicol, ciprofloxacin, and doxycycline. PCR analysis identified the mcr-1 gene in 8% (7/87) E. coli isolates. Further, whole genome sequencing was conducted on 17 isolates, including multidrug resistance (MDR) E. coli and/or mcr-1 gene carriers. This analysis unveiled a diverse array of ARGs. Alongside the mcr-1 gene, the bla_CTX-M55 gene was particularly noteworthy as it confers resistance to third generation cephalosporins, including ceftriaxone. MDR E. coli genomes exhibited other ARGs encoding resistance to fosfomycin (fosA3), quinolones (qnrB19, qnrS1, qnrE1), tetracyclines (tetA, tetB, tetD, tetM), sulfonamides (sul1, sul2, sul3), amphenicols (cmlA1, floR), lincosamides (inuE), as well as various aminoglycoside resistance genes. Additionally, Multi Locus Sequence Typing (MLST) revealed a high diversity of E. coli strains, including ST10, a pandemic clone. This information provides evidence of the dissemination of highly significant ARGs in public health. Therefore, it is imperative to implement measures aimed at mitigating and preventing the transmission of MDR bacteria carrying ARGs to urban environments.

Biofilm formation, antibiotic resistance and genotyping of Shiga toxin-producing Escherichia coli isolated from retail chicken meats

1. The Shiga toxin-producing Escherichia coli (STEC) is a hazardous zoonotic agent for chicken meat consumers. This study determined the serogroups and evaluated the virulence genes, antibiotic resistance, biofilm-forming profiles and genetic relationships of STEC isolates in chicken meat.2. A total of 100 samples belonging to dressed-whole chicken and different parts of the chicken (wing, breast, thigh, drumstick) were collected between September and November 2019 from different retail markets in Kayseri, Türkiye.3. Phenotypic (identification, disc diffusion test, Congo red agar and microtitre plate tests) and molecular tests (identification, serogrouping, virulence factors, biofilm, antibiotic susceptibility, 16S rRNA sequencing and enterobacterial repetitive intergenic consensus-PCR for typing of the isolates) were carried out.4. E. coli was isolated from 35% of the samples and 35% of the samples harboured at least one STEC. Among 35 STEC isolates, 3 (8.5%), 6 (17.1%), 2 (5.7%) and 3 (8.5%) were found to be positive for fliCH2, fliCH8, fliCH11, fliCH19 genes, respectively. Out of 35 STEC positive isolates, 4 (11.4%) were identified as E. coli O157, from which 2 (5.7%) were E. coli O157:H7. E. coli O157 was detected in two (10%), one (5%), one (5%) of the thigh, drumstick and whole chicken samples, respectively.5. Biofilm-forming ability was reported in 33 (94.2%) of 35 E. coli isolates, whilst the biofilm-associated genes detected among 35 STEC isolates included csgA (88.5%), fimH (88.5%), bcsA (85.7%), agn43 (14.2%) and papC (8.5%). The STEC strains showed resistance against ampicillin (88.5%) and erythromycin (88.5%), followed by tetracycline (74.2%) and gentamicin (25.7%). However, the distribution of isolates harbouring bla_CMY, ere(A), tet(A) and aac(3)-IV antibiotic resistance genes was found to be 17.1%, 11.4%, 85.7% and 5.7%, respectively.6. ERIC-PCR showed that E. coli strains obtained from different parts and whole of chicken samples had genetic diversities. ERIC-PCR patterns grouped strains of 35 STEC into eight clusters designated A-H, with 73% similarity. Proper hygiene measures and staff training are essential for public health during poultry processing and in retail stores to control STEC.

Antibiotic resistance of uropathogens among the community-dwelling pregnant and nonpregnant female: a step towards antibiotic stewardship

BACKGROUND

Indiscriminate and widespread use of antibiotics has resulted in emergence of many antibiotic-resistant organisms. Antibiotic administration during pregnancy is mostly avoided, unless there is compelling medical condition. We hypothesized that the uropathogens isolated from pregnant women would be more susceptible to antibiotics compared to those isolated from nonpregnant women, thus will be helpful in formulating separate empiric guideline for pregnant women based on the resistance pattern.

METHODS

This was a prospective cross-sectional study conducted over a period of 2 years in which females with the clinical diagnosis of either cystitis or asymptomatic bacteriuria during pregnancy were included from the community settings. Uropathogen species and their antimicrobial resistance pattern were compared between the pregnant and nonpregnant groups. After accounting for centre-to-centre variation and adjusting for age and socio-economic status, the adjusted odds ratio for antibiotic resistance was calculated and compared between pregnant and nonpregnant women using logistic regression analysis.

RESULTS

A total of 1758 women (pregnant: 43.3%; nonpregnant: 56.6%) were screened in the study over a period of 2 years, out of which 9.3% (163/1758) were having significant bacteriuria. Escherichia coli and Klebsiella pneumoniae were the two commonest uropathogen in both the groups; their prevalence being 83.6% in pregnant women and 85.2% in nonpregnant women, respectively. Resistance against ampicillin, cefixime, cefoxitin, ceftazidime, ceftriaxone and amoxicillin-clavulanic acid were found significantly lower in the pregnant women compared to nonpregnant. After adjusting the age and socio-economic status accounting for centre-to-centre variation, the odds of resistance for cefixime, amoxicillin-clavulanic acid and co-trimoxazole were found lower and statistically significant among the pregnant women group.

CONCLUSIONS

The antimicrobial resistance was significantly higher among the community-dwelling nonpregnant women compared to pregnant women in case of few antibiotics. The study highlighted the need of building local antibiogram that could help to initiate the empirical treatment and thus prevent emergence of antimicrobial resistance.

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

Pathogenicity Islands in Uropathogenic Escherichia coli Clinical Isolate of the Globally Disseminated O25:H4-ST131 Pandemic Clonal Lineage: First Report from Egypt

Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infections (UTIs). The pathogenesis of UTIs relies upon UPEC's acquisition of virulence determinants that are commonly inserted into large chromosomal blocks which are termed 'pathogenicity islands' (PAIs). In this study, we investigated the virulence-associated genes embedded in the chromosome of a UPEC Egyptian strain, EC14142. Additionally, we present a detailed characterization of the PAIs in the EGY_EC14142 chromosome. The isolate displayed a multidrug-resistant phenotype, and whole genome sequencing indicated that it belonged to the globally disseminated O25:H4-ST131 pandemic lineage and the H30-Rx clade. EGY_EC14142 carried genes that are responsible for resistance to aminoglycosides, fluoroquinolones, extended-spectrum β-lactams, macrolides, folate pathway antagonists, and tetracyclines. It encoded five PAIs with a high similarity to PAI II536, PAI IV536, PAI V536, PAI-536-icd, and PAIusp. The genome analysis of EGY_EC14142 with other closely related UPEC strains revealed that they have a high nucleotide sequence identity. The constructed maximum-likelihood phylogenetic tree showed the close clonality of EGY_EC14142 with the previously published ST131 UPEC international isolates, thus endorsing the broad geographical distribution of this clone. This is the first report characterizing PAIs in a UPEC Egyptian strain belonging to the globally disseminated pandemic clone O25:H4-ST131.

Characterization of virulence factors and antibiotic resistance pattern of uropathogenic Escherichia coli strains in a tertiary care center

Background: Urinary tract infection(UTI) is one of the commonly prevalent bacterial infection in humans.The uropathogenic E. coli (UPEC) expresses a range of virulence factors that contribute to their pathogenicity . The emergence of multidrug resistance (MDR)-associated UTI is increasing.This study monitors the distribution of virulence factors among UPEC strains to note the antibiogram, outcome and type of associated UTI. Methods:A prospective cross-sectional time-bound study of six months was done on clinically significant urinary isolates of Escherichia coli. Detection of haemolysin production and serum resistance was done by phenotypic methods. Genotypic characterization of the virulence genes ( papC, iutA, hlyA, cnf1) was done by multiplex PCR. Demographic data, clinical history, antibiogram and type of UTI was collected from clinical case records. Results:75 E.coli isolates from patients with suspected UTIs were included. Females had a higher preponderance of UTI (66.7%). 93% of patients were adults and the remaining 7% were from paediatrics.  24 (32%) isolates showed haemolysis by plate haemolysis and all isolates were serum-resistant. Out of 75 isolates, 65 were positive for at least one of four targeted genes, while remaining ten isolates were negative for all four genes.Multidrug resistance was found in 40 (53.3%) isolates. 97.4% of the UTI cases had a favourable clinical outcome at discharge. Mortality due to urosepsis was 2.6%. Conclusion:Association of hemolysin production with resistance to imipenem and norfloxacin in UPEC strains was significant.Presence of hlyA gene is positively associated with ceftazidime resistance. Nitrofurantoin, piperacillin, tazobactam, and cefaperazone sulbactam are possible candidates for empirical therapy of UTIs. Drugs like aminoglycosides, carbapenems and fosfomycin may be used as reserve drugs in the treatment of MDR-UTI.However, inappropriate usage can increase antibiotic resistance. Hence proper selection of antibiotics in hospitals taking into account the local antibiogram is needed to reduce the emergence of antibiotic resistance.

Characterization of virulence factors and antibiotic resistance pattern of uropathogenic Escherichia coli strains in a tertiary care center

Background: Urinary tract infections (UTI) are the most prevalent bacterial infection in humans. The uropathogenic E. coli (UPEC) expresses a range of virulence factors that contribute to their pathogenicity . The emergence of multidrug resistance (MDR)-associated UTI is increasing. This study monitors the distribution of virulence factors among UPEC strains to note the antibiogram, outcome and type of associated UTI. Methods: A prospective cross-sectional time-bound study of six months was done on clinically significant urinary isolates of Escherichia coli. Detection of haemolysin production and serum resistance was done by phenotypic methods. Genotypic characterization of the virulence genes ( papC, iutA, hlyA, cnf1) was done by multiplex PCR. Demographic data, clinical history, antibiogram and type of UTI was collected from clinical case records. Results:75 E.coli isolates from patients with suspected UTIs were included. Females had a higher preponderance of UTI (66.7%). 93% of patients were adults and the remaining 7% were from paediatrics.  24 (32%) isolates showed haemolysis by plate haemolysis and all isolates were serum-resistant. Out of 75 isolates, 65 were positive for at least one of four targeted genes, while remaining ten isolates were negative for all four genes. Multidrug resistance was found in 40 (53.3%) isolates. 97.4% of the UTI cases had a favourable clinical outcome at discharge. Mortality due to urosepsis was 2.6%. Conclusion: Association of hemolysin production with resistance to imipenem and norfloxacin in UPEC strains was significant. Presence of hlyA gene is positively associated with ceftazidime resistance. Nitrofurantoin, piperacillin, tazobactam, and cefaperazone sulbactam are possible candidates for empirical therapy of UTIs. Drugs like aminoglycosides, carbapenems and fosfomycin may be used as reserve drugs in the treatment of MDR-UTI. However, inappropriate usage can increase antibiotic resistance. Hence proper selection of antibiotics in hospitals taking into account the local antibiogram is needed to reduce the emergence of antibiotic resistance.

Comparison of the Clinical and Genotypic Characteristics of Uropathogenic Escherichia coli Strains According to Sex in Korea

In this study, we compared the microbiological, genotypic, and antibiotic resistance characteristics of uropathogenic Escherichia coli (UPEC) strains in patients with pyelonephritis in Korea according to sex based on data corresponding to the February 2015 to June 2018 period. Based on Escherichia coli phylogenetic group analysis, gene virulence detection, and subgroup analyses by sex, we observed that the antibiotic resistance percentages and proportions corresponding to extended-spectrum beta-lactamase producing UPEC were higher in males than in females. In addition, phylogenetic group B2 showed predominance in both the male and female groups, which further showed similar adhesion molecule distributions. Toxin-associated factors, hlyA and cnf1, were more common in males. In clinical presentations, urinary predisposing factors, complicated urinary tract infections (UTIs), concomitant bacteremia, and persistent fever were also more common with males. Although females and males showed UPEC genotypic differences, there were no differences between them with respect to poor outcomes. Persistent fever was associated with community-acquired infection and bacteremic UTI and relapsed UTI within 3 months was associated with urinary tract stone. In future, it will be necessary to conduct multicenter studies, involving more cases on UPEC to validate our results.

Genotypic assay to determine some virulence factors of Uropathogenic E. coli (UPEC) isolates

A total of 179 urine samples were collected from patients suffering from urinary tract infections were admitted and visit Al-Hilla General Teaching Hospital in Al-Hilla City, during a period from April 2021 to December 2021, from both sex (male and female). Out of 179,123 (68.7%) were positive culture, whereas 56 (31.3%) samples showed no bacterial growth, To confirm the identification of E. coli by use selective media (EMB agar medium, biochemical tests, automated Vitek 2 system and 16s RNA specific primer by the presence of (1492 bp) compared with allelic ladder, it was found that, E. coli were deliberated the main an etiological causes UTI to other types bacteria which constitute 56/123 (45.5%), [45/56 (80.4%) from female and 11/56 (19.6%) from male], while 67/123 (54.4%) were related to other types of bacteria. Molecular detection of some virulence factors genes were studied, out of 56 E. coli isolates, hlyA gene was detected in 21/56 (37.5%) isolates by the presence of (1177 bp) and sat gene was detected in 35/56 (62.5%) isolates by the presence of (410 bp) compared with allelic ladder.

Phylogenetic Group Distribution of Uropathogenic Escherichia coli and Related Antimicrobial Resistance Pattern: A Meta-Analysis and Systematic Review

The phylogenetic classification of Escherichia coli isolates is of great importance not only for understanding the populations of E. coli but also for clarifying the relationship between strains and diseases. The present study aimed to evaluate the prevalence of phylogenetic groups, antibiotic susceptibility pattern, and virulence genes among uropathogenic E. coli (UPEC) isolated from different parts of Iran through a systematic review and meta-analysis. Several international electronic sources, including Web of Science, PubMed, Scopus, and Embase, were searched (2000–2020) in order to identify the studies compatible with our inclusion criteria. The meta-analysis was performed using the metaprop program in the STATA (version 11) software. Based on our comprehensive search, 28 studies meeting the eligibility criteria were included in the meta-analysis. The pooled prevalence of phylogroups B₂, D, B₁, and A was 39%, 26%, 18%, and 8%, respectively. In addition, there was a significant heterogeneity among different phylogroups. However, according to the results of Begg’s and Egger’s tests, there were no significant publication bias in phylogroups B₂, D, B₁, and A. This research provided the first comprehensive study on phylogroups of UPEC isolated in Iran. Our findings indicated that phylogroup B₂ and group D were the most predominant phylogenetic groups among UPEC isolates in various regions of Iran. In addition, we observed that certain phylogenetic groups are more antibiotic resistant than the others. It was also observed that the dissemination of virulent phylogroup B₂ and D should be controlled via comprehensive infection control measures. Additionally, certain strategies should be developed for monitoring the antibiotic therapy.

Antibiotic resistance, phylogenetic typing, and virulence genes profile analysis of uropathogenic Escherichia coli isolated from patients in southern Iraq

Of the most common infectious diseases that occur mainly by uropathogenic Escherichia coli (UPEC) is urinary tract infections (UTIs). The purpose of this study was to investigate virulence factors, antibiotic resistance, and phylogenetic groups among UPEC strains isolated from patients with UTI in southern Iraq. A total of 100 UPEC isolates were collected from urine samples of UTI patients from various hospitals in southern Iraq, and confirmed by morphological and biochemical tests. Antimicrobial susceptibility testing on isolates was performed by disk diffusion method. Multiplex PCR techniques were used to evaluate the phylogenetic groups based on Clermont method and to detect the presence of six virulence factor genes. The majority of isolates belonged to the phylogenetic groups B2 (46%) and C (13%). The most prevalent virulence factors were fimH (96%), followed by aer (47%), papC (36%), cnf1 (17%), hly (15%), and afa (8%). Phenotypic testing showed that the isolates were most resistant to piperacillin, ticarcillin, amoxicillin/clavulanic acid (92%, 91%, and 88%, respectively) and most sensitive to amikacin and imipenem, respectively. The maximum antibiotic resistance and virulence factors were observed in the phylogenetic group B2. The results showed that the UPEC isolates had all six virulence factors with high frequency and the highest drug resistance. Besides, the results showed a direct relationship between virulence factors, gene diversity, phylogenetic background, and antimicrobial resistance in the UPEC isolates.

Differences of virulence factors, and antimicrobial susceptibility according to phylogenetic group in uropathogenic Escherichia coli strains isolated from Korean patients

Background

Escherichia coli is among the most common uropathogens. Increased antibiotic resistance in Gram negative bacilli is global concern. Alternative therapeutic options including vaccines against uropathogenic E. coli (UPEC) have been developed. In this study, we compared the genotypic characteristics and antimicrobial susceptibility of UPEC according to phylogenetic groups.

Methods

We retrospectively reviewed the medical records of pyelonephritis patients with UPEC between February 2015 and June 2018. The study was conducted at a medical center in Korea. We compared the clinical and genotypic characteristics of UPEC according to phylogenetic groups. The phylogenetic groups and 29 virulence factors were identified using multiplex polymerase chain reaction.

Results

Phylogenetic group analysis revealed that most uropathogenic E. coli belonged to groups B2 and D: B2 (276, 77.7%), D (62, 17.5%), B1 (12, 3.4%), and A (5, 1.4%). Among the virulence factors, fyuA, fimH, traT, iutA, papG allele II, and papC were the most frequently observed. Phylogenetic group B2 was more closely related to virulence factors, including fimH, sfa/focED, focG, hlyA, cnf1, fyuA, and PAI, than group D. Groups B2 and D showed similar clinical presentations and complications. Group B2 had mostly healthcare-associated infections and antimicrobial resistance. Group D mostly had community-acquired infections. The K1 serotype was prevalent in group B2, and K5 was the most prevalent in group D.

Conclusions

Phylogenetic group B2 had more proportions and types of virulence factors than group D. Group B2 showed a high presentation of virulence factors related to adhesions and toxins. An increased presentation of antimicrobial resistance and healthcare-associated infections was also noted. Considering the genetic characteristics of UPEC, alternative therapeutic options targeting frequent virulence factors might be considered in addition to antibiotics.

Antibiotic resistance patterns of Escherichia coli isolates from the clinic through the wastewater pathway

Antimicrobial resistance (AMR) remains one of the leading global health threats. This study compared antimicrobial resistance patterns among E. coli isolates from clinical uropathogenic Escherichia coli (UPEC) to hospital wastewater populations and throughout an urban wastewater treatment facility - influent, pre- and post-chlorinated effluents. Antibiotic susceptibility of 201 isolates were analyzed against eleven different antibiotics, and the presence of twelve antibiotic resistant genes and type 1 integrase were identified. AMR exhibited the following pattern: UPEC (46.8%) > hospital wastewater (37.8%) > urban post-chlorinated effluent (27.6%) > pre-chlorinated effluent (21.4%) > urban influent wastewater (13.3%). However, multi-drug resistance against three or more antimicrobial classes was more prevalent among hospital wastewater populations (29.7%) compared to other sources. E. coli from wastewaters disinfected with chlorine were significantly correlated with increased trimethoprim-sulfamethoxazole resistance in E. coli compared to raw and treated wastewater populations. bla_CTX-M-1 group was the most common extended spectrum beta-lactamase in E. coli from hospital wastewater (90%), although UPEC strains also encoded bla_CTX-M-1 group (50%) and bla_TEM (100%) genes. Among tetracycline-resistant populations, tetA and tetB were the only resistance genes identified throughout wastewater populations that were associated with increased phenotypic resistance. Further characterization of the E. coli populations identified phylogroup B2 predominating among clinical UPEC populations and correlated with the highest AMR, whereas the elevated rate of multi-drug resistance among hospital wastewater was mostly phylogroup A. Together, our findings highlight hospital wastewater as a rich source of AMR and multi-drug resistant bacterial populations.

Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes

Escherichia coli is a major causative agent of environmental bovine mastitis and this disease causes significant economic losses for the dairy industry. There is still debate in the literature as to whether mammary pathogenic E. coli (MPEC) is indeed a unique E. coli pathotype, or whether this infection is merely an opportunistic infection caused by any E. coli isolate being displaced from the bovine gastrointestinal tract to the environment and, then, into the udder. In this study, we conducted a thorough genomic analysis of 113 novel MPEC isolates from clinical mastitis cases and 100 bovine commensal E. coli isolates. A phylogenomic analysis indicated that MPEC and commensal E. coli isolates formed clades based on common sequence types and O antigens, but did not cluster based on mammary pathogenicity. A comparative genomic analysis of MPEC and commensal isolates led to the identification of nine genes that were part of either the core or the soft-core MPEC genome, but were not found in any bovine commensal isolates. These apparent MPEC marker genes were genes involved with nutrient intake and metabolism [adeQ, adenine permease; nifJ, pyruvate-flavodoxin oxidoreductase; and yhjX, putative major facilitator superfamily (MFS)-type transporter], included fitness and virulence factors commonly seen in uropathogenic E. coli (pqqL, zinc metallopeptidase, and fdeC, intimin-like adhesin, respectively), and putative proteins [yfiE, uncharacterized helix-turn-helix-type transcriptional activator; ygjI, putative inner membrane transporter; and ygjJ, putative periplasmic protein]. Further characterization of these highly conserved MPEC genes may be critical to understanding the pathobiology of MPEC.

Detection of Phylogenetic Groups and Drug Resistance Genes of Escherichia coli Causing Urinary Tract Infection in Southwest Iran

Background: Many bacteria can cause urinary tract infections (UTIs), among which Escherichia coli is the most common causative agent. Escherichia coli strains are divided into eight phylogenetic groups based on the new Quadroplex-PCR method, which are different in terms of patterns of resistance to antibiotics, virulence, and environmental characteristics. Objectives: This study aimed to determine the phylogenetic groups and the prevalence of drug resistance genes in E. coli strains causing UTIs. Methods: In this descriptive cross-sectional study, 129 E. coli isolates obtained from the culture of patients with UTIs were evaluated for phylogenetic groups using the new method of Clermont et al. The identification of phylogenetic groups and antibiotic resistance genes was performed using the multiplex polymerase chain reaction (PCR) method. Results: In this study, concerning the distribution of phylogenetic groups among E. coli isolates, the phylogenetic group B2 (36.4%) was the most common phylogenetic group, followed by phylogroups C (13.2%), clade I (10.1%), D (9.3%), and A (3.1%) while groups B1 and F were not observed in any of the isolates, and 20.2% had an unknown state. Also, out of 129 E. coli isolates, the total frequency of tetA, tetB, sul1, sul2, CITM, DfrA, and qnr resistance genes was 59.7%, 66.7, 69, 62, 30.2, 23.3, and 20.2%, respectively. In this study, there was a significant relationship between antibiotics (P = 0.026), cefotaxime (P = 0.003), and nalidixic acid (P = 0.044) and E. coli phylogenetic groups. No significant relationship was observed between E. coli phylogenetic groups and antibiotic resistance genes. Conclusions: The results of this study showed that strains belonging to group B2 had the highest prevalence among other phylogroups, and also, the frequency of antibiotic resistance genes and drug-resistant isolates had a higher prevalence in this phylogroup. These results show that phylogroup B2 has a more effective role in causing urinary tract infections compared to other phylogroups, and this phylogroup can be considered a genetic reservoir of antibiotic resistance.

Escherichia coli urinary tract infections: Host age-related differences in bacterial virulence factors and antimicrobial susceptibility

BACKGROUND

Urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are one of the most common outpatient bacterial infections. Although bacterial and host factors are reported to be associated with UTI pathogenesis, little is known about the host age-related differences in bacterial virulence factors and antimicrobial susceptibility.

METHODS

PCRs were carried out to detect K1 capsule antigen, 15 virulence factors, and phylogenetic groups in E. coli isolates. Antimicrobial susceptibility of selected agents was determined by the disk diffusion method. Isolates were divided into 6 groups based on their host age.

RESULTS

The results showed that virulence factors PapGII, PapGIII, Cnf1, Aer, Usp, Iha, OmpT, HlyA, and Sat, had highest frequencies in the host age group 0-3. Phylogenetic group B2 dominated in our isolates (59.6%) followed by group D (20.7%). In addition, 77.4% of strains isolated from 0 to 3 age group belonged to phylogenetic group B2. Antimicrobial susceptibility tests showed that E. coli strains isolated were significantly more resistant to antimicrobial agents as host age increased. Phylogenetic group B2 isolates were more susceptible to antimicrobial agents, compared to A, B1, and D isolates.

CONCLUSION

We found E. coli isolated from elders were more resistant to antimicrobial agents and had less virulence factors.

Virulence genes and phylogenetic groups of uropathogenic Escherichia coli isolates from patients with urinary tract infection and uninfected control subjects: a case-control study

Background

Urinary Tract Infection (UTI) is one of the most common bacterial infectious diseases which causes considerable morbidity and costly health problems. Uropathogenic Escherichia coli (UPEC), the most common pathogen causing UTI, is a highly heterogeneous group of extraintestinal pathogenic E. coli (ExPEC) which may carry a variety of virulence factors and belonging to different phylogenetic backgrounds. The current study aimed to investigate the frequency and association between various virulence factors (VFs) and phylogenetic groups of UPEC and commensal isolates.

Methods

UPEC and commensal E. coli strains isolated from UTI and feces of healthy humans were compared for the presence of VFs and phylogenetic groups. Association between virulence genes was investigated and cluster analysis was employed.

Results

According to the results, among a 30 virulence markers tested, the pathogenicity-associated island (PAI), papAH, papEF, fimH, fyuA, and traT genes prevalence were statistically significant in UPEC isolates. A strong association was found between the B2 and D phylogenetic groups and clinical isolates of UPEC; while, commensal isolates were mostly associated with phylogenetic group A. The aggregated VFs scores were more than twice higher in the UPEC isolates in comparison with the commensal isolates. Interestingly, the B2 group in both UPEC and commensal isolates had the highest VF scores. A strong positive association was found between several virulence genes. The clustering results demonstrated that UPEC or commensal E. coli isolates were highly heterogeneous due to different composition of their virulence gene pool and pathogenicity islands.

Conclusion

Genetic structure and VFs of UPEC strains vary from region to region; therefore, to control the UTI, the epidemiological aspects and characterization of the UPEC isolates need to be investigated in different regions. Since UPEC isolates are generally originate from the commensal strains, it may be feasible to reduce the UTI burden by interfering the intestinal colonization, particularly in the highly pathogenic clonal lineages such as B2.

Plasmid-Borne and Chromosomal ESBL/AmpC Genes in Escherichia coli and Klebsiella pneumoniae in Global Food Products

Plasmid-mediated extended-spectrum beta-lactamase (ESBL), AmpC, and carbapenemase producing Enterobacteriaceae, in particular Escherichia coli and Klebsiella pneumoniae, with potential zoonotic transmission routes, are one of the greatest threats to global health. The aim of this study was to investigate global food products as potential vehicles for ESBL/AmpC-producing bacteria and identify plasmids harboring resistance genes. We sampled 200 food products purchased from Finland capital region during fall 2018. Products originated from 35 countries from six continents and represented four food categories: vegetables (n = 60), fruits and berries (n = 50), meat (n = 60), and seafood (n = 30). Additionally, subsamples (n = 40) were taken from broiler meat. Samples were screened for ESBL/AmpC-producing Enterobacteriaceae and whole genome sequenced to identify resistance and virulence genes and sequence types (STs). To accurately identify plasmids harboring resistance and virulence genes, a hybrid sequence analysis combining long- and short-read sequencing was employed. Sequences were compared to previously published plasmids to identify potential epidemic plasmid types. Altogether, 14 out of 200 samples were positive for ESBL/AmpC-producing E. coli and/or K. pneumoniae. Positive samples were recovered from meat (18%; 11/60) and vegetables (5%; 3/60) but were not found from seafood or fruit. ESBL/AmpC-producing E. coli and/or K. pneumoniae was found in 90% (36/40) of broiler meat subsamples. Whole genome sequencing of selected isolates (n = 21) revealed a wide collection of STs, plasmid replicons, and genes conferring multidrug resistance. bla_CTX–M–15-producing K. pneumoniae ST307 was identified in vegetable (n = 1) and meat (n = 1) samples. Successful IncFII plasmid type was recovered from vegetable and both IncFII and IncI1-Iγ types from meat samples. Hybrid sequence analysis also revealed chromosomally located beta-lactamase genes in two of the isolates and indicated similarity of food-derived plasmids to other livestock-associated sources and also to plasmids obtained from human clinical samples from various countries, such as IncI type plasmid harboring bla_TEM–52C from a human urine sample obtained in the Netherlands which was highly similar to a plasmid obtained from broiler meat in this study. Results indicate certain foods contain bacteria with multidrug resistance and pose a possible risk to public health, emphasizing the importance of surveillance and the need for further studies on epidemiology of epidemic plasmids.