Detection of pap, sfa, afa, foc, and fim Adhesin-Encoding Operons in Uropathogenic Escherichia coli Isolates Collected From Patients With Urinary Tract Infection

Role of Small Non-Coding RNA in Gram-Negative Bacteria: New Insights and Comprehensive Review of Mechanisms, Functions, and Potential Applications

Small non-coding RNAs (sRNAs) are a key part of gene expression regulation in bacteria. Many physiologic activities like adaptation to environmental stresses, antibiotic resistance, quorum sensing, and modulation of the host immune response are regulated directly or indirectly by sRNAs in Gram-negative bacteria. Therefore, sRNAs can be considered as potentially useful therapeutic options. They have opened promising perspectives in the field of diagnosis of pathogens and treatment of infections caused by antibiotic-resistant organisms. Identification of sRNAs can be executed by sequence and expression-based methods. Despite the valuable progress in the last two decades, and discovery of new sRNAs, their exact role in biological pathways especially in co-operation with other biomolecules involved in gene expression regulation such as RNA-binding proteins (RBPs), riboswitches, and other sRNAs needs further investigation. Although the numerous RNA databases are available, including 59 databases used by RNAcentral, there remains a significant gap in the absence of a comprehensive and professional database that categorizes experimentally validated sRNAs in Gram-negative pathogens. Here, we review the present knowledge about most recent and important sRNAs and their regulatory mechanism, strengths and weaknesses of current methods of sRNAs identification. Also, we try to demonstrate the potential applications and new insights of sRNAs for future studies.

Genome characterization of a multi-drug resistant Escherichia coli strain, L1PEag1, isolated from commercial cape gooseberry fruits (Physalis peruviana L.)

Introduction

Foodborne infections, which are frequently linked to bacterial contamination, are a serious concern to public health on a global scale. Whether agricultural farming practices help spread genes linked to antibiotic resistance in bacteria associated with humans or animals is a controversial question.

Methods

This study applied a long-read Oxford Nanopore MinION-based sequencing to obtain the complete genome sequence of a multi-drug resistant Escherichia coli strain (L1PEag1), isolated from commercial cape gooseberry fruits (Physalis peruviana L.) in Ecuador. Using different genome analysis tools, the serotype, Multi Locus Sequence Typing (MLST), virulence genes, and antimicrobial resistance (AMR) genes of the L1PEag1 isolate were determined. Additionally, in vitro assays were performed to demonstrate functional genes.

Results

The complete genome sequence of the L1PEag1 isolate was assembled into a circular chromosome of 4825.722 Kbp and one plasmid of 3.561 Kbp. The L1PEag1 isolate belongs to the B2 phylogroup, sequence type ST1170, and O1:H4 serotype based on in silico genome analysis. The genome contains 4,473 genes, 88 tRNA, 8 5S rRNA, 7 16S rRNA, and 7 23S rRNA. The average GC content is 50.58%. The specific annotation consisted of 4,439 and 3,723 genes annotated with KEEG and COG respectively, 3 intact prophage regions, 23 genomic islands (GIs), and 4 insertion sequences (ISs) of the ISAs1 and IS630 families. The L1PEag1 isolate carries 25 virulence genes, and 4 perfect and 51 strict antibiotic resistant gene (ARG) regions based on VirulenceFinder and RGI annotation. Besides, the in vitro antibiotic profile indicated resistance to kanamycin (K30), azithromycin (AZM15), clindamycin (DA2), novobiocin (NV30), amikacin (AMK30), and other antibiotics. The L1PEag1 isolate was predicted as a human pathogen, matching 464 protein families (0.934 likelihood).

Conclusion

Our work emphasizes the necessity of monitoring environmental antibiotic resistance, particularly in commercial settings to contribute to develop early mitigation techniques for dealing with resistance diffusion.

Detection of phylogrouping, adhesin, and extended spectrum β-lactamases genes in hospital acquired uropathogenic Escherichia coli isolates

BACKGROUND

It has been interesting to compare the levels of antimicrobial resistance and the virulence characteristics of uropathogenic Escherichia coli (UPEC) strains of certain phylogenetic groups. The purpose of this study was to identify the frequency of phylogenetic groups, adhesin genes, antibiotic sensitivity patterns, and extended spectrum-lactamases (ESBLs) genes in hospital-acquired UPEC.

METHODS

After UPEC isolation, the disc diffusion method was used to assess its susceptibility to antibiotics. Combination disc testing confirmed the existence of ESBL producers. Polymerase chain reaction (PCR) was used to detect genes for adhesin and ESBLs.

RESULTS

One hundred and twenty-eight E. coli were isolated which had the highest resistance to tetracycline (96%) followed by cefoxitin (93%), cefepime (92%), ceftazidime (79%), aztreonam (77%) and sulfamethoxazole -trimethoprim (75%). About 57% of isolates were phenotypically ESBLs positive and they were confirmed by PCR. B2 phylogroup (41%) was the most frequent in E. coli isolates then group D (30%), group A (18%), and lastly group B1 (11%). ESBLs genes were more significantly prevalent in phylogroups B2 and D than other phylogroups (P < 0.001). Regarding adhesin genes, both fim H and afa were more significantly associated with group B2 than other groups (P < 0.009, < 0.032), respectively. In ESBL-positive isolates, both genes were more significantly detected compared to negative ones (P < 0.001).

CONCLUSION

Phylogroups B2 and D of UPEC are important reservoirs of antimicrobial resistance and adhesion genes. Detection of ESBL-producing E. coli is important for appropriate treatment as well as for effective infection control in hospitals.

Uropathogenic Escherichia coli (UPEC)-Associated Urinary Tract Infections: The Molecular Basis for Challenges to Effective Treatment

Urinary tract infections (UTIs) are among the most common bacterial infections, especially among women and older adults, leading to a significant global healthcare cost burden. Uropathogenic Escherichia coli (UPEC) are the most common cause and accounts for the majority of community-acquired UTIs. Infection by UPEC can cause discomfort, polyuria, and fever. More serious clinical consequences can result in urosepsis, kidney damage, and death. UPEC is a highly adaptive pathogen which presents significant treatment challenges rooted in a complex interplay of molecular factors that allow UPEC to evade host defences, persist within the urinary tract, and resist antibiotic therapy. This review discusses these factors, which include the key genes responsible for adhesion, toxin production, and iron acquisition. Additionally, it addresses antibiotic resistance mechanisms, including chromosomal gene mutations, antibiotic deactivating enzymes, drug efflux, and the role of mobile genetic elements in their dissemination. Furthermore, we provide a forward-looking analysis of emerging alternative therapies, such as phage therapy, nano-formulations, and interventions based on nanomaterials, as well as vaccines and strategies for immunomodulation. This review underscores the continued need for research into the molecular basis of pathogenesis and antimicrobial resistance in the treatment of UPEC, as well as the need for clinically guided treatment of UTIs, particularly in light of the rapid spread of multidrug resistance.

Dynamic single cell analysis in a proximal-tubule-on-chip reveals heterogeneous epithelial colonization strategies of uropathogenic Escherichia coli under shear stress

The urinary tract is a hydrodynamically challenging microenvironment and uropathogenic Escherichia coli (UPEC) must overcome several physiological challenges in order to adhere and establish a urinary tract infection. Our previous work in vivo revealed a synergy between different UPEC adhesion organelles, which facilitated effective colonization of the renal proximal tubule. To allow high-resolution real-time analysis of this colonization behavior, we established a biomimetic proximal-tubule-on-chip (PToC). The PToC allowed for single-cell resolution analysis of the first stages of bacterial interaction with host epithelial cells, under physiological flow. Time-lapse microscopy and single-cell trajectory analysis in the PToC revealed that while the majority of UPEC moved directly through the system, a minority population initiated heterogeneous adhesion, identified as either rolling or bound. Adhesion was predominantly transient and mediated by P pili at the earliest time-points. These bound bacteria initiated a founder population which rapidly divided, leading to 3D microcolonies. Within the first hours, the microcolonies did not express extracellular curli matrix, but rather were dependent on Type 1 fimbriae as the key element in the microcolony structure. Collectively, our results show the application of Organ-on-chip technology to address bacterial adhesion behaviors, demonstrating a well-orchestrated interplay and redundancy between adhesion organelles that enables UPEC to form microcolonies and persist under physiological shear stress.

Urinary tract virulence genes in extended-spectrum beta-lactamase E. coli from dairy cows, beef cattle, and small ruminants

Extended-spectrum β-lactamase Escherichia coli is an important cause of urinary tract infections in humans. ESBL producers E. coli were reported in food-producing animals, but no previous study reported the virulence potential of these isolates. Thus, this study determined the virulence potential of ESBL producers E. coli isolates from 518 beef feces, 610 dairy cow feces, 305 dairy cow milk, 503 sheep milk and 445 goat milk samples. A total of 278 isolates; specifically, 130 from beef feces, 39 from the cow's feces, 42 from cow's milk, 44 from sheep milk and 23 from goats' milk were isolated and then tested for 14 virulence genes by polymerase chain reaction. After that, the correlation of virulence genes presence among the isolates was determined statistically. Overall, 97% of the isolates carried fimH, 39% carried iroN _{E. coli} and 32% carried papC. The kpsMT K1, cnf1, papAH, papG allele II & III, papG allele II, and kpsMT II were carried by 6 to 23% of the isolates, while less than 6% of the isolates carried papG allele III, papG allele I, Univcnf, iutA and hlyA. About 68.2% of the isolates carried two or more virulence genes and 41.8% carried three or more. Moreover, the isolates had 71 different profiles of virulence genes, where the most common profiles were fimH alone (86 isolate), fimH + iroN _{E. coli} (35 isolate), fimH + papC (20 isolate), and fimH + papC + iroN _{E. coli} (13 isolate). The adhesion, capsule synthesis and toxins secretion genes were significantly associated (p ˂ 0.01) with each other. These results call for awareness about the risk of food animals as reservoirs of ESBL uropathogenic E. coli that would threaten public health and limits the treatment options for urinary tract infections.

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.

Evaluation of Biofilm Formation and Virulence Genes and Association with Antibiotic Resistance Patterns of Uropathogenic Escherichia coli Strains in Southwestern Iran

Background: Uropathogenic Escherichia coli (UPEC) strains, encoding superficial and secretory virulence factors, can lead to colonization and facilitation of bacterial growth in the host urinary tract, causing Urinary Tract Infection (UTI). Objectives: This study determined the ability of biofilm formation by the Congo red agar method, the presence of virulence genes using the multiplex polymerase chain reaction (PCR) method, and the relationship between biofilm formation and antibiotic resistance patterns and virulence genes in E. coli clinical isolates in Yasuj. Methods: This cross-sectional study was performed on 144 UPEC isolates collected in 2017. Biofilm formation was detected by the Congo red agar phenotypic assay and virulence factors by the multiplex PCR method. Antibiotic resistance tests were performed by the Kirby-Bauer method. Results: Out of 144 isolates of E. coli, 22 (19.4%) isolates showed to be strong biofilm producers, 27 (23.8%) moderate biofilm producers, and 64 (56.3%) weak biofilm producers. A significant relationship was observed between biofilm-producing strains and resistance to ampicillin (P = 0.020) and cotrimoxazole (P = 0.038). The virulence genes in strong biofilm producers included iutA (95%), FimH (93%), ompT (90%), PAI (90%), and TraT (81%) genes. The phylogroup B2 carried the most virulence genes. A significant correlation was observed between E. coli phylogenetic groups and aer (P = 0.019), iroN (P = 0.042), and ompT (P = 0.032) virulence genes. Conclusions: The results of this study showed a high prevalence of virulence genes, and antibiotic-resistant E. coli strains capable of biofilm formation. The results of this study may help elucidate the pathogenesis of UPEC and facilitate better treatment strategies for patients with UTIs in this geographic area.

Genetic diversity and virulence characteristics of biofilm-producing uropathogenic Escherichia coli

Uropathogenic E. coli (UPEC) strains exhibit different levels of biofilm formation that help adhesion of the bacteria to uroepithelial cells. We investigated the genetic diversity and virulence-associated genes (VAGs) of biofilm-producing UPEC. A collection of 107 biofilm-producing (BFP) UPEC strains isolated from patients with UTI in Iran were divided into three groups of strong, moderate, and weak BFPs after a quantitative microtiter plate assay, and the involvement of curli and cellulose in adhesion of the strains to T24 cell line was confirmed by the construction of csgD and yedQ mutants of two representative UPEC strains. BFP strains were tested for their genetic diversity, phylogenetic groups, and the presence of 15 VAGs. A significant decrease in adhesion of csgD and yedQ mutant strains confirmed the role of biofilm production in adhesion to uroepithelial cells. A high diversity was found among all three groups of strong (Di = 0.998), moderate (Di = 0.998), and weak (Di = 0.988) BFPs with majority of the strains belonging to phylogroups B2 (44.9%) and A (24.3%). Strong BFP strains carried significantly higher level papEF, hlyA, and iutA than other BFP groups. In contrast, the presence of fimH, focG, sfaS, set-1, and cvaC was more pronounced among weak BFP strains. There exists a high genetic diversity among the BFP strains with different VGA profiles. However, the high prevalence of phylogroup A among BFP strains suggests the fitness of commensal E. coli strains to cause UTI in this country.

Phenotypic and Genotypic Properties of Fluoroquinolone-Resistant, qnr-Carrying Escherichia coli Isolated from the German Food Chain in 2017

Fluoroquinolones are the highest priority, critically important antimicrobial agents. Resistance development can occur via different mechanisms, with plasmid-mediated quinolone resistance (PMQR) being prevalent in the livestock and food area. Especially, qnr genes, commonly located on mobile genetic elements, are major drivers for the spread of resistance determinants against fluoroquinolones. We investigated the prevalence and characteristics of qnr-positive Escherichia (E.) coli obtained from different monitoring programs in Germany in 2017. Furthermore, we aimed to evaluate commonalities of qnr-carrying plasmids in E. coli. We found qnr to be broadly spread over different livestock and food matrices, and to be present in various sequence types. The qnr-positive isolates were predominantly detected within selectively isolated ESBL (extended spectrum beta-lactamase)-producing E. coli, leading to a frequent association with other resistance genes, especially cephalosporin determinants. Furthermore, we found that qnr correlates with the presence of genes involved in resistance development against quaternary ammonium compounds (qac). The detection of additional point mutations in many isolates within the chromosomal QRDR region led to even higher MIC values against fluoroquinolones for the investigated E. coli. All of these attributes should be carefully taken into account in the risk assessment of qnr-carrying E. coli from livestock and food.

A One Health Perspective for Defining and Deciphering Escherichia coli Pathogenic Potential in Multiple Hosts

E. coli is one of the most common species of bacteria colonizing humans and animals. The singularity of E. coli 's genus and species underestimates its multifaceted nature, which is represented by different strains, each with different combinations of distinct virulence factors. In fact, several E. coli pathotypes, or hybrid strains, may be associated with both subclinical infection and a range of clinical conditions, including enteric, urinary, and systemic infections. E. coli may also express DNA-damaging toxins that could impact cancer development. This review summarizes the different E. coli pathotypes in the context of their history, hosts, clinical signs, epidemiology, and control. The pathotypic characterization of E. coli in the context of disease in different animals, including humans, provides comparative and One Health perspectives that will guide future clinical and research investigations of E. coli infections.

Distribution of phylogenetic groups, adhesin genes, biofilm formation, and antimicrobial resistance of uropathogenic Escherichia coli isolated from hospitalized patients in Thailand

Background

Urinary tract infections (UTIs) are the most common bacterial infections and are often caused by uropathogenic Escherichia coli (UPEC). We investigated the distribution of phylogenetic groups, adhesin genes, antimicrobial resistance, and biofilm formation in E. coli isolated from patients with UTIs.

Methods

In the present study, 208 UPEC isolated from Thai patients were classified into phylogenetic groups and adhesin genes were detected using multiplex PCR. Antimicrobial susceptibility testing was performed using agar disk diffusion. The Congo red agar method was used to determine the ability of the UPEC to form biofilm.

Results

The most prevalent UPEC strains in this study belonged to phylogenetic group B2 (58.7%), followed by group C (12.5%), group E (12.0%), and the other groups (16.8%). Among adhesin genes, the prevalence of fimH (91.8%) was highest, followed by pap (79.3%), sfa (12.0%), and afa (7.7%). The rates of resistance to fluoroquinolones, trimethoprim-sulfamethoxazole, and amoxicillin-clavulanate were  65%, 54.3%, and 36.5%, respectively. The presence of adhesin genes and antibiotic resistance were more frequent in groups B2 and C compared to the other groups. Of the 129 multidrug-resistant UPEC strains, 54% were biofilm producers. Our findings further indicated that biofilm production was significantly correlated with the pap adhesin gene (p ≤ 0.05).

Conclusion

These findings provide molecular epidemiologic data, antibiotic resistance profiles, and the potential for biofilm formation among UPEC strains that can inform further development of the appropriate prevention and control strategies for UTIs in this region.

Isolation, Characterization and Genomic Analysis of a Novel Bacteriophage VB_EcoS-Golestan Infecting Multidrug-Resistant Escherichia coli Isolated from Urinary Tract Infection

Escherichia coli (E. coli) is one of the most common uropathogenic bacteria. The emergence of multi-drug resistance among these bacteria resulted in a worldwide public health problem which requires alternative treatment approaches such as phage therapy. In this study, phage VB_EcoS-Golestan, a member of Siphoviridae family, with high lytic ability against E. coli isolates, was isolated from wastewater. Its burst size was large and about 100 plaque-forming units/infected cell, rapid adsorption time, and high resistance to a broad range of pH and temperatures. Bioinformatics analysis of the genomic sequence suggests that VB_EcoS-Golestan is a new phage closely related to Escherichia phages in the Kagunavirus genus, Guernseyvirinae subfamily of Siphoviridae. The genome size was 44829 bp bp that encodes 78 putative ORFs, no tRNAs, 7 potential promoter sequences and 13 Rho-factor-independent terminators. No lysogenic mediated genes were detected in VB_EcoS-Golestan genome. Overall VB_EcoS-Golestan might be used as a potential treatment approach for controlling E. coli mediated urinary tract infection, however, further studies are essential to ensure its safety.

Distribution of virulence genes and phylogenetics of uropathogenic Escherichia coli among urinary tract infection patients in Addis Ababa, Ethiopia

Background

Urinary tract infection (UTI) is a common cause of morbidity worldwide. Uropathogenic Escherichia coli (UPEC) bacteria are the major cause of urinary tract infections. UPEC strains derive from different phylogenetic groups and possess an arsenal of virulence factors that contribute to their ability to overcome different defense mechanisms and cause disease. The objective of this study was to identify phylogroup and virulence genes of UPEC among urinary tract infection patients.

Methods

A cross sectional study was conducted from January 1, 2017 to October 9, 2017. E. coli bacteria were isolated from UTI patients using culture and conventional biochemical tests. Identification of phylogroup and genes that encodes for virulence factors was done using multiplex polymerase chain reaction (PCR). Data was processed and analyzed with SPSS version16.0 and Epi-info version 3.4.1 software.

Results

The most common urologic clinical manifestation combinations in this study were dysuria, urine urgency and urgency incontinence. The frequent UPEC virulence gene identified was fimH 164 (82%), followed by aer 109 (54.5%), hly 103 (51.5%), pap 59 (29.5%), cnf 58 (29%), sfa 50 (25%) and afa 24 (12%).There was significant association between pap gene and urine urgency (p-0.016); sfa and dysuria and urine urgency (p-0.019 and p-0.043 respectively); hly and suprapubic pain (p-0.002); aer and suprapubic pain, flank pain and fever (p-0.017, p-0.040, p-0.029 respectively). Majority of E. coli isolates were phylogroup B2 60(30%) followed by D 55(27.5%), B1 48(24%) and A 37(18.5%). There was significant association between E. coli phylogroup B2 and three virulence genes namely afa, pap, and sfa (p-0.014, p-0.002, p-0.004 respectively).

Conclusion

In this study the most frequent E. coli virulence gene was fimH, followed by aer, hly, pap, cnf, sfa and afa respectively. There was significant association between E. coli virulence genes and clinical symptoms of UTI. The phylogenetic analysis indicates majority of uropathogenic E. coli isolates were phylogroup B2 followed by phylogroup D. Phylogroup B2 carries more virulence genes. Hence, targeting major UPEC phylogroup and virulence genes for potential vaccine candidates is essential for better management of UTI and further research has to be conducted in this area.

Virulence and Resistance Determinants of Uropathogenic Escherichia coli Strains Isolated from Pregnant and Non-Pregnant Women from Two States in Mexico

BACKGROUND/PURPOSE

Uropathogenic E. coli (UPEC) is the main cause of urinary tract infection (UTI) and it is known that pregnant women have a higher risk for UTI. UPEC has a variety of virulence and antibiotic resistance factors that facilitate its pathogenic success and it is crucial to know which are the susceptibility patterns, Extended-Spectrum-β-Lactamase (ESBL) production, virulence genes, pathogenicity islands (PAI), phylogenetic groups and serotypes among strains isolated from pregnant and non-pregnant women.

METHODS

One hundred fifty UPEC strains were isolated from pregnant and non-pregnant women from two different Mexican states (Sonora and Puebla). Strains were analyzed using the Kirby-Bauer method for the determination of antibiotic susceptibility and ESBL. Virulence genes, PAIs and phylogenetic groups were determined using a multiplex PCR. Strains were serotyped by an agglutination assay. Blood agar and CAS agar were used for phenotypic assays.

RESULTS

92.7% of UPEC strains showed multidrug-resistant (MDR), 6.7% extremely-resistant (XDR) and 0.6% pandrug-resistant (PDR). The highest resistance was determined to be for β-lactam antibiotics (>72% in both states) and 44.5% of the UPEC strains were ESBL+. The predominant virulence genes found were fimH (100%), iucD (85%) and iha (60%). The strains isolated from pregnant women from Puebla presented a large percentage of genes associated with upper urinary tract infections. PAIs were found in 51% and 68% of the strains from Sonora and Puebla, respectively. All the strains were siderophores producers and 41.5% produced hemolysis. The serotypes found were diverse and belonged to phylogroups A, B2 and C.

CONCLUSION

The UPEC strains from this study are MDR with tendency to XDR or PDR, they can cause upper UTIs and are serotypically and phylogenetically diverse, which supports the need to develop new strategies for UTI treatment in pregnant and non-pregnant Mexican women.

In vitro assessment of pathogenicity and virulence encoding gene profiles of avian pathogenic Escherichia coli strains associated with colibacillosis in chickens

BACKGROUND

Avian pathogenic Escherichia coli (APEC) strains have been associated with various disease conditions in avian species due to virulence attributes associated with the organism.

AIMS

This study was carried out to determine the in vitro pathogenic characteristics and virulence encoding genes found in E. coli strains associated with colibacillosis in chickens.

METHODS

Fifty-two stock cultures of E. coli strains isolated from chickens diagnosed of colibacillosis were tested for their ability to produce haemolysis on blood agar and take up Congo red dye. Molecular characterization was carried out by polymerase chain reaction (PCR) amplification of virulence encoding genes associated with APEC.

RESULTS

Eleven (22%) and 41 (71%) were positive for haemolysis on 5% sheep red blood agar and Congo red agar, respectively. Nine virulence-associated genes were detected as follows: FimH (96%), csgA (52%), iss (48%), iut (33%), tsh (21%), cva (15%), kpsII (10%), pap (2%), and felA (2%).

CONCLUSION

The APEC strains exhibited virulence properties and harbored virulence encoding genes which could be a threat to the poultry population and public health. The putative virulence genes were diverse and different in almost all isolate implying that pathogenesis was multi-factorial and the infection was multi-faceted which could be a source of concern in the detection and control of APEC infections.

Characterization of antibiotic resistance and virulence factors of Escherichia coli strains isolated from Iranian inpatients with urinary tract infections

Background

Urinary tract infections (UTIs) are one of the most frequent human infectious diseases causing considerable amount of morbidity and mortality. The present study aimed to investigate the occurrence of antibiotics resistance and virulence genes among Escherichia coli strains isolated from UTIs in the north of Iran.

Methods

This cross-sectional study was performed at 5 teaching hospitals in Rasht in the north of Iran. Totally, 129 E. coli isolates were identified by standard microbiologic tests. Antimicrobial susceptibility pattern was determined using disk diffusion method. The presence of virulence genes was detected by PCR method.

Results

The results of antibiotic susceptibility showed that the highest resistance rates were to ampicillin (78.3%) followed by nalidixic acid (74.4%) and trimethoprim/sulfamethoxazole (69.8%). On the other hand, the highest susceptibility was toward nitrofurantoin (96.1%) and imipenem (92.2%). Further analysis revealed that the rate of ESBL-producing and multiple-drug resistant isolates was 51.2% and 84.5%, respectively. Molecular analysis revealed that traaT (87.6%) gene was the most prevalent virulence factors followed by fyuA (86%) and kpsmt (76%) genes. Also, fimH gene was the most frequently detected adhesion-associated gene with 74.4%.

Conclusion

In summary, our results showed a remarkable rate of drug resistance and heterogeneity for virulence factors among E. coli strains isolated from UTIs in the north of Iran. The emergence of such strains can be a predictive marker for their persistence in the hospital and consequently a significant threat for hospitalized patients.

Microbiome patterns reveal the transmission of pathogenic bacteria in hilsa fish (Tenualosa ilisha) marketed for human consumption in Bangladesh

AIMS

This study conducted bacterial community, virulence and antibiogram profiling inside the hindgut and skin of freshly caught hilsa fish and those sold at markets.

METHODS AND RESULTS

The results of 16S rRNA-based high-throughput sequencing showed a higher number of bacterial genera in marketed fish samples than in fresh fish samples. The total operational taxonomic units, genus counts and diversity index were significantly higher (P > 0·05) in marketed fish, which also had abundant pathogenic bacterial groups. Skin samples had a lower profusion of pathogenic bacteria than gut samples. A total of 52 bacterial isolates from nine species were identified in this study, of which 25 were from a Chittagong market and 22 were from a Dhaka market, whereas only five were from fresh hilsa. The polymerase chain reaction amplification of 12 species-specific virulence genes in the 52 isolates, namely, aer, hly, chxA, toxB, rtxC, sfa, uge, norB, trx, toxA, ipaH, sigA and coa, indicated a high number of positive samples containing Vibrio cholerae, Aeromonas spp., Klebsiella pneumoniae, Escherichia coli and Staphylococcus aureus. Antibiogram profiling of these bacteria against 10 commercial antibiotics showed high-resistance patterns of the isolates against sulfamethoxazole, kanamycin, neomycin, ampicillin and tetracycline.

CONCLUSION

The results reveal the spread of multidrug-resistant bacteria in hilsa fish marketed for human consumption in Bangladesh.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study highlights the risk of spreading environmentally and clinically pathogenic bacteria in fish sold for human consumption in Bangladesh. Such bacteria come from aquatic pollution and poor handling, storage and transportation practices that may predispose fish to major outbreaks of infectious and waterborne diseases.

Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports

Extraintestinal pathogenic E. coli (ExPEC) are facultative pathogens that are part of the normal human intestinal flora. The ExPEC group includes uropathogenic E. coli (UPEC), neonatal meningitis E. coli (NMEC), sepsis-associated E. coli (SEPEC), and avian pathogenic E. coli (APEC). Virulence factors (VF) related to the pathogenicity of ExPEC are numerous and have a wide range of activities, from those related to bacteria colonization to those related to virulence, including adhesins, toxins, iron acquisition factors, lipopolysaccharides, polysaccharide capsules, and invasins, which are usually encoded on pathogenicity islands (PAIs), plasmids and other mobile genetic elements. Mechanisms underlying the dynamics of ExPEC transmission and the selection of virulent clones are still poorly understood and require further research. The time shift between colonization of ExPEC and the development of infection remains problematic in the context of establishing the relation between consumption of contaminated food and the appearance of first disease symptoms. What appears to be most difficult is to prove that ExPEC strains cause disease symptoms and to examine the mechanism of transition from the asymptomatic colonization of the intestines to the spreading of the bacteria outside the digestive system. A significant problem for researchers who are trying to ascribe ExPEC transmission to food, people or the environment is to draw the distinction between colonization of ExPEC and infection. Food safety is an important challenge for public health both at the production stage and in the course of its processing and distribution. Examination of the genetic similarity of ExPEC strains will allow to determine their origin from different sources. Many levels of genotyping have been proposed in which the typing of strains, plasmids and genes is compared in order to obtain a more complete picture of this complex problem. The aim of our study was to characterize E. coli strains isolated from humans, animals and food for the presence of bacterial genes encoding virulence factors such as toxins, and iron acquisition systems (siderophores) in the context of an increasing spread of ExPEC infections.

Distribution of virulence genes and their association with antimicrobial resistance among uropathogenic Escherichia coli isolates from Iranian patients

BACKGROUND

Urinary tract infections (UTIs) are one of the most frequent diseases encountered by humans worldwide. The presence of multidrug-resistant (MDR) uropathogenic Escherichia coli (UPEC) harboring several virulence factors, is a major risk factor for inpatients. We sought to investigate the rate of antibiotic resistance and virulence-associated genes among the UPECs isolated from an Iranian symptomatic population.

METHODS

A total of 126 isolates from inpatients with UTI from different wards were identified as UPEC using the conventional microbiological tests. After identification of UPECs, all the isolates were subjected to antimicrobial susceptibility test and polymerase chain reaction (PCR) to identify the presence of 9 putative virulence genes and their association with the clinical outcomes or antimicrobial resistance.

RESULTS

The data showed that the highest and the lowest resistance rates were observed against ampicillin (88.9%), and imipenem (0.8%), respectively. However, the frequency of resistance to ciprofloxacin was found to be 55.6%. High prevalence of MDR (77.8%) and extended-spectrum β-lactamase (ESBL) (54.8%) were substantial. PCR results revealed the frequency of virulence genes ranged from 0 to 99.2%. Among 9 evaluated genes, the frequency of 4 genes (fimH, sfa, iutA, and PAI marker) was > 50% among all the screened isolates. The iutA, pap GII, and hlyA genes were more detected in the urosepsis isolates with significantly different frequencies. The different combinations of virulence genes were characterized as urovirulence patterns. The isolates recovered from pyelonephritis, cystitis, and urosepsis cases revealed 27, 22, and 6 virulence patterns, respectively. A significant difference was determined between ESBL production with pap GII, iutA, and PAI marker genes.

CONCLUSIONS

Our study highlighted the MDR UPEC with high heterogeneity of urovirulence genes. Considering the high rate of ciprofloxacin resistance, alternative drugs and monitoring of the susceptibility profile for UPECs are recommended.

Detection of Antimicrobial Susceptibility and Integrons Among Extended-spectrum β-lactamase Producing Uropathogenic Escherichia coli Isolates in Southwestern Iran

Objectives

Urinary tract infections (UTIs) are one of the most prevalent infectious diseases and can lead to a high rate of morbidity and mortality. The emergence of multiple-drug resistant strains, particularly extended-spectrum beta-lactamases (ESBLs) producing strains, has become a global healthcare concern. Our study sought to investigate the antimicrobial resistance pattern and presence of integrons and fimH determinants among uropathogenic Escherichia coli (UPEC) isolates obtained from hospitalized Iranian patients.

Methods

This cross-sectional study was performed on 121 E. coli isolates recovered from patients with clinical symptoms of UTIs, referred to Shiraz Nemazee Hospital, in 2016-17. The isolates were identified by standard microbiologic tests and confirmed by API 20E strip. Antimicrobial susceptibility testing was determined using the disk diffusion method. The presence of fimH and classes 1-3 integron encoding genes was determined using the polymerase chain reaction.

Results

Ampicillin (9.1%) and nalidixic acid (19.0%) showed the lowest level of antibiotic susceptibility. The highest level of susceptibility was toward imipenem (77.7%). The rate of ESBL-producing isolates was 42.1%. There was a significant association between production of ESBLs and higher antibiotic resistance in the tested isolates. Of the investigated virulence and resistance genes, fimH, intI1, and intI2 were positive in 98.3%, 59.5%, and 7.4% of isolates, respectively.

Conclusions

The remarkable rate of ESBL-producing UPEC isolates accompanied with the presence of integrons suggest the necessity of restricted infection control policies to prevent further dissemination of resistant strains.

Altered Regulation of the Diguanylate Cyclase YaiC Reduces Production of Type 1 Fimbriae in a Pst Mutant of Uropathogenic Escherichia coli CFT073

The pst gene cluster encodes the phosphate-specific transport (Pst) system. Inactivation of the Pst system constitutively activates the two-component regulatory system PhoBR and attenuates the virulence of pathogenic bacteria. In uropathogenic Escherichia coli strain CFT073, attenuation by inactivation of pst is predominantly attributed to the decreased expression of type 1 fimbriae. However, the molecular mechanisms connecting the Pst system and type 1 fimbriae are unknown. To address this, a transposon library was constructed in the pst mutant, and clones were tested for a regain in type 1 fimbrial production. Among them, the diguanylate cyclase encoded by yaiC (adrA in Salmonella) was identified to connect the Pst system and type 1 fimbrial expression. In the pst mutant, the decreased expression of type 1 fimbriae is connected by the induction of yaiC This is predominantly due to altered expression of the FimBE-like recombinase genes ipuA and ipbA, affecting at the same time the inversion of the fim promoter switch (fimS). In the pst mutant, inactivation of yaiC restored fim-dependent adhesion to bladder cells and virulence. Interestingly, the expression of yaiC was activated by PhoB, since transcription of yaiC was linked to the PhoB-dependent phoA-psiF operon. As YaiC is involved in cyclic di-GMP (c-di-GMP) biosynthesis, an increased accumulation of c-di-GMP was observed in the pst mutant. Hence, the results suggest that one mechanism by which deletion of the Pst system reduces the expression of type 1 fimbriae is through PhoBR-mediated activation of yaiC, which in turn increases the accumulation of c-di-GMP, represses the fim operon, and, consequently, attenuates virulence in the mouse urinary tract infection model.IMPORTANCE Urinary tract infections (UTIs) are common bacterial infections in humans. They are mainly caused by uropathogenic Escherichia coli (UPEC). We previously showed that interference with phosphate homeostasis decreases the expression of type 1 fimbriae and attenuates UPEC virulence. Herein, we identified that alteration of the phosphate metabolism increases production of the signaling molecule c-di-GMP, which in turn decreases the expression of type 1 fimbriae. We also determine the regulatory cascade leading to the accumulation of c-di-GMP and identify the Pho regulon as new players in c-di-GMP-mediated cell signaling. By understanding the molecular mechanisms leading to the expression of virulence factors, we will be in a better position to develop new therapeutics.