Uropathogenic Escherichia coli pathogenicity islands and other ExPEC virulence genes may contribute to the genome variability of enteroinvasive E. coli

Phage isolation, characterization, and antibiotic resistance profiling in Avian pathogenic Escherichia coli: Integrating data for a possible novel AMR surveillance model

Colibacillosis, brought on by Avian Pathogenic Escherichia coli (APEC), is a significant risk to poultry farming. The management of colibacillosis is made more difficult by the increasing levels of antimicrobial resistance (AMR) in APEC isolates. The antibiotic resistance profiles, antibiotic resistance gene (ARG) presence, and phage susceptibility of 130 APEC isolates were examined in this investigation. The highest resistance against antibiotics was detected against tetracycline and nalidixic acid, with 86.15% and 85.38%, respectively, among isolates. A high frequency of ARGs was found in the data, especially the positively correlated blaTEM (95.38%) and tetA (85.38%) genes. The 20 bacteriophages we recovered were further described, with PhEcoAP90 having the widest host range. A 14 ± 1.41 nm tail and a 52.20 ± 2.94 nm head were revealed by TEM examination. A one-step growth experiment observed a 20-min latent period and a 58 PFU/cell burst size. PhEcoAP90 showed instability at high temperatures and extreme pH values. These results imply that although PhEcoAP90 exhibits potential as an antibiotic alternative for managing APEC infections, its use in severe settings may be restricted. To help combat AMR in chicken farming, we also suggest a unique AMR surveillance system that includes phage sensitivity, ARG prevalence, and antibiotic resistance profiles. In conclusion, our research emphasizes the need for integrated AMR surveillance systems in the poultry industry and the promise of phages as efficient alternative therapeutic approaches in regulating AMR in APEC.

Developing the PIP-eco: An integrated genomic pipeline for identification and characterization of Escherichia coli pathotypes encompassing hybrid forms

Pathogenic Escherichia coli (E. coli) strains are distinguished by their diverse virulence factors, which contribute to a wide spectrum of diseases. These pathogens evolve through the horizontal transfer of virulence factors, resulting in the emergence of hybrid pathotypes with complex and heterogeneous characteristics. Recognizing their profound impact on public health, this study introduces the PIP-eco pipeline, a comprehensive analytical tool designed for the precise identification and characterization of E. coli pathotypes. This PIP-eco pipeline advances beyond traditional molecular techniques by facilitating detailed analysis of both single and hybrid pathotypes. It integrates targeted marker gene analysis, virulence factor-based phylogenetic analysis, and pathogenicity islands (PAIs) profiling to elucidate the genetic diversity of E. coli pathotypes and support their accurate classification. This integrative approach enables PIP-eco to uncover connections among various E. coli pathotypes, highlight shared virulence factors, and provide insights into their evolutionary trajectories. By utilizing experimentally validated marker genes, the pipeline ensures robust identification of pathotypes, particularly those of hybrid pathotypes. Additionally, PAI analysis offers comprehensive genetic investigations, revealing strain-specific variations and potential virulence mechanisms. As a result, the PIP-eco pipeline emerges as a useful tool for dissecting the evolutionary dynamics of E. coli and characterizing complex pathotypes, addressing the critical need for accurate detection and understanding of hybrid pathotypes.

TRS-PCR profiles correlate with polymorphisms of the genomic o454-nlpD region, virulence factors repertoire, and phylogenetic groups among uropathogenic Escherichia coli strains isolated from patients from Lodz region, Poland

Extraintestinal urinary tract infections are mainly caused by uropathogenic strains of E. coli. UPECs are a heterogeneous group of strains possessing various genes associated with virulence traits. It was demonstrated that changes in the composition of the o454-nlpD region and genetic variation in the mutS-rpoS chromosomal region in ExPEC strains are correlated with their virulence, particularly in those with the pattern III o454-nlpD region and belonging to phylogenetic group B2. In this study, we investigated the presence and distribution of the o454-nlpD genomic polymorphism in our collection of 124 uropathogenic E. coli strains, examining the correlation of o454-nlpD region types with the virulence factors studied. Our findings revealed a positive association between certain virulence factors in UPEC strains and the presence of pattern III in the o454-nlpD region. Additionally, all these strains were classified under phylogenetic group B2. We also showed that the highly pathogenic group of E. coli identified by examining the polymorphism of the o454-nlpD region coincides with the highly pathogenic group of uropathogens we identified in the averaged TRS-PCR analysis.

Detection and analysis of Shiga toxin producing and enteropathogenic Escherichia coli in cattle from Tierra del Fuego, Argentina

Shiga toxin producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are pathovars that affect mainly infants' health. Cattle are the main reservoir of STEC. Uremic hemolytic syndrome and diarrheas can be found at high rates in Tierra del Fuego (TDF). This study aimed to establish the prevalence of STEC and EPEC in cattle at slaughterhouses in TDF and to analyze the isolated strains. Out of 194 samples from two slaughterhouses, STEC prevalence was 15%, and EPEC prevalence was 5%. Twenty-seven STEC strains and one EPEC were isolated. The most prevalent STEC serotypes were O185:H19 (7), O185:H7 (6), and O178:H19 (5). There were no STEC eae + strains (AE-STEC) or serogroup O157 detected in this study. The prevalent genotype was stx2c (10/27) followed by stx1a/stx2hb (4/27). Fourteen percent of the strains presented at least one stx non-typeable subtype (4/27). Shiga toxin production was detected in 25/27 STEC strains. The prevalent module for the Locus of Adhesion and Autoaggregation (LAA) island was module III (7/27). EPEC strain was categorized as atypical and with the ability to cause A/E lesion. The ehxA gene was present in 16/28 strains, 12 of which were capable of producing hemolysis. No hybrid strains were detected in this work. Antimicrobial susceptibility tests showed that all strains were resistant to ampicillin and 20/28 were resistant to aminoglycosides. No statistical differences could be seen in the detection of STEC or EPEC either by slaughterhouse location or by production system (extensive grass or feedlot). The rate of STEC detection was lower than the one reported for the rest of Argentina. STEC/EPEC relation was 3 to 1. This is the first study on cattle from TDF as reservoir for strains that are potentially pathogenic to humans.

The pathogenesis of prevalent aerobic bacteria in aerobic vaginitis and adverse pregnancy outcomes: a narrative review

Background

Aerobic vaginitis is a common cause of vaginal discharge in reproductive-age women, increasing the risk of negative pregnancy outcomes such as premature delivery, abortion, premature rupture of membranes and stillbirth. However, the aetiology and pathogenesis of aerobic vaginitis causing negative pregnancy outcomes are still unclear, and there is no unified and standardized treatment method for aerobic vaginitis in the pregnancy period.

Methods

We conducted a literature search of published studies in the English language focusing on aerobic vaginitis and its association with adverse pregnancy outcomes utilizing PubMed and Web of Science from January 1973 through June 2021. The common pathogenic bacteria of aerobic vaginitis during pregnancy, such as group B Streptococcus, Escherichia coli, Staphylococcus aureus, Enterococcus faecalis and Klebsiella pneumoniae, as well as the related adverse pregnancy outcomes and existing treatments were reviewed.

Results

A total of 4534 articles were identified, and 97 studies that had inclusion criteria were subjected to careful review. The pathogenic bacteria of aerobic vaginitis can produce different toxins or affect the local immunity of patients and then lead to the occurrence of infection. Fresh wet mount microscopy is the preferred diagnostic method for aerobic vaginitis. Clindamycin is a common antibiotic used for aerobic vaginitis in pregnant women. The use of products combining probiotics has achieved excellent treatment success.

Conclusions

Future research in this field can provide insights regarding the mechanism of aerobic vaginitis-induced adverse pregnancy outcomes in humans and ways to prevent their occurrence.

Aerobic vaginitis is an infection of the vagina that increases the risk of negative pregnancy outcomes. The aetiology and pathogenesis of aerobic vaginitis causing negative pregnancy outcomes are still unclear. This paper reviews the common pathogenic bacteria of aerobic vaginitis during pregnancy, and the related adverse pregnancy outcomes. We also review the existing treatment. Currently, it is believed that the microflora in aerobic vaginitis is composed of commensal aerobic microorganisms of intestinal origin, and the most frequently encountered bacteria are group B Streptococcus, Escherichia coli, Staphylococcus aureus, Enterococcus faecalis and Klebsiella pneumoniae. The pathogenic bacteria of aerobic vaginitis can produce different toxins or affect the local immunity of patients and then lead to the occurrence of infection. Fresh wet mount microscopy is the preferred diagnostic method for aerobic vaginitis. Clindamycin is a common antibiotic used for aerobic vaginitis in pregnant women. The use of products combining probiotics has achieved excellent treatment success. This study provides a reference for future research and early diagnosis and treatment during pregnancy. Future research in this field can provide insights regarding the mechanisms of aerobic vaginitis-induced adverse pregnancy outcomes in humans and ways to prevent their occurrence.

Molecular Epidemiology of Extraintestinal Pathogenic Escherichia coli Causing Hemorrhagic Pneumonia in Mink in Northern China

The molecular epidemiology and biological characteristics of Escherichia coli associated with hemorrhagic pneumonia (HP) mink from five Chinese Provinces were determined. From 2017 to 2019, 85 E. coli strains were identified from 115 lung samples of mink suffering from HP. These samples were subjected to serotyping, antimicrobial susceptibility, detection of virulence genes, phylogenetic grouping, whole-genome sequencing, drug resistant gene, multilocus sequence typing (MLST) and biofilm-forming assays. E. coli strains were divided into 18 serotypes. Thirty-nine E. coli strains belonged to the O11 serotype. Eighty-five E. coli strains were classified into seven phylogenetic groups: E (45.9%, 39/85), A (27.1%, 23/85), B1 (14.1%, 12/85), B2 (3.7%, 3/85), D (3.7%, 3/85), F (2.4%, 2/85) and clade I (1.2%, 1/85). MLST showed that the main sequence types (STs) were ST457 (27/66), All E. coli strains had ≥4 virulence genes. The prevalence of virulence was 98.8% for yijp and fimC, 96.5% for iucD, 95.3% for ompA, 91.8% for cnf-Ⅰ, 89.4% for mat, 82.3% for hlyF, and 81.2% for ibeB. The prevalence of virulence genes iss, cva/cvi, aatA, ibeA, vat, hlyF, and STa was 3.5-57.6%. All E. coli strains were sensitive to sulfamethoxazole, but high resistance was shown to tetracycline (76.5%), chloramphenicol (71.8%), ciprofloxacin (63.5%) and florfenicol (52.9%), resistance to other antibiotics was 35.3-16.5%. The types and ratios of drug-resistance genes were tet(A), strA, strB, sul2, oqxA, blaTEM-1B, floR, and catA1 had the highest frequency from 34%-65%, which were consistent with our drug resistance phenotype tetracycline, florfenicol, quinolones, chloramphenicol, the bla-NDM-I and mcr-I were presented in ST457 strains. Out of 85 E. coli strains, six (7.1%) possessed a strong ability, 12 (14.1%) possessed a moderate ability, and 64 (75.3%) showed a weak ability to form biofilm. Our data will aid understanding of the epidemiological background and provide a clinical basis for HP treatment in mink caused by E. coli.

Occurrence of Escherichia coli and Salmonella species in Some Livestock (Poultry) Feeds in Mando, Kaduna, Nigeria

The study aimed at assessing the proximate composition, isolation, characterization of some Enterobacteriaceae from two (2) brands of poultry feeds marketed in Mando, Kaduna, Nigeria. A total of sixteen (16) samples of two (2) different poultry feeds (starter and finisher) from four (4) poultry farms in mando were collected and subjected to proximate and microbiological analysis. The proximate analysis was carried out using standard techniques and procedures. All the feed samples were cultured on separate media which include Eosin methylene blue (EMB), nutrient Agar (NA) and Salmonella-Shigella Agar (SSA) media using standard procedures. The antibiogram of the selected antibiotics was evaluated against the test isolates. The result of proximate analysis of the starter and finisher feeds indicated that the Dry matter of starter feed had the highest percentage composition of 95.02% and crude fiber of the finisher feed had the lowest composition of 3.78%. The highest number of bacterial load was recorded to be 10.0×104 CFU/g for the feed sample A (starter feed) and 12.0x104CFU/g was recorded for the feed sample B (finisher feed) which had the highest number of bacterial load recorded among the two (2) different poultry feeds analyzed. The bacteria isolates were identified as Salmonella species and Escherichia coli. Total viable count (TVC) of Salmonella species and E. coli in the feed samples (starter and finisher) ranges from 3.0×104CFU/g to 12.0×104CFU/g. Both organisms (Salmonella species, E. coli) were found as 37.5% and 25% of the analyzed feeds (Broiler starter and broiler finisher) samples, respectively. There was no level of significant (p>0.05) difference between the level of contamination of Salmonella species and E. coli in the two different feeds analyzed, as p=0.06 and p=0.13 for Salmonella species, and E. coli respectively. Sample A and B (Starter and Finisher) feeds had the highest number of Salmonella species occurrence with six ( 6) positive samples while E. coli was recorded in four (4) samples of A and B (Starter and Finisher) feeds. The result of the antibiogram indicated that ciprofloxacin (30 µg), Gentamycin (30µg), Perfloxacin (30µg) and Tarvid (30µg) was effective against Salmonella species and Escherichia coli. The significant of spread of the species of the Enterobacteriaceae in livestock feeds requires the need for effective quality assurance and control, good hygiene practices in production and proper handling of the poultry feeds.

Diversity of Hybrid- and Hetero-Pathogenic Escherichia coli and Their Potential Implication in More Severe Diseases

Although extraintestinal pathogenic Escherichia coli (ExPEC) are designated by their isolation site and grouped based on the type of host and the disease they cause, most diarrheagenic E. coli (DEC) are subdivided into several pathotypes based on the presence of specific virulence traits directly related to disease development. This scenario of a well-categorized E. coli collapsed after the German outbreak of 2011, caused by one strain bearing the virulence factors of two different DEC pathotypes (enteroaggregative E. coli and Shiga toxin-producing E. coli). Since the outbreak, many studies have shown that this phenomenon is more frequent than previously realized. Therefore, the terms hybrid- and hetero-pathogenic E. coli have been coined to describe new combinations of virulence factors among the classic E. coli pathotypes. In this review, we provide an overview of these classifications and highlight the E. coli genomic plasticity that results in some mixed E. coli pathotypes displaying novel pathogenic strategies, which lead to a new symptomatology related to E. coli diseases. In addition, as the capacity for genome interrogation has grown in the last few years, it is clear that genes encoding some virulence factors, such as Shiga toxin, are found among different E. coli pathotypes to which they have not traditionally been associated, perhaps foreshowing their emergence in new and severe outbreaks caused by such hybrid strains. Therefore, further studies regarding hetero-pathogenic and hybrid-pathogenic E. coli isolates are necessary to better understand and control the spread of these pathogens.

Phylogenetic Characterization and Multilocus Sequence Typing of Extended-Spectrum Beta Lactamase-Producing Escherichia coli from Food-Producing Animals, Beef, and Humans in Southwest Nigeria

Multidrug-resistant extended-spectrum beta lactamase (ESBL)-producing Escherichia coli strains are emerging globally in both humans and animals. Antimicrobial susceptibility testing and ESBL screening were performed on pure cultures of 216 E. coli isolates from human and animal fecal samples as well as beef. Polymerase chain reaction was performed for the detection of resistance genes. Representative isolates of ESBL-producing E. coli were randomly selected for multilocus sequence typing and pulsed field gel electrophoresis (PFGE). Sixty of the isolates were identified as ESBL producers, and seven resistance genes were amplified in them: TEM (61.7%), blaCTX-M-15 (51.7%), AAC-6-LB (43.3%), blaCTX-M-1 (38.3%), blaCTX-M-9 (33.3%), blaCTX-M-2 (21.7%), and SHV (11.7%); they were classified into four phylogroups: A (25%), B1 (45%), B2 (20%), and D (10%). Thirty of these isolates were clustered into 10 sequence types with ST131 being mostly prevalent. Six PFGE types were discovered, each of which was shared by isolates from different subjects and had the same phylogroups and resistance gene profiles. There was a dissemination of PFGE types across various groups among humans, animals, and beef. This underlines the fact that the spread of ESBL E. coli could be from humans to animals, from animals to humans, as well as across animal species.

Effect and Analysis of Bacterial Lysates for the Treatment of Recurrent Urinary Tract Infections in Adults

Urinary tract infection (UTI) is a relevant public health problem, economically and socially affecting the lives of patients. The increase of antimicrobial bacterial resistance significantly hinders the treatment of UTIs, raising the need to search for alternative therapies. Bacterial lysates (BL) obtained from Escherichia coli and other pathogens have been used to treat different infectious diseases with promising results. This work aims to evaluate the effect and composition of an autologous BL for the treatment and control of recurrent UTIs in adults. The results show remission in 70% of the patients within the first three months after the administration of BL, while the infection is maintained under control for 6-12 months. The analysis by liquid chromatography-mass spectrometry (LC-MS) of the BL fractions recognized by the sera of patients shows the presence of cytosolic proteins, fimbriae, OMPs, and LPS. Our study demonstrates that the autologous BL contributed to the treatment and control of recurrent UTIs in adults, and its composition shows that different surface components of E. coli are potential immunogens that could be used to create a polyvalent protective vaccine.

Snapshot of Phylogenetic Groups, Virulence, and Resistance Markers in Escherichia coli Uropathogenic Strains Isolated from Outpatients with Urinary Tract Infections in Bucharest, Romania

BACKGROUND

Urinary tract infections (UTIs) caused by Uropathogenic Escherichia coli (UPEC) are among the most common infections worldwide, including Romania. To the best of our knowledge, this is the first study performed on a significant number of community-acquired (CA) UPEC strains isolated from Romanian outpatients, aiming to evaluate and establish potential correlations among the phylogenetic groups (PG), resistance profiles, and the virulence factors (VF) genes of the CA-UPEC isolates.

MATERIALS/METHODS

The present study was performed on a total of 787 UPEC nonrepetitive isolates consecutively isolated during one month from outpatients with CA-UTIs, visiting one of the biggest laboratories in Bucharest, Romania, receiving patients from all over the country. The strains identification was performed by MALDI TOF and the susceptibility patterns were tested using Microscan according to CLSI guidelines. PCR assays were performed to detect the presence of different VFs (fimH gene encoding for type 1 fimbriae, afaBC for A fimbriae, sfaDE for S fimbriae, KpsMTII for capsule, hlyA for haemolysin A, hlyD for haemolysin D, and cnf-1 for tumor necrosis factor), the phylogenetic groups (PG) A, B1, B2, and D, and the extended spectrum beta-lactamases (ESBLs) genes.

RESULTS

The 787 CA-UPEC strains were isolated predominantly from female patients (90.95%) of >30 years (~74%). The resistance rates were 47.52% for ampicillin, 41.16% for tetracycline, 24.39% for cotrimoxazole, 19.18% for amoxicillin-clavulanic acid, 15.50% for cefazolin, 14.99% for ciprofloxacin, and 14.86% for levofloxacin; 35.19% of the investigated strains were MDR and 9.03% ESBL producers (from which 42.25% were positive for blaCTX-M, 38.02% for blaTEM, and 19.71% for blaSHV). FimH was the most frequent virulence gene (93.90%) followed by hlyD (44.34%); afaBC (38.24%); KpsMTII (32.65%); sfaDE (23.88%); hlyA (12.45%); and cnf-1 (7.75%). The distribution of the analyzed UPEC strains in phylogenetic groups was different for non-MDR and MDR strains. Overall, 35% of the strains belonged to the phylogenetic group B2 (harboring the yjaA gene); 27% to group B1 (confirmed by the presence of the TspE4C2 fragment); 16% to group D; and 22% to group A. The CA-UPEC strains included in PG B1 and PG B2 proved to be the most virulent ones, the number of strains carrying multiple VFs (>3) being significantly larger as compared to strains belonging to PG A and PG D) (p<0,0001). The presence of one or two ESBL genes was significantly associated (p =0.0024) with PGs A and D.

CONCLUSIONS

Our findings showed that the community UPEC strains circulating in Bucharest, Romania, belong predominantly to group B2 and >90% harbored the fimH gene. High MDR resistance rates were observed, as well as extended VF profiles, highlighting the importance of this type of studies for improving the epidemiological surveillance and the therapeutic or prophylactic management of the respective infections, in the context of antibiotic resistance emergence.

The relationship between phylogenetic classification, virulence and antibiotic resistance of extraintestinal pathogenic Escherichia coli in İzmir province, Turkey

Background

Extraintestinal pathogenic Escherichia coli (ExPEC) is an important bacterium and responsible for many bloodstream infections, including urinary tract infections and even fatal bacteremia. The aim of this research was to investigate whether ExPEC strains isolated from Turkish blood cultures have a relationship between 16S rRNA based phylogenetic clusters and antibiotic resistance profiles, virulence factors or clonal lineages.

Methods

Phenotypically identified ExPEC blood culture isolates (n = 104) were included in this study. The 16S rRNA partial sequence analysis was performed for genotypic identification of ExPEC isolates. Antibiotic susceptibility and Extended-Spectrum β-Lactamase testing of isolates were performed. Phylogenetic classification (A, B1, B2 and D), Multi Locus Sequence Typing analysis and virulence-associated genes were investigated.

Results

Based on 16S rRNA partial sequence analysis, 97 out of 104 (93.26%) ExPEC isolates were confirmed as E. coli. Ampicillin (74.22%) and cefuroxime axetil (65.97%) resistances had the highest frequencies among the ExPEC isolates. In terms of phylogenetic classification of ExPEC, D (38.14%, 37/97) was the most prevalent group after A (29.89%, 29/97), B2 (20.61%, 20/97), and B1 (11.34%, 11/97). The sequence types of the 20 ExPEC isolates belonging to the B2 phylogenetic group were analyzed by Multi Locus Sequence Typing. Ten isolates out of 20 (50.0%) were identified as ST131. The other STs were ST95 (n = 1), ST14 (n = 1), ST10 (n = 1), ST69 (n = 1), ST1722 (n = 2), ST141 (n = 1), ST88 (n = 1), ST80 (n = 1), and ST998 (n = 1). Of the ST131 strains, six (60%, 6/10) represented serogroup O25. The most common virulence factor genes were serum resistance factor gene, traT (55.7%) aerobactin siderophore receptor and yersiniabactin encoding genes iutA (45.3%) and fyuA (50.5%), respectively. In addition, PAI (41.2%), iroN (23.7%), hlyA (15.4%), kpsII (13.4%), ompT (13.4%), papG (12.4%), iss (9.3%), cnf1 (7.2%), ibeA (2.06%), and sfaS (2.06%) genes were present in the ExPEC isolates.

Conclusion

The 16S rRNA-based phylogenetic relationship tree analysis showed that a large cluster was present among 97 ExPEC isolates along with related reference strains. There were 21 main clusters with 32 closely related subclusters. Based on our findings, different clonal lineages of ExPEC can display different antibiotic susceptibilities and virulence properties. We also concluded that virulence factors were not distributed depending on phylogenetic groups (A, B1, B2, and D). The ExPEC isolates belonging to the same phylogenetic group and sequence type could display different resistance and virulence characteristics.