Rapid and simple determination of the Escherichia coli phylogenetic group

Investigating the effect of sub MIC concentrations of ciprofloxacin, ceftriaxone and imipenem on the expression of virulence and toxin-antitoxin genes of Escherichia coli strains isolated from blood infections in leukemia patients

Bloodstream infections (BSIs) pose significant risks to individuals with leukemia, and Escherichia coli stands out as a prevalent cause in these infections. This research sought to explore the impact of sub-inhibitory concentrations (sub-MIC) of ciprofloxacin, imipenem, ceftriaxone, and the combined use of ceftriaxone and ciprofloxacin on the expression of virulence factors and toxin-antitoxin genes in E. coli strains obtained from leukemia patients. Twelve clinical strains of E. coli that demonstrated resistance to ciprofloxacin, imipenem, and ceftriaxone and contained the chosen virulence and toxin-antitoxin genes were included in the study. The minimum inhibitory concentration (MIC) of ciprofloxacin, imipenem, and ceftriaxone was determined using the microbroth dilution method. Furthermore, the expression levels of virulence genes (iutA, traT, afaA, hlyA) and toxin-antitoxin genes (relE, mazF) were assessed via Real-time PCR both before and after exposure to ciprofloxacin, ceftriaxone, and imipenem. According to our findings, the sub-MIC concentrations of ciprofloxacin, imipenem, and ceftriaxone resulted in decreased expression levels of virulence factor genes (iutA, traT, afaA) and toxin-antitoxin genes (relE, mazF), with the exception of an increase in hlyA gene expression. The findings indicate that prophylactic and experimental use of sub-MICs of ciprofloxacin, imipenem, ceftriaxone, and a combination of ciprofloxacin and ceftriaxone can diminish the expression of virulence factors and toxin-antitoxin genes in E. coli. Further research is necessary to explore the interactions between antibiotic resistance and virulence genes, particularly in the blood infections.

Impact of vaccination on the ecology of Escherichia coli in commercial Turkey production

Escherichia coli is a bacterium ubiquitous to the healthy intestinal microflora in animals. Some E. coli can cause disease in poultry, but disease manifestation is a result of the balance between stress level in the bird and the virulence potential of E. coli strains present. The collection of diseases caused by E. coli is referred to as colibacillosis, which has continually burdened the poultry industry through significant morbidity, mortality, condemnations, and reduced performance. Avian pathogenic E. coli (APEC) refers to strains with shared genetic traits enhancing their ability to cause colibacillosis and have been well characterized. However, less is known about the overall ecology of E. coli in poultry production and how ecology changes following mitigation strategies such as vaccination. We examined commensal and environmental E. coli isolates from samples collected as part of a field trial consisting of 8 flocks (4 control and 4 vaccinated) located within a single, vertically integrated, turkey production company. Our results revealed no significant differences in APEC status or proportions of high-risk clones in response to vaccination. APEC prevalence was significantly higher during the growout versus brood period. When we looked at Clermont phylogroups, no significant differences were seen in the prevalence of phylogroups B1, C, D, E, F, and G between the control and vaccinated groups. Phylogroup B2 prevalence was significantly higher while phylogroup A prevalence was significantly lower in the vaccinated group compared to the control group during the growout period, but only for isolates from cloacal swabs. Phylogroups A, B1, B2, C, and E showed differences in prevalence between the brood and growout periods, but no relationships were consistently significant across all sample types. These findings suggest that application of a live attenuated vaccine has limited effects on the overall ecology of E. coli and APEC prevalence within healthy birds.

A virulent escherichia coli O121-B2-ST131 strain causes hemorrhagic pneumonia in mink: evidence from pathogenicity and animal challenge experiments

In recent years, rapid fatal hemorrhagic pneumonia (HP) has been increasingly reported in mink. In several studies, the virulence factors of strains isolated from diseased tissues have been identified as extraintestinal pathogenic Escherichia coli (ExPEC). The molecular characteristics of the strains were also analyzed, but whether ExPEC is the etiological agent of HP has not been confirmed in an animal challenge model. In this study, we characterized the antibiotic resistance, virulence characteristics, and pathogenicity of a bacterial strain isolated from a typical case of mink HP, and designated it L1. Our study revealed that isolate L1 has high levels of antibiotic resistance, to multiple antibiotics, including ampicillin, tylosin, kanamycin, and so on. Numerous virulence genes were detected in isolate L1, including those encoding adhesins (focG, afa/draB, mat, crl), invasins (ibeA, einv), and toxin (cnf1). ExPEC isolate L1 belongs to the O121 serogroup and was classified in the B2 phylogroup and sequence type 131 (ST131). Animal experiments showed that L1 is highly pathogenic to mice, and induced fatal HP in mink. A mouse model of isolate L1 infection showed lethargy, depression, and then death. The sick minks showed similar clinical signs and died soon after nasal bleeding and hematemesis, with a large amount of congestion and consolidation in the lungs. Using animal challenge experiments based on Koch's postulates, we demonstrate for the first time that ExPEC is a causative agent of rapid fatal HP in minks. Our research provides important insights into the identification and control of rapid fatal HP in minks and effective antibiotic treatments for infected animals.

Antimicrobial resistance and genetic diversity of Escherichia coli isolated from marine bivalves

Escherichia coli can contaminate the marine environment through sewage and accumulate in bivalve molluscs. We assessed antimicrobial resistance (AMR) mechanisms and genetic diversity of 69 E. coli isolates recovered from in natura, boiled, and purchased Perna perna mussels in Niterói city, Brazil. All isolates were sensitive to cefoxitin, imipenem, meropenem, and fosfomycin. In contrast, 61 (88.4%) isolates were not susceptible to streptomycin. We found ten (14.5%) multidrug-resistant (MDR) isolates. Extended-spectrum beta-lactamase (ESBL) production was detected in 30 (43.5%) isolates, with 14 (46.7%) isolates carrying ESBL genes (blaTEM, blaCTX-M9, blaSHV, blaCTX-M2, and blaCTX-M8/25). Quinolone/fluoroquinolone resistance was observed in 12 (17.4%) isolates, with qnrS and qnrB genes identified. Nine (13%) isolates were resistant to folate pathway inhibitors, with sul1 and sul2 genes identified. Only one (1.5%) isolate had the intI integrase gene. Most isolates had the A/C replicon (73.9%) and belonged to phylogenetic group B1 (50.7%). PFGE analysis revealed the existence of 54 genotypes, with four clusters containing isolates from different sources. The presence of ESBL-producing strains, AMR genes, and diverse plasmid replicons highlights the role of marine environments in AMR dissemination. Continuous AMR surveillance in marine ecosystems is crucial to mitigate public health risks linked to seafood consumption.

Avian pathogenic Escherichia coli (APEC) isolated from chicks and embryos in the hatchery

Avian pathogenic Escherichia coli (APEC) is the most common cause of omphalitis. This disease affects newborn chicks up to the 7th day of life, causing high mortality and reduced performance of broilers. The study aimed to determine the frequency of APEC occurrence in embryos and newly hatched chicks. E. coli isolates were subjected to PCR to identify the minimal predictive virulence factors, phylogenetic groups, and predictive identification of the clonal complex (CC) ST131, ST117, and ST95. The phenotypic analysis assessed the antimicrobial resistance profile. A total of 254 samples were analyzed and 60.63% (n = 154/254) were positive for E. coli, of which 35.71% (n = 55/154) were classified as APEC (60% (n = 33/55) isolated in the yolk sac of day-old chicks, 29.09% (n = 16/55) in pipped eggs and 10.91% (n = 6/55) in embryonated eggs). The B2 phylogenetic group accounted for 21.81% (n = 12/55), with an increase in the contamination by B2 strains during the incubation process, from 6.25% (n = 1) to 30.30% (n = 10). We also identified 14.54% (n = 8/55) strains for the G group. The sequence types ST131 and ST117 were observed at the same frequency (10.90%, n = 6), followed by ST95 (3.6%, n = 2). A total of 27.27% were considered multidrug-resistant strains (MDR). The highest resistance rate was amoxicillin (43.64%, n = 24) and tetracycline (25.45%, n = 14). To a lesser extent, levels of resistance to critical drugs commonly used in hatcheries were identified, such as ceftiofur (20%, n = 11) and gentamicin (7%, n = 4).

Whole-genome analysis of five Escherichia coli strains isolated from focal duodenal necrosis in laying hens reveals genetic similarities to the E. coli O25:H4 ST131 strain

Focal duodenal necrosis (FDN) is an intestinal disease causing significant economic losses in the table-egg industry due to reduced egg production in laying hens. Its etiology and pathogenesis remain poorly understood. Between 2021 and 2023, 111 Escherichia coli isolates were collected from FDN lesions and screened for the presence of virulence genes using PCR panels. Five strains-FDN-4, FDN-9, FDN-11, FDN-24, and FDN-50-were selected for whole-genome sequencing due to their high virulence gene content. Core-genome analyses found that the five FDN E. coli belong to different phylogroups and strain types (ST), but they all share multiple complete operons involved in key pathogenic functions, including host cell adhesion and invasion, iron acquisition, motility, biofilm formation, and acid resistance. Comparative genomic analyses identified FDN-4 as the most genetically distinct strain, closely resembling EC958, an O25b:H4 ST131 uropathogenic E. coli (UPEC) commonly associated with extended-spectrum beta-lactamase production. FDN-4 and EC958 share unique chromosomal virulence genes absent in the other FDN strains, all located within genomic islands. This study provides the first complete genomic characterization of E. coli isolated from FDN lesions and highlights FDN-4 as a genetically distinct strain with similarities to O25b:H4 ST131 UPEC.IMPORTANCEThis study presents the first complete genomic characterization of Escherichia coli isolated from focal duodenal necrosis (FDN) lesions. Notably, FDN-4 is the first E. coli strain from a poultry disease (FDN) to show significant similarity to O25b:H4 ST131 strains, commonly classified as uropathogenic E. coli and often associated with extended-spectrum beta-lactamase production. However, caution is warranted when attributing direct transmission routes between poultry and humans.

Emergence of multidrug resistant Escherichia coli coharboring fosA3 and ESBL genes from retail ducks along slaughter line

The excessive and indiscriminate use of antimicrobial agents in poultry production has increased antimicrobial resistance in E. coli, posing a significant threat to public health. This study investigated the prevalence of multidrug-resistant (MDR) E. coli co-harboring fosA3 and extended-spectrum β-lactamases (ESBLs) genes in large-scale retail duck slaughterhouses in Sichuan Province, China. The antimicrobial susceptibility to 9 categories and 16 types of antimicrobial agents was assessed by using the broth microdilution method. Phylogenetic grouping and pulsed-field gel electrophoresis (PFGE) were used to investigate the phylogenetic groups and genetic characteristics of the isolates. Moreover, whole-genome sequencing (WGS) was performed on 35 representative E. coli isolates. Among 1, 059 samples collected, 895 E. coli were isolated by MacConkey (MAC) agar and eosin methylene blue (EMB) agar and PCR identification, and 150 strains of MDR E. coli co-carrying fosA3 and ESBL genes were finally screened for further analysis. The results indicated that 141 isolates were resistant to fosfomycin and exhibited high resistance to β-lactam antibiotics. All isolates demonstrated MDR patterns, with 148 isolates resistant to six or more classes of antimicrobial agents. The majority (70/150, 46.67 %) belonged to phylogenetic group B1. Based on an 85 % similarity threshold, all isolates were categorized into 40 distinct PFGE types. Genomic analysis revealed 27 different serotypes and 19 sequence types (STs), with O8 (14.29 %, 5/35) and ST155 (22.86 %, 8/35) being the most common. The IncFIB (AP001918) was the most prevalent plasmid replicon type, identified in 74.29 % (26/35) of the isolates. In addition, 49 acquired antimicrobial resistance genes (ARGs) associated with resistance to 11 types of antimicrobial agents were identified and chromosomal mutation of p.S83L in gyrA gene (88.57 %, 31/35) was the most common. Furthermore, 110 virulence factors (VFs) were identified, with those related to iron uptake and storage, adhesion, secretion and endotoxin production being the most prevalent. This study underscored the importance of rational use of antimicrobial agents in poultry farming and provided critical insights into the distribution of ARGs and VFs among retail duck-derived MDR E. coli.

Traditional marketed meats as a reservoir of multidrug-resistant Escherichia coli

This study aimed to analyze Escherichia coli from marketed meat samples in Peru. Sixty-six E. coli isolates were recovered from 21 meat samples (14 chicken, 7 beef), and antimicrobial resistance levels and the presence of mechanisms of antibiotic resistance, as well as clonal relationships and phylogeny of colistin-resistant isolates, were established. High levels of antimicrobial resistance were detected, with 93.9% of isolates being multi-drug resistant (MDR) and 76.2% of samples possessing colistin-resistant E. coli; of these, 6 samples from 6 chicken samples presenting mcr-1-producer E. coli. Colistin-resistant isolates were classified into 22 clonal groups, while phylogroup A (15 isolates) was the most common. Extended-spectrum β-lactamase- and pAmpC-producing E. coli were found in 18 and 8 samples respectively, with blaCTX-M-55 (28 isolates; 16 samples) and blaCIT (8 isolates; 7 samples) being the most common of each type. Additionally, blaCTX-M-15, blaCTX-M-65, blaSHV-27, blaOXA-5/10-like, blaDHA, blaEBC and narrow-spectrum blaTEM were detected. In addition, 5 blaCTX-M remained unidentified, and no sought ESBL-encoding gene was detected in other 6 ESBL-producer isolates. The tetA, tetE and tetX genes were found in tigecycline-resistant isolates. This study highlights the presence of MDR E. coli in Peruvian food-chain. The high relevance of CTX-M-55, the dissemination through the food-chain of pAmpC, as well as the high frequency of unrelated colistin-resistant isolates is reported.

Antimicrobial resistance in community-acquired enteric pathogens among children aged ≤ 10-years in low-and middle-income countries: a systematic review and meta-analysis

Introduction

Antimicrobial resistance (AMR) is a global health priority. This systematic review summarizes the prevalence of AMR in enteric pathogens originating from the community, specifically among ≤10-year-old children in low-and middle-income countries (LMICs). In addition, it presents the proportions of pooled resistance in Campylobacter spp., Escherichia coli, Shigella spp., and Salmonella spp. (CESS) to clinically relevant antibiotics.

Methods

Six online repositories, namely PubMed, Medline, Web of Science, Cochrane Library, CABI, and EMBASE were searched for articles published between January 2005 and September 2024. Random-effects meta-analysis models were constructed to estimate the pooled AMR proportions for CESS pathogens, and a subgroup analysis by region was also carried out.

Results

A total of 64 publications from 23 LMICs met our inclusion criteria. The pooled estimates of E. coli AMR for clinically important antibiotics were as follows: sulfamethoxazole/trimethoprim (SXT) 71% [95%CI: 57-82%]; ampicillin (AMP) 56% [95%CI: 44-67%]; ciprofloxacin (CIP) 10% [95%CI: 5-20%]; and ceftriaxone (CRO) 8% [95%CI: 2-31%]. The proportions of AMR detected in Shigella spp. were AMP 76% [95%CI: 60-87%]; nalidixic acid (NA) 9% [95%CI: 2-31%]; CIP 3% [95%CI: 0-15%]; and CRO 2% [95%CI: 0-19%]. The proportions of Salmonella spp. AMR were AMP 55% [95%CI: 35-73%] and SXT 25% [95%CI: 15-38%]. The proportions of Campylobacter spp. AMR were erythromycin (ERY) 33% [95%CI: 12-64%] and CIP 27% [95%CI: 8-61%]. There was high variability in the regional subgroup analysis, with high interstudy and regional heterogeneity I2 ≥ 75%.

Conclusion

Our results shed light on drug-resistant enteric bacterial pathogens in young children, providing evidence that CESS pathogens are becoming increasingly resistant to clinically important antimicrobials. Regional differences in resistance patterns between these community isolates highlight the need for strong national and regional surveillance to detect regional variations and inform treatment and appropriate antibiotic stewardship programs. The limitations of our findings include high regional variability, significant interstudy heterogeneity, and underrepresentation of certain LMICs.

Systematic review registration

https://inplasy.com/inplasy-2024-2-0051/, registration number: INPLASY202420051.

Agriculturally Sourced Multidrug-Resistant Escherichia coli for Use as Control Strains

Bacteriological control strains with known characteristics ensure consistency and reproducibility of assay performance across different laboratories and are an important cornerstone of quality control in the microbiology laboratory. Ideally, control strains should be representative of the assay target and be widely available from reputable sources. However, for work involving antibiotic resistance most controls come from human and veterinary clinical sources and are not optimized for work in agriculturally impacted environments or not widely available. The objective of this work was to identify and make widely available two E. coli isolates sourced from agricultural production settings that could be used as external controls supporting method development, research and environmental monitoring for extended spectrum β-lactamase producing (ESBL) and tetracycline resistant Escherichia coli. Previously collected E. coli suspects were screened based on antimicrobial susceptibility testing data, then confirmed as E. coli and characterized both phenotypically and genotypically. The positive control strain, ARS-C301 was ESBL positive and contained the CTX-M-55 and tet(A) genes, and the negative control strain, ARS-C101 was negative for both targets. Here we introduce two agriculturally sourced, fully characterized, and genetically sequenced control strains for use as laboratory controls in research involving extended-spectrum β-lactamase producing (ESBL) and tetracycline-resistant Escherichia coli isolated from the environment, available via publicly accessible culture collections, and commercially as a quantitative pellet.

Extended-spectrum β-lactamase-producing Escherichia coli isolated from captive primates: characteristics and horizontal gene transfer ability analysis

The rapid spread of extended-spectrum β-lactamases (ESBLs)-producing Escherichia coli (ESBL-EC) around the world has become a significant challenge for humans and animals. In this study, we aimed to examine the characteristics and horizontal gene transfer (HGT) capacity of ESBL-EC derived from captive primates. We screened for ESBL-EC among a total of 444 multidrug-resistant (MDR) E. coli strains isolated from 13 zoos in China using double-disk test. ESBL genes, mobile genetic elements (MGEs), and virulence-associated genes (VAGs) in ESBL-EC were detected through polymerase chain reaction (PCR). Furthermore, conjugation experiments were conducted to examine the HGT capacity of ESBL-EC, and the population structure (phylogenetic groups and MLST) was determined. Our results showed that a total of 69 (15.54%, 69/444) ESBL-EC strains were identified, and 5 variants of blaCTX and 3 variants of blaTEM were detected. The highest detection rate was blaCTX-M-55 (49.28%, 34/69), followed by blaCTX-M-15 (39.13%, 27/69). Ten MGEs were detected and the most prevalent was IS26 (78.26%, 54/69), followed by ISEcp1 (60.87%, 42/69). Eighteen combinations of MGEs were detected, in which ISEcp1 + IS26 was predominant (18.84%, n = 13). A total of 15 VAGs were detected and the most prevalent was fimC (84.06%, 58/69), followed by sitA (78.26%, 54/69). Furthermore, HGT ability analysis results showed that 40.58% (28/69) of ESBL-EC strains exhibited the ability to engage in conjugative transfer. Plasmid typing revealed that IncFIB (78.57%, 22/28) had the highest detection rates. Furthermore, antibiotic resistance genes (ARGs) of blaTEM-135, tetA and qnrS; MGEs of IS26, trbC and ISCR3/14 showed high rates of conjugative transfer. The population structure analysis showed that the phylogroup B1 and ST2161 were the most prevalent. ESBL-EC poses a potential threat to captive primates and may spread to other animals, humans, and the environment. It is imperative to implement measures to prevent the transmission of ESBL-EC among captive primates.

Longitudinal study of avian pathogenic Escherichia coli (APEC) serogroups associated with disease in Georgia poultry using molecular serology and virulence gene analysis

Avian pathogenic Escherichia coli (APEC) is a significant cause of morbidity, mortality, and production loss to the poultry industry worldwide. Here, we characterized 569 E. coli isolates from avian-diagnosed colibacillosis cases from the state of Georgia, USA. In total, 339 isolates were assigned into 32 serogroups with the majority classifying as O78, O2, O25, O8, O1, O86, O18, and O15. Serogroup O25 was found to link with broilers, while broiler breeders were more often associated with serogroup O1 and pet/ hobby birds with serogroup O8. In addition, some serogroups (O1) were more prevalent in the summer and fall. Analysis for virulence-associated genes (VAGs) found 23.20% of isolates did not harbour any genes linked with the APEC pathotype, while ColV plasmid-associated genes (iroN, ompT, hlyF, iss, and aerJ) were frequently detected among most isolates (with 80-96% prevalence) and some of these genes were linked with serogroup. Phylogenetic analysis, classified isolates into phylogenetic groups B2 (34%), F (19%), A (15%), and G (9%). The phylogenetic group B2 isolates also harboured the highest number of VAGs. This study highlights that the current APEC-causing disease in birds in the State of Georgia has identified several emerging serogroups possessing several VAGs that could potentially lead to challenges in colibacillosis control.RESEARCH HIGHLIGHTSSeveral emerging APEC serogroups were observed in Georgia poultry populations.An association between APEC serogroups and bird type was observed.The prevalence of different APEC serogroups was influenced by season.A multiplex PCR assay targeting common serogroups of APEC in Georgia poultry was developed.

Comparative genomic and phenotypic description of Escherichia ruysiae: a newly identified member of the gut microbiome of the domestic dog

Introduction

Escherichia ruysiae is a newly identified species within the Escherichia genus, yet its presence in domestic animals remains largely unexamined. This study characterizes four isolates detected for the first time in the domestic dog (Canis lupus familiaris), focusing on their phenotypic and genomic features.

Methods

We used culturomic methods to isolate four E. ruysiae isolates that were initially identified as Escherichia coli using MALDI-TOF mass spectrometry. Whole-genome sequencing confirmed that the isolates belonged to E. ruysiae, not E. coli. Phenotypic characterization included enzymatic activity assays and antimicrobial susceptibility testing. Comparative genomic analyses were performed on these four isolates, along with 14 additional E. ruysiae and representative genomes from the five other Escherichia species in order to assess genetic diversity and functional gene distribution.

Results and discussion

All strains exhibited similar enzymatic activities and resistance to clindamycin, erythromycin, and metronidazole. The pangenome analysis revealed that most missing gene orthologs are related to motility followed by metabolism, including synthetases, reductases, phosphatases, permeases, transferases, and epimerases, as well as structural genes like efflux pumps and transporters. Phylogroup typing using the ClermonTyping method identified two main groups within the E. ruysiae species, Clade III and IV. Typical virulence genes associated with E. coli are absent in these strains. The multiple approaches used in this study expand our understanding of the diverse aspects of the recently described species, E. ruysiae.

Serogrouping and Molecular Characterization of ESBL-Producing Avian Pathogenic Escherichia coli from Broilers and Turkeys with Colibacillosis in Algeria

Avian colibacillosis caused by avian pathogenic Escherichia coli (APEC) strains is a bacterial disease responsible for enormous economic losses in the poultry industry, due to high mortality rates in farms, antibiotic therapy costs, and seizures at slaughterhouses. The aim of this study was to characterize the serogroups and molecular features of extended spectrum β-lactamase (ESBL)-producing APEC isolates recovered from 248 liver samples of 215 broilers and 33 turkeys with colibacillosis lesions in northeast Algeria. For this, microbiological tests were carried out, according to the recommended standards: E. coli isolates were recovered using standard microbiological protocols, and identification was carried out by MALDI-TOF MS. Serogrouping was performed using a rapid agglutination slide and the antisera of three O somatic groups (O1, O2, O78). Antimicrobial susceptibility was determined by the disk diffusion method. PCR assays and sequencing were used to detect antimicrobial resistance genes, integrons, phylogrouping, and MLST. Conjugation experiments were also conducted to determine the transferability of the retrieved ESBL-encoding genes. Overall, 211 (85.1%) APEC isolates were collected (one per positive sample), and 164 (77.7%) of them were typable. The O2 and O1 serogroups were the most detected (46.1% in broiler typable isolates and 61.5% in turkey typable isolates). Seventeen APEC isolates were ESBL-producers and harbored the following genes (number of isolates): blaCTX-M-1 (14), blaCTX-M-15 (2), and blaSHV-12 (1). They belonged to phylogroups D (10 isolates), B1 (6 isolates), and B2 (1 isolate). The MLST of 13 ESBL producers revealed seven STs: ST23, ST38, ST48, ST117, ST131, ST1146, and ST5087. The ESBL-encoding genes were transferred by conjugation among 15 ESBL-producing isolates, and transconjugants acquired either the IncK or IncI1 plasmids. Concerted efforts from all poultry actors are needed to establish surveillance monitoring strategies to mitigate the spread of ESBL-producing isolates implicated in avian colibacillosis.

Antimicrobial Susceptibility Profiles of Commensal Escherichia coli Isolates from Turkeys in Hungarian Poultry Farms Between 2022 and 2023

Background: The global spread of antimicrobial resistance (AMR) has prompted the critical importance of regular monitoring. Escherichia coli, a widely distributed facultative anaerobic pathogen, is significant both in terms of the clinical diseases that it causes and as a reservoir of antimicrobial resistance, with notable implications for both animal and public health. Within the poultry industry, the turkey sector is an emerging and internationally significant branch. Methods: Our objective was to assess the antimicrobial resistance profile of commensal Escherichia coli strains isolated from large-scale turkey flocks in Hungary using minimum inhibitory concentration (MIC) determination. Results: A total of 470 isolates were analyzed, revealing that 61.5% of the strains were resistant to amoxicillin, while 18.5% were resistant to amoxicillin-clavulanic acid. The resistance observed against enrofloxacin (62.8%) and ceftriaxone (24%) is concerning. Comparison with human resistance data showed a similar resistance rate for amoxicillin and ampicillin, as well as amoxicillin-clavulanic acid and cephalosporins. However, for other active substances, the situation was significantly worse in veterinary medicine. Conclusions: The lower resistance to amoxicillin-clavulanic acid indicates that most strains are β-lactamase producers. Our findings underscore the necessity of regular and comprehensive surveillance, which can establish temporal trends over time. Incorporating data on antibiotic usage into future studies could facilitate the exploration of relevant correlations. Additionally, the next-generation sequencing of multidrug-resistant strains could help elucidate the genetic basis of resistance.

Molecular analysis of acute pyelonephritis-excessive innate and attenuated adaptive immunity

This study investigated the molecular basis of disease severity in acute pyelonephritis (APN), a common and potentially life-threatening bacterial infection. Two cohorts of infants with febrile urinary tract infection were included. Renal involvement was defined by DMSA scans and molecular disease determinants by gene expression analysis and proteomic screens, at diagnosis and after 6 mo. Innate immune hyper-activation, systemically and locally in the urinary tract, was defined as a cytokine storm. Neutrophil degranulation and renal toxicity genes were strongly regulated, with overexpression in the APN group (first DMSA+). Adaptive immune attenuation in the APN group further supported the notion of an immune imbalance. DNA exome genotyping identified APN and febrile urinary tract infection as genetically distinct and scarring associated genes, but the activation of renal toxicity genes during acute infection was unrelated to the development of renal scarring. The results define APN as a hyper-inflammatory disorder with the characteristics of a cytokine storm combined with adaptive immune attenuation. The findings are consistent with innate immune dysfunctions and neutrophil disorders identified as determinants of APN susceptibility in genetic models.

Comparative genomics of clinical hybrid Escherichia coli strains in Norway

The global rise of hybrid Escherichia coli (E. coli) is a major public health concern, as enhanced virulence from multiple pathotypes complicates the traditional E. coli classification system and challenges clinical diagnostics. Hybrid strains are particularly concerning as they can infect both intestinal and extraintestinal sites, complicating treatment and increasing the risk of severe disease. This study analyzed virulence-associated genes (VAGs) in 13 E. coli isolates from fecal samples of patients with symptoms of gastrointestinal (GI) infection in Norwegian hospitals and clinics. Whole genome sequencing (WGS) was conducted using Oxford Nanopore's MinION and Illumina's MiSeq platforms. Eleven strains harbored molecular diagnostic markers of atypical enteropathogenic E. coli (aEPEC), enteroinvasive E. coli (EIEC), Shiga toxin-producing E. coli (STEC), enterotoxigenic E. coli (ETEC), or typical enteropathogenic E. coli (tEPEC). Two of those isolates were identified as triple intestinal hybrids with molecular diagnostic markers for aEPEC, EIEC, and STEC. Notably, two isolates lacked any IPEC-specific molecular diagnostic markers, yet were suspected of causing the patient's GI infection. Furthermore, genes associated with extraintestinal pathogenic E. coli (ExPEC)-including adhesins, toxins, protectins, siderophores, iron acquisition systems, and invasins-were identified in all the isolates. Thus, most of the isolates were classified as hybrid aEPEC/ExPEC, STEC/ExPEC, tEPEC/ExPEC, or aEPEC/EIEC/STEC/ExPEC. These findings emphasize the genomic plasticity of E. coli and highlight the need to revise the classification system for enteric pathogens.

Antimicrobial Resistance and Molecular Characterization of Escherichia coli from Healthy Chickens in Shandong, China from 2009 to 2014

Antimicrobial resistance (AMR) is a great threat to animal and public health. Here, we conducted a surveillance of Escherichia coli isolated from healthy chickens during 2009-2014 to identify the characteristics of AMR. A total of 351 (95.64%) E. coli isolates were obtained from 367 healthy chicken fecal samples collected from 6 farms located in Shandong Province, China. The susceptibility to 10 antimicrobials, the prevalence of antibiotic resistance genes (ARGs), phylogenetic clustering, and multilocus sequence typing were evaluated. The isolates exhibited high resistant rates (>95%) to ampicillin, cefotaxime, ciprofloxacin, ceftiofur, and enrofloxacin. The most prevalent ARGs were blaCTX-M (36.36%), aac(6')-Ib-cr (30.79%), qnrS (29.62%), oqxAB (27%), mcr-1 (15.83%), blaTEM (9.09%), qnrC (3.52%), qnrD (0.88%), and qepA (0.29%). Phylogenetic clustering analysis indicated that the most prevalent group was group D (37.89%), followed by group B1 (34.76%), A (24.22%), and B2 (3.13%). Fifty-seven sequence types (STs) were identified among the 124 blaCTX-M-positive strains, and the dominant STs were ST354 (13.71%), ST117 (5.65%), ST155, ST2309, and ST2505 (4.84% each). There was a significant association between 17 pairs of AMR phenotypes, 14 pairs of ARGs, and 11 pairs of AMR-ARGs. The strongest association was found between ST602 and qnrC (odds ratios: 22.2). This study implied that E. coli isolated from healthy chickens could potentially serve as a reservoir of AMR and ARGs, and significant associations exist among AMR, ARGs, phylogenetic groups, and STs. Our study highlighted the need for routine surveillance of AMR in healthy chickens, and promoting appropriate antibiotic use and implementing regular monitoring of resistance in broilers are crucial for fostering the development of the poultry industry and safeguarding public health.

Phylogenetic groups and extraintestinal virulence genes of inflow Escherichia coli entering a municipal drinking water treatment facility (St. Paul, MN, USA)

Extraintestinal pathogenic Escherichia coli (ExPEC), a leading cause of urinary tract infections, sepsis and neonatal meningitis, circulates between diverse hosts and the environment. Consequently, identifying ExPEC reservoirs and transmission pathways has potentially great public health importance. Here, we used PCR-based methods to characterize 104 E. coli isolates from inflow water to the St. Paul, MN (USA), municipal drinking water treatment plant. Isolates were analysed for major phylogenetic groups and multiple extraintestinal virulence genes. Additionally, from the 65 (of 104) water samples that yielded multiple E. coli colonies, we screened E. coli population DNA for virulence genes. Thirty-three percent of isolates represented virulence-associated groups B2 and D, and 8% (95% CI: 3%, 15%) qualified molecularly as ExPEC. The ExPEC isolates, all from group B2 or D, had a median virulence gene score of 11.0 and collectively contained all but four of the 28 studied extraintestinal virulence genes. Population DNA screening increased the proportion of samples positive for individual virulence genes and, presumptively, for ExPEC [14% (95% CI: 10%, 30%) vs. 8%, P=0.03]. These findings identify a previously underappreciated potential mechanism for community-wide dissemination of ExPEC and underscore the importance of consistent disinfection of municipal drinking water.

Molecular Epidemiology and Antibiotic Resistance Associated with Avian Pathogenic Escherichia coli in Shanxi Province, China, from 2021 to 2023

Avian Pathogenic Escherichia coli (APEC) constitutes a major etiological agent of avian colibacillosis, which significantly hinders the development of the poultry industry. Conducting molecular epidemiological studies of APEC plays a crucial role in its prevention and control. This study aims to elucidate the molecular epidemiological characteristics of Avian Pathogenic Escherichia coli in Shanxi Province. In this study, 135 APEC strains were isolated and identified from 150 liver samples of diseased and deceased chickens exhibiting clinical symptoms, which were collected from farms in Shanxi Province between 2021 and 2023. The isolates were then analyzed for phylogenetic clustering, drug resistance, resistance genes, virulence genes, and biofilm formation capabilities. The results revealed that the proportions of the A, B1, B2, and D evolutionary subgroups were 26.67%, 32.59%, 17.78%, and 15.56%, respectively. The drug resistance testing results indicated that 92% of the isolates exhibited resistance to cotrimoxazole, kanamycin, chloramphenicol, amoxicillin, tetracycline, and other antibiotics. In contrast, 95% of the strains were sensitive to ofloxacin, amikacin, and ceftazidime. The most prevalent resistance genes included tetracycline-related (tetA) at 88.15%, followed by beta-lactam-related (bla-TEM) at 85.19%, and peptide-related (mcr1) at 12.59%. The virulence gene analysis revealed that ibeB, ompA, iucD, and mat were present in more than 90% of the isolates. The results revealed that 110 strains were biofilm-positive, corresponding to a detection rate of 81.48%. No significant correlation was found between the drug resistance genes, virulence genes, and the drug resistance phenotype. A moderate negative correlation was observed between the adhesion-related gene tsh and biofilm formation ability (r = -0.38). This study provides valuable insights into the prevention and control of avian colibacillosis in Shanxi Province.

When E. coli strikes: a necropsy analysis of a juvenile giraffe's fatal infection

BACKGROUND

As bacterial infections pose a major health risk to captive populations, disease prevention and management play a crucial role in the ex situ conservation of giraffes (Giraffa camelopardalis). This study describes the case of a giraffe that developed septicemia after an umbilical cord infection caused by Escherichia coli. To our knowledge, pathological changes in diseased giraffes caused by E. coli, which is an opportunistic pathogenic organism, have not been reported. This is the first report presenting an analysis of necropsies and subsequent microbiological investigations.

CASE PRESENTATION

The baby giraffe's mother died shortly after birth, so it had to be fed milk powder. The giraffe was healthy at first but developed symptoms like depression, loss of appetite, and lameness at 8 days old. At 14 days of age, the juvenile giraffe showed astasia and gradually died, with a disease course of 7 days. Postmortem examination revealed opisthotonus and navel swelling. Serofibrinous arthritis, serofibrinous necrotizing inflammation of periarticular soft tissue, serous omphalitis, and severe adventitia hemorrhage of the umbilical artery were observed. Severe serofibrinous pericarditis, pleuritis, and peritonitis were also observed. The interstitium of the pulmonary lobule widened because it was filled with a pale yellow translucent gelatinous exudate. Histopathologically, the calf had diffuse serous interstitial pneumonia, serous necrotizing umbilical arteritis, degenerative hepatitis with mild fibrosis, degenerative nephritis, hemorrhagic lymphadenitis, necrotizing enteritis, and necrotizing thyroiditis. Blue-stained clumps of bacteria of varying sizes and neutrophil infiltration were scattered or diffused in the interstitial connective tissue and edematous serosa of all tissues and organs, as well as in small vessels and lymphatic vessels, which were filled with many neutrophils (lymphatic spread). Single gram-negative Escherichia coli were cultured from all tissues of the animal. Polymerase chain reaction results of 16S rRNA of the isolated Escherichia coli had 99.79% homology to KJB03889.1.

CONCLUSIONS

The gross, histopathologic, microscopic, and polymerase chain reaction sequencing features reported in a juvenile giraffe were consistent with colibacillosis, which is a rare disease of giraffes. The gross, histopathologic, microscopic, and polymerase chain reaction sequencing features reported in a juvenile giraffe. This case serves as a paradigmatic illustration of a giraffe suffering from neglect and inadequate treatment, leading to severe consequences. In instances of giraffe Escherichia coli septicemia, it is imperative to thoroughly assess for underlying diseases, particularly in the absence of obvious predisposing factors. The rise of multidrug resistant organisms has constrained the efficacy of empirical antibiotic treatment, highlighting the importance of promptly conducting culture and sensitivity testing and employing antibiotic therapy guided by susceptibility results.

Analysis of phylogroups, biofilm formation, virulence factors, antibiotic resistance and molecular typing of uropathogenic Escherichia coli strains isolated from patients with recurrent and non-recurrent urinary tract infections

BACKGROUND

Uropathogenic Escherichia coli (UPEC) is the predominant cause of urinary tract infections (UTIs), and the recurrence of these infections poses significant treatment challenges.

OBJECTIVE

This study aimed to compare the phylogroups, biofilm formation, virulence factors, and antibiotic resistance of UPEC strains in patients with recurrent versus non-recurrent UTIs in Hamadan City, Western Iran.

MATERIALS AND METHODS

A total of 110 E. coli isolates were collected from urine cultures across three major hospitals and laboratories. The isolates were confirmed through biochemical tests, and their antibiotic resistance profiles were evaluated using the disk diffusion method. Biofilm production was assessed using the microtiter plate method, while virulence genes and phylogroup determination were analyzed via PCR. Real-time PCR was employed to compare the expression levels of the pap and fimH virulence genes.

RESULTS

The results indicated that 73% of isolates were from non-recurrent UTI patients, with a higher incidence in females and children under 10 years. A significant difference was detected in the underlying diseases and the expression of the pap between the recurrent and non-recurrent groups. Antibiotic resistance was notably significant, particularly against Ampicillin-sulbactam, Trimethoprim-Sulfamethoxazole, Nalidixic acid, and Ciprofloxacin, with 77% of strains classified as multi-drug resistant (MDR). Despite differences in the rates of ESBL production between recurrent (53%) and non-recurrent (42.5%) strains, no significant differences were observed in antibiotic resistance, biofilm formation, virulence factors, or phylogroups between the two groups. Phylogenetic analysis revealed a predominance of phylogroups B2 and D, with high genetic diversity among the isolates.

CONCLUSION

The study highlights the traits of UPEC strains in recurrent and non-recurrent UTIs, showing high antibiotic resistance and genetic diversity among isolates. The study found notable differences in underlying diseases and the expression of the pap gene between recurrent and non-recurrent groups, suggesting that these factors may play a crucial role in the recurrence of infections. Further investigation into these differences could enhance our understanding and management of recurrent UTIs.

Prevalence of Shiga-Toxigenic Escherichia coli in Bovine Manure in the Mid-Atlantic Region of the United States

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen and known to reside naturally in cattle. The application of untreated biological soil amendments of animal origin on fresh produce fields results in unique food safety challenges. It is critical to identify farm manure management practices to mitigate pre-harvest pathogen contamination. The objective of this study was to quantify the prevalence and level of STEC in cattle manure in the Mid-Atlantic region of the United States. A total of 161 bovine manure samples were collected from 13 cattle farms between 2016 and 2018. The samples were enriched with non-selective and selective media and quantified following a Most-Probable Number (MPN) assay. Among the recovered STEC isolates, PCR was performed to determine the presence of stx, eae, and rfbE. Clermont PCR was performed to identify phylogenetic groups of isolates. Of the 13 farms, 11 had STEC populations between <1.0 and >5.6 log MPN/g. Farm, humidity, and sampling year significantly (p < 0.05) influenced STEC populations in bovine manure. Of the 108 isolates, 50% were stx+ and 14% eae+. Phylogenetic group analysis revealed that 46% of the isolates belonged to group A, 19% to B1, 7% to B2, and 28% to D. Group D had the highest prevalence of stx+ and eae+ and group B1 had the lowest prevalence. Results suggest STEC geographical distribution in the Mid-Atlantic region is farm-specific, and climatic conditions can be critical for its survival and dissemination.

Research note: Prevalence and genetic characteristics of pathogenic E. coli isolates from domestic pigeons in central China

Pigeon has become popular as a food recently, due to their highly nutritive valuE. colibacillosis, which is caused by pathogenic E. coli, is one of the most important bacterial diseases in pigeon breeding. However, data on E. coli isolates from pigeons are currently limited. In order to understand the prevalence and genetic characteristics of pathogenic E. coli in pigeon farms, a total of 199 E. coli strains were isolated from domestic pigeons in central China. Among them, 30.15 % isolates (60/199) were identified to belong to phylogroups B2 and D, which were recognized as pathogenic E. coli. To further characterize these 60 pathogenic E. coli, whole genome sequencing and antimicrobial susceptibility testing were carried out. These isolates covered 12 serotypes, and the dominant serotypes were O166 (30/60), O17 (7/60) and O7 (7/60). Eleven sequence types (ST) were identified, and ST646, ST38 and ST2001 were the dominant genotypes. Among these 60 pathogenic E. coli strains, high resistance rates to florfenicol (96.7 %), tetracycline (96.7 %), ampicillin (98.3 %) and trimethoprim (96.7 %) were observed. Twenty-six resistance genes were identified, and the most popular resistance genes included floR (58/60), tetA (58/60), blaTEM-1 (58/60), dfrA (57/60) and sul2 (53/60). Virulence gene analysis revealed five different iron uptake systems in these strains, and all the O166 serotype strains contained three iron uptake systems. In addition, diarrhoeagenic E. coli-associated gene eaeH was detected in 96.67 % of the pathogenic isolates, highlighting their foodborne threat. Overall, this study extends our knowledge of the epidemiology of pathogenic E. coli in domestic pigeons.

Epidemiological and molecular characteristics of extraintestinal pathogenic escherichia coli isolated from diseased cattle and sheep in Xinjiang, China from 2015 to 2019

Escherichia coli has become a common causative agent of infections in animals, inflicting serious economic losses on livestock production and posing a threat to public health. Escherichia coli infection is common and tends to be complex in Xinjiang, a major region of cattle and sheep breeding in China. This study aims to explore the current status and molecular characteristics of Escherichia coli infection in cattle and sheep in Xinjiang, as part of the disease prevention and control strategy. Herein we isolated Extraintestinal pathogenic Escherichia coli (ExPEC) from the liver, spleen, lung, heart, and lymph nodes of infected cattle and sheep (Xinjiang, China), and phylogenetic grouping, serotyping, and multilocus sequence typing were performed to determine epidemic and molecular characteristics. We also assessed their biofilm formation ability. A total of 132 strains of ExPEC were identified from diseased cattle and sheep, belonging to 7 phylogenetic groups. A and B1 are advantageous groups. Further, 22 serogroups were found, with O101 (26/132), O154 (14/132), and O65 (8/132) being the predominant ones. Among the seven sequence types identified by multilocus sequence typing, ST10 was the most common, followed by ST23 and ST457. Of 132, 105 (79.5%) strains were able to form biofilms: 15 strains (11.4%) were strong, 28 (21.2%) were medium, and 62 (47%) were weak biofilm producers. These findings will contribute to a better understanding of the molecular epidemiology of ExPEC in Xinjiang, China, and can be applied to the development, prevention, and disease control of future diagnostic tools and vaccine.

Decomposition of the pangenome matrix reveals a structure in gene distribution in the Escherichia coli species

Thousands of complete genome sequences for strains of a species that are now available enable the advancement of pangenome analytics to a new level of sophistication. We collected 2,377 publicly available complete genomes of Escherichia coli for detailed pangenome analysis. The core genome and accessory genomes consisted of 2,398 and 5,182 genes, respectively. We developed a machine learning approach to define the accessory genes characterizing the major phylogroups of E. coli plus Shigella: A, B1, B2, C, D, E, F, G, and Shigella. The analysis resulted in a detailed structure of the genetic basis of the phylogroups' differential traits. This pangenome structure was largely consistent with a housekeeping-gene-based MLST distribution, sequence-based Mash distance, and the Clermont quadruplex classification. The rare genome (consisting of genes found in <6.8% of all strains) consisted of 163,619 genes, about 79% of which represented variations of 315 underlying transposon elements. This analysis generated a mathematical definition of the genetic basis for a species.

IMPORTANCE

The comprehensive analysis of the pangenome of Escherichia coli presented in this study marks a significant advancement in understanding bacterial genetic diversity. By employing machine learning techniques to analyze 2,377 complete E. coli genomes, the study provides a detailed mapping of core, accessory, and rare genes. This approach reveals the genetic basis for differential traits across phylogroups, offering insights into pathogenicity, antibiotic resistance, and evolutionary adaptations. The findings enhance the potential for genome-based diagnostics and pave the way for future studies aimed at achieving a global genetic definition of bacterial phylogeny.

Advancing Understanding of Escherichia coli Pathogenicity in Preterm Neonatal Sepsis

Neonatal sepsis is a major cause of mortality in preterm infants, with Escherichia coli as one of the leading pathogens. Few studies have examined the interplay between virulence factors, resistance profiles, phylogroups, and clinical outcomes in this population. We analyzed 52 E. coli strains isolated from 49 preterm neonates diagnosed with sepsis at a tertiary-level hospital in Mexico. Strains underwent phylogenetic classification, virulence gene profiling, and antimicrobial resistance testing. PFGE was used to assess genetic relatedness and outbreak clusters. Clinical data were correlated with molecular findings. Phylogroups A and B2 accounted for 46% of strains. Phylogroup A exhibited notable virulence, with high prevalence of the pathogenicity island described in virulent extra-intestinal E. coli strains (PAI), aerobactin siderophore receptor AerJ (iutA), and yersiniabactin siderophore receptor (fyuA) genes, alongside significant resistance profiles. PFGE identified two dominating branches. Branch A, comprising phylogroups A and B2, displayed high resistance and was prevalent in the neonatal intensive care unit. Branch C, with phylogroups A and D, showed less multidrug resistance but was significantly associated with maternal chorioamnionitis. This study redefines E. coli pathogenicity in neonatal sepsis, highlighting the virulence of traditionally non-pathogenic phylogroups. High virulence strains were associated with more severe outcomes. These findings underscore the need for enhanced strategies in targeted prevention, improved diagnostics, and tailored treatments for high-risk preterm populations.

Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients

The E. coli strains harboring the polyketide synthase (pks) island encode the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involves whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organisms. Fifteen E. coli strains isolated from patients with ulcerative colitis (UC) were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks-positive (pks+) isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158 + 13) pks+ isolates belonged to phylogroup B2, and most of the isolates belong to sequence types ST73 and ST95. One isolate from a UC patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks+ isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the0020preponderance of virulence genes and a reduced number of antimicrobial genes in pks+ isolates. This study significantly contributes to understanding the evolution of pks islands in E. coli.

The pathogenicity traits of avian pathogenic Escherichia coli O25-ST131 associated with avian colibacillosis in Georgia poultry and their genotypic and phenotypic overlap with other extraintestinal pathogenic E. coli

AIMS

To characterize Escherichia coli O25 ST131 (O25-ST131) isolated from Georgia poultry-a "global high-risk" clonal strain.

METHODS AND RESULTS

Using multiplex PCR to detect target genes in 98 isolates of avian pathogenic E. coli (APEC) O25 recovered from avians diagnosed with colibacillosis (n = 87) and healthy chicks (n = 11) in Georgia, USA. Eighty-eight isolates were classified as sequence type ST131 clade b and 56% (n = 49) belong to the phylogenetic group B2. Overall, 17% were identified as uropathogenic E. coli (UPEC)-like and 94% of the isolates formed strong to moderate biofilms. The extended-spectrum β-lactamases encoding genes, blaCTX M-15 (24%), carbapenemases encoding genes, and blaOXA48 (16%) were also detected. The isolates harbored FIB (88%), FIC (28%), A/C (14%), and FIIA (6%) plasmid replicons. Interestingly, 78% of the isolates were found to be resistant to chicken serum and 92% showed capabilities for growth in human urine. The isolates showed phenotypic resistance to several antibiotics including chloramphenicol (63%), ciprofloxacin (57%), trimethoprim-sulfamethoxazole (28%), streptomycin (17%), and cefoxitin and meropenem (14%) using the national antimicrobial resistance monitoring system panel.

CONCLUSIONS

Overall, our study provides evidence of the virulence of these global "high-risk" clones in Georgia poultry with some isolates showing genotypic overlap between APEC and UPEC. Also, this clone harbored several virulence genes, antimicrobial-resistant genes, and plasmids. Interestingly, the majority of APEC O25-ST131 isolates can survive and grow in both chicken serum and human urine and warrant further investigation of their potential pathogenicity for both chickens and humans.

Residence-colonization trade-off and niche differentiation enable coexistence of Escherichia coli phylogroups in healthy humans

Despite abundant literature on pathogenicity and virulence of the opportunistic pathogen Escherichia coli, much less is known about its ecological and evolutionary dynamics as a commensal. Based on two detailed longitudinal datasets on the gut microbiota of healthy adults followed for months to years in France and the USA, we identified a robust trade-off between the ability to establish in a new host (colonization) and to remain in the host (residence). Major E. coli lineages (phylogroups or subgroups) exhibited similar fitness but diverse strategies, from strong colonisers residing few days in the gut to poor colonisers residing for years. Strains with the largest number of extra-intestinal virulence associated genes and highest pathogenicity also resided for longest in hosts. Furthermore, the residence of a strain was more strongly reduced when it competed with other strains from the same phylogroup than from another phylogroup, suggesting niche differentiation between phylogroups. Based on a discrete-state Markov model developed to describe E. coli dynamics in a host population, we found that the trade-off and niche differentiation acted together as equalizing and stabilizing mechanisms allowing phylogroups to coexist over long periods of time. Our model also predicted that external disturbances may disproportionately affect resident strains, such as the extraintestinal pathogenic ones of subgroup B2.3. Our results call for further studies outside high-income countries, where the prevalence of this phylogroup is much lower. More generally, the trade-off between colonization and persistence could play a role in the diversification of other bacterial species of the microbiome.

Genetic diversity and antibiotic resistance patterns of Escherichia coli isolates causing septicemia: A phylogenetic typing and PFGE analysis

INTRODUCTION

This study aims to analyze clinical isolates of E. coli causing septicemia across various phylogroups utilizing the PFGE method.

MATERIALS AND METHODS

A total of 100 clinical isolates were collected. The presence of CTX-M, TEM, SHV, KPC, MBL and OXA-48 genes was detected by PCR. Additionally, phylotyping, serotyping, and virulence-typing assay were done by PCR and PFGE methods to investigate the genetic diversity of the isolates.

RESULTS

The O1 serotype and the HlyA gene were the most prevalent serotype and virulence gene, respectively. Notably, 34% of the isolates harbored SHV, TEM, and CTX-M-1 β-lactamase genes. All isolates showed resistance to amoxicillin and tetracycline, but no resistance to fosfomycin was seen. The most and least common phylotypes, according to PFGE analysis, belonged to phylogroups B2 and B1, respectively.

CONCLUSION

The data offers valuable insights into the genetic diversity and antibiotic resistance patterns of E. coli isolates responsible for septicemia.

Escherichia coli: An arduous voyage from commensal to Antibiotic-resistance

Escherichia coli (E. coli), a normal intestinal microbiota is one of the most common pathogen known for infecting urinary tract, wound, lungs, bone marrow, blood system and brain. Irrational and overuse of commercially available antibiotics is the most imperative reason behind the emergence of the life threatening infections caused due to antibiotic resistant pathogens. The World Health Organization (WHO) identified antimicrobial resistance (AMR) as one of the 10 biggest public health threats of our time. This harmless commensal can acquire a range of mobile genetic elements harbouring genes coding for virulence factors becoming highly versatile human pathogens causing severe intestinal and extra intestinal diseases. Although, E. coli has been the most widely studied micro-organism, it never ceases to astound us with its ability to open up new research avenues and reveal cutting-edge survival mechanisms in diverse environments that impact human and surrounding environment. This review aims to summarize and highlight persistent research gaps in the field, including: (i) the transfer of resistant genes among bacterial species in diverse environments, such as those associated with humans and animals; (ii) the development of resistance mechanisms against various classes of antibiotics, including quinolones, tetracyclines, etc., in addition to β-lactams; and (iii) the relationship between resistance and virulence factors for understanding how virulence factors and resistance interact to gain a better grasp of how resistance mechanisms impact an organism's capacity to spread illness and interact with the host's defences. Moreover, this review aims to offer a thorough overview, exploring the history and factors contributing to antimicrobial resistance (AMR), the different reported pathotypes, and their links to virulence in both humans and animals. It will also examine their prevalence in various contexts, including food, environmental, and clinical settings. The objective is to deliver a more informative and current analysis, highlighting the evolution from microbiota (historical context) to sophisticated diseases caused by highly successful pathogens. Developing more potent tactics to counteract antibiotic resistance in E. coli requires filling in these gaps. By bridging these gaps, we can strengthen our capacity to manage and prevent resistance, which will eventually enhance public health and patient outcomes.

Molecular characterization of uropathogenic Escherichia coli (UPEC) strains isolated from companion dogs and cats in Korea

IMPORTANCE

Urinary tract infections (UTIs) are common and significant health issues in pets. Although extensive international research exists on their prevention and treatment, a notable gap remains in analyzing the characteristics of the causative bacteria.

OBJECTIVE

To investigate the phylogroup, antimicrobial resistance (AMR), and molecular genotype of Escherichia coli isolates from dogs and cats with UTIs in animal clinics in Korea.

METHODS

Uropathogenic E. coli (UPEC) strains were analyzed for phylogenetic grouping polymerase chain reaction, AMR, transferable resistance plasmids, and multilocus sequence typing.

RESULTS

Sixty-seven UPECs were isolated from urine samples of dogs (n = 57) and cats (n = 10). Regarding age, the incidence of UTI was the highest in the 11 to 15 years range (46.3%, 31/67). Regarding sex, it accounted for 58.2% (n = 39) in female dogs and 11.9% (8/67) in female cats. Phylogroup B2 was the most frequent (n = 51, 75.0%) among all strains, followed by D (16.2%), A (7.4%), and B1 (1.5%). Thirty-seven (55.2%) UPECs were multidrug-resistant (MDR), and 24 (35.8%) of them belonged to phylogroup B2. Extended-spectrum cephalosporin and carbapenemase genes were detected in 18 (26.9%) UPECs and plasmids carrying these resistance genes were conjugated between strains. Thirty sequence types (STs) were identified among the total strains. Among the UPECs (n = 51) with phylogroup B2, 23 STs were identified, with ST73 being the most frequent (n = 12, 17.9%), followed by ST131 (n = 9, 13.4%).

CONCLUSIONS AND RELEVANCE

Phylogroup B2 strains, particularly ST73 and ST121, were most prevalent in UPECs from Korean companion dogs and cats. For MDR UPECs, appropriate antibiotic selection is essential for the treatment of UTIs.

Abundance of fecal indicator bacteria and diversity of Escherichia coli associated with poultry farms and pasture land cover in streams of northwestern South Carolina

Livestock can contribute fecal indicator bacteria (FIB) to waterbodies. However, few studies have examined the relationship between watershed land use or land cover involving livestock production and the genetic diversity of Escherichia coli in freshwater ecosystems. Our major goal was to determine if FIB abundance and E. coli phylogenetic group distributions in headwater streams are related to livestock production in rural watersheds in South Carolina. In both 2017 and 2018, grab samples were collected from streams at summer baseflow. In 2017, we collected samples from watersheds with or without poultry rearing facilities (PRFs). In 2018, we collected samples from streams draining watersheds with mixed forest and pasture cover and from streams in mostly forested watersheds. In both summers, we measured concentrations of total coliforms, E. coli, and Enterococcus. We also categorized E. coli isolates into one of four phylogenetic groups (A, B1, B2, D). Streams with PRFs in their watersheds had significantly higher concentrations of Enterococcus but not total coliforms or E. coli than streams in watersheds without PRFs. Also, B2 isolates were less frequent and B1 isolates were more frequent in watersheds with PRFs than in those without. Streams draining mixed forest/pasture watersheds had significantly higher concentrations of total coliforms and E. coli but not Enterococcus, as well as higher frequencies of B1 isolates, than streams in mostly forested watersheds. Overall, the most frequent E. coli phylogenetic groups in watersheds with animal production appeared consistent with the phylogenetic groups that are especially abundant in poultry or mammalian livestock feces.

Antimicrobial Susceptibility Profiles of Commensal Escherichia coli Isolates from Chickens in Hungarian Poultry Farms Between 2022 and 2023

Background: Widespread use of antibiotics has led to a global increase in resistance. The Escherichia coli bacterium is a facultative pathogen that often develops antibiotic resistance and is easily transmitted, not only in animal health but also in public health. Within the poultry sector, domestic fowl is widespread and one of the most dynamically growing sectors, which is why regular, extensive monitoring is crucial. Among economically important livestock, poultry as a major source of animal protein for humans is a frequent carrier of Escherichia coli, also with sporadically detected clinical disease. Methods: Our research evaluates the susceptibility of commensal Escherichia coli strains, isolated from large domestic fowl flocks in Hungary, to antibiotics of animal and public health importance, by determining the minimum inhibitory concentration value. Results: A total of 410 isolates were tested, with the highest level of resistance being found for florfenicol (62.7%). Particularly alarming are the resistance rates to enrofloxacin (52.9%), colistin (30.7%), and ceftriaxone (23.9%). We also found a resistance of 56.1% to amoxicillin and 22.2% to amoxicillin-clavulanic acid, which suggests that the majority of strains are β-lactamase-producing. When compared with the national human resistance data, we found with similar values for amoxicillin and amoxicillin-clavulanic acid, but the resistance rates of aminoglycosides, fluoroquinolones, and potency sulfonamide were worse in animal health. Conclusions: In conclusion, our results suggest that periodic surveys should be carried out and that long-term trends can be established that allow the monitoring of resistance patterns over time. For multidrug-resistant strains, new generation sequencing can be used to investigate the genetic background of resistance.

Molecular characterization of avian pathogenic Escherichia coli isolates from broiler farms in Northern Palestinian territories

Background and Aim

Colibacillosis is caused by avian pathogenic Escherichia coli (APEC), which results in significant losses for the poultry sector. It has zoonotic potential and acts as a source of antibiotic resistance and virulence genes for other E. coli. This study aimed to assess phylogenetic groups, virulence factors, and resistance phenotypes of APEC strains isolated from broiler farms in Northern Palestine.

Materials and Methods

A total of 65 APEC isolates were recovered from diseased chickens with typical colibacillosis symptoms from broiler farms located in the northern region of Palestine from May to July 2024. Strains were identified using classical and molecular techniques. Antibiotic resistance was detected using the disk diffusion method. Phylotyping and virulence genotyping of the APEC isolates were performed using a polymerase chain reaction (PCR).

Results

This study showed a high detection rate of APEC strains (100%) in chickens. The most APEC strains, 56/65 (86.2%), belonged to group D. Other strains were assigned to groups B2 (5/65, 7.7%), B1 (3/65, 4.6%), and A (1/65, 1.5%). Antibiotic resistance ranged from 27.7% for Polymyxin E (colistin) to 100% for Amoxicillin. Polymyxin E (colistin) and fosfomycin are the most effective drugs. The most common virulence gene was iroN, which was detected in 61 isolates (93.8%). The APEC strains in Palestine exhibit a wide variety of resistance patterns and genetic variations.

Conclusion

Controlling APEC infections is essential for public health, especially when APEC isolates can pass on resistance and virulence genes to dangerous bacteria such as E. coli that are particular to humans. It is essential to understand APEC pathogenesis, antimicrobial therapy, and the development of measures to control colibacillosis.

Daily and Weekly Urine Variations in Bacterial Growth Susceptibility in Postmenopausal Women With no History of Urinary Tract Infection: A Pilot Study

OBJECTIVE

To evaluate bacterial growth in the bladder as a major virulence factor during urinary tract infections (UTIs), we assessed the variability of uropathogenic bacterial growth in urine samples over multiple timepoints from 3 postmenopausal women with no history of UTI.

METHODS

Following IRB approval, postmenopausal women who never had a UTI provided mid-stream urine samples 3 times daily (8 a.m., 12 p.m., and 4 p.m.), twice a week over 2 weeks, as well as dietary intake logs. Each sample was studied for pH and bacterial growth using 3 uropathogenic Escherichia coli (E.coli) strains (LRPF007, KE40, UTI89), 1 uropathogenic Enterococcus faecalis strain (HRH40), and 1 non-pathogenic E. coli strain (W3110).

RESULTS

Similar mean growth yields were observed for the uropathogenic strains (mean ∆OD600 =0.1-0.13) with high variability (standard deviation [SD]= 0.12-0.28) and lower mean growth for the non-pathogenic strain (mean ∆OD600 =0.05). Urine from each individual at different collection times never had the same bacterial growth potential for any bacterial strain. There were significant associations between urine pH decrease with higher fat (P = .017), vitamin D (P = .02), magnesium (P = .049), fluid (P = .013), and ash (P = .01) intake.

CONCLUSION

Major variations were observed in the bacterial growth response in the urine of the same individuals. These variations imply a requirement for a normalization procedure, eg, growth in synthetic urine, for analysis of bacterial growth in urine. There were significant associations between decreased urine pH and several nutrients found in foods that are classified as highly acidic.

Interrelation Between Pathoadaptability Factors and Crispr-Element Patterns in the Genomes of Escherichia coli Isolates Collected from Healthy Puerperant Women in Ural Region, Russia

Escherichia coli is a commensal and opportunistic bacterium widely distributed around the world in different niches including intestinal of humans and animals, and its extraordinary genome plasticity led to the emergence of pathogenic strains causing a wide range of diseases. E. coli is one of the monitored species in maternity hospitals, being the main etiological agent of urogenital infections, endometriosis, puerperal sepsis, and neonatal diseases. This study presents a comprehensive analysis of E. coli isolates obtained from the maternal birth canal of healthy puerperant women 3-4 days after labor. According to whole genome sequencing data, 31 sequence types and six phylogenetic groups characterized the collection containing 53 isolates. The majority of the isolates belonged to the B2 phylogroup. The data also includes phenotypic and genotypic antibiotic resistance profiles, virulence factors, and plasmid replicons. Phenotypic and genotypic antibiotic resistance testing did not demonstrate extensive drug resistance traits except for two multidrug-resistant E. coli isolates. The pathogenic factors revealed in silico were assessed with respect to CRISPR-element patterns. Multiparametric and correlation analyses were conducted to study the interrelation of different pathoadaptability factors, including antimicrobial resistance and virulence genomic determinants carried by the isolates under investigation. The data presented will serve as a valuable addition to further scientific investigations in the field of bacterial pathoadaptability, especially in studying the role of CRISPR/Cas systems in the E. coli genome plasticity and evolution.

Characterization of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Diarrhoeal Faeces from 0 to 5-Year-Old Children Attending Public Hospitals in Franceville, Gabon

BACKGROUND

In Gabon, studies on the characterization of extended-spectrum beta-lactamase-producing Escherichia coli in young children with diarrhoea are almost nonexistent. The objective was to evaluate the prevalence of antibiotic resistance to extended-spectrum beta-lactamase-producing Escherichia coli in children at public hospitals in Franceville, Gabon.

METHODS

Seventy diarrhoea faecal samples were collected from children aged 0-5 years. The culture and isolation of colonies were carried out on MacConkey agar. The colonies were identified using VITEK 2. The determination of the extended-spectrum beta-lactamase's profiles was accomplished using the double disk method. The identification of phylogroups and pathotypes was performed by PCR. Identification of the ESBL genes was performed by sequencing.

RESULTS

A total of 26 strains of Escherichia coli (33.0%) were identified from 78 bacterial isolates. Twenty (77.0%) Escherichia coli strains carried extended-spectrum beta-lactamases blaCTX-M-15 and 5.0% carried blaSHV-12 subtypes. Phylogroup D (62.0%) was predominant, followed by B1 (12.0%), B2 (8.0%) and E (4.0%). The bacterial pathogens causing diarrhoea were enterohemorrhagic E. coli (12.0%), typical enteropathogenic Escherichia coli (8.0%), atypical enteropathogenic Escherichia coli (4.0%), Enteroaggregative Escherichia coli (4.0%) and enteroinvasive E. coli (4.0%).

CONCLUSIONS

This study showed a high prevalence of extended-spectrum beta-lactamase, Escherichia coli of phylogroup D and pathotype enterohemorrhagic Escherichia coli in children under 5 years old in public hospitals in Franceville, most probably due to the misuse or inappropriate consumption of beta-lactams.

Prevalence and molecular characterization of ESBL/pAmpC producing faecal Escherichia coli strains with widespread detection of CTX-M-15 isolated from healthy poultry flocks in Eastern Algeria

The intensification of livestock farming has led to the widespread use of massive amounts of antibiotics worldwide. Poultry production, including white meat, eggs and the use of their manure as fertiliser, has been identified as one of the most crucial reservoirs for the emergence and spread of resistant bacteria, including E. coli in poultry as an important opportunistic pathogen representing the greatest biological hazard to human and wildlife health. Thus, this study aimed to analyse E. coli in the faecal carriage of healthy poultry flocks and to investigate the phenotypic and genotypic characteristics of antimicrobial resistance, including integrons genes and phylogenetic groups. A total of 431 cloacal swabs from apparently healthy poultry from four regions in Eastern Algeria from December 2021 to October 2022. 360 E. coli were isolated; from broilers (n = 151), broiler breeders (n = 91), laying hens (n = 72), and breeding hens (n = 46). Among this, 281 isolates exhibited multidrug resistance (MDR) phenotype, 17 of the 360 E. coli isolates exhibited ESBL, and one isolate exhibited both ESBL/pAmpC. A representative collection of 183 among 281 MDR E. coli was selected for further analysis by PCR to detect genes encoding resistance to different antibiotics, and sequencing was performed on all positive PCR products of blaCTX-M and blaCMY-2 genes. Phylogenetic groups were determined in 80 E. coli isolates (20 from each of the four kinds of poultry). The blaCTX-M gene was found in 16 (94.11 %) ESBL-producing E. coli isolates within 11 strains co-expressing the blaSHV gene and 8 strains co-expressing the blaTEM gene. Sequence analysis showed frequent diversity in CTX-M-group-1, with blaCTX-M-15 being the most predominant (n = 11), followed by blaCTX-M-1 (n = 5). The blaCMY-2 gene was detected only in one ESBL/pAmpC isolate. Among the 183 tested isolates, various antimicrobial resistance genes were found (number of strains) blaTEM (n = 121), blaSHV (n = 12), tetA (n = 100), tetB (n = 29), sul1(n = 67), sul2 (n = 32), qnrS (n = 45), qnrB (n = 10), qnrA (n = 1), catA1(n = 13), aac-(6')-Ib (n = 3). Furthermore, class 1 and class 2 integrons were found in 113 and 2 E. coli, respectively. The isolates were classified into multiple phylogroups, including A (35 %), B1 (27.5 %), B2 and D each (18.75 %). The detection of integrons and different classes of resistance genes in the faecal carriage of healthy poultry production indicates that commensal E. coli could potentially act as a reservoir for antimicrobial resistance, posing a significant One Health challenge encompassing the interconnected domains of human, animal health and the environment. Here, we present the first investigation to describe the diversity of blaCTX-M producing E. coli isolates with widespread detection of CTX-M-15 and CTX-M-1 in healthy breeders (Broiler and breeding hens) in Eastern Algeria.

High Prevalence of Antimicrobial Resistance Genes in Multidrug-Resistant Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Clinical Isolates after COVID-19 Pandemic, North Iran

Background

Amid the COVID-19 pandemic, the surge in hospital admissions and widespread use of broad-spectrum antibiotics have heightened the risk of hospital-acquired infections from multidrug-resistant (MDR) organisms, particularly Escherichia coli. It is imperative to implement stringent measures to curb the spread of antimicrobial resistance in hospitals and devise robust treatment strategies for patients grappling with such infections. To confront this challenge, a comprehensive study was undertaken to examine MDR extended-spectrum beta-lactamase (MDR-ESBL)-producing Escherichia coli isolates from patients with nosocomial infections following the COVID-19 pandemic in Northern Iran.

Materials and Methods

The current study was conducted as a cross-sectional study. A total of 12,834 samples were collected from patients with healthcare-associated infections at four designated corona centers in Northern Iran, following the COVID-19 pandemic. Antimicrobial resistance was determined using standard broth micro-dilution, while resistance genes were accurately detected using the multiplex PCR method.

Results

The results indicated that meropenem and ciprofloxacin had a resistance rate of 100% and 98.2%, respectively, while piperacillin-tazobactam showed the highest sensitivity rate at 54.4%. The frequency of specific genes, including bla IMP , bla TEM , AcrA, AcrB, bla CTX , bla OXA-58 , aaclb, bla SHV, and aacla, were found to be 100%, 100%, 99.1%, 99.1%, 91.2%, 80.7%, 64.9%, 44.7%, and 37.7%, respectively.

Conclusions

In the current study, over 50% of MDR-ESBL-producing Escherichia coli isolates exhibited resistance to antibiotics. A combination of antibiotics, including piperacillin-tazobactam and colistin, is recommended for treating extensively drug-resistant Escherichia coli infections.

Extended-spectrum beta-lactamase- and carbapenemase-producing Escherichia coli isolates causing hospital- and community-acquired infections in Tunisia (2001-2019): expansion of CTX-M-15-C2 and CTX-M-27-C1 ST131 subclades

The prevalence of infections caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) and carbapenemase-producing E. coli (CP-EC) is increasing worldwide. We investigated the epidemiology of ESBL-EC and CP-EC causing hospital-acquired (HA) infections in a large teaching hospital in Tunisia over the last two decades and compared it with a collection of 107 community-acquired (CA) ESBL-EC isolates. Between 2001 and 2019, the incidence of HA ESBL-EC increased significantly from 0.08 to 0.32 cases per 1,000 patient days, due entirely to the rapid emergence and expansion of ST131, which accounted for 42.3% (157/371) of HA ESBL-EC. Most ESBL-EC harbored the CTX-M type (92%) with a predominance of blaCTX-M-15. The C2/H30-Rx subclone (n = 103, 65.6%) accounted for 90% of ST131 isolates between 2003 and 2012 and was exclusively associated with CTX-M-15, whereas cluster C1-M27, which was associated with CTX-M-27, emerged in 2013 and expanded gradually to 55% of ST131 in 2019. ST131 prevalence was higher among CA ESBL-EC than HA ESBL-EC (63.6% vs. 42.3%, P = 0.002). CA C2 subclone and non-ST131 isolates showed higher virulence scores than HA isolates. The incidence of CP-EC remained stable over the study period with a mean of 0.08 cases per 1,000 patient days. Among the 38 identified CP-EC isolates, only 16.2% belonged to the ST131 clone and 81.5% produced OXA-48-like carbapenemases. ST131 is the major driver of ESBL-EC spread in both hospital and community settings in Tunisia, mainly linked to the expansion of the CTX-M-15-C2 and CTX-M-27-C1 subclades. The emergence of CP-EC requires ongoing genomic surveillance.

IMPORTANCE

We aimed to investigate the microbiological features of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) and carbapenemase-producing E. coli (CP-EC) causing hospital- and community-acquired infections in Tunisia over the last two decades. The study captured the emergence and expansion of the CTX-M-15-C2 ST131 subclade and successively the CTX-M-27-C1 ST131 subclade, which were responsible for the steady increase in the prevalence of ESBL-EC. However, the incidence of CP-EC remained stable over the study period with a highly diverse content in carbapenemase genes dominated by blaOXA-48-like. This is the first study to provide comprehensive data on the epidemiology of ESBL-EC and CP-EC in a North African country.

Diagnosis of extraintestinal pathogenic Escherichia coli pathogenesis in urinary tract infection

Extra-intestinal pathogenic Escherichia coli (ExPEC) is a virulent pathogen found in humans that causes the majority of urinary tract infections, and other infections such as meningitis and sepsis. ExPEC can enter the urinary tract through two modes: ascending from the bladder or descending from the kidneys. Human anatomical structures generally prevent the transmission of pathogens between the extra-intestinal area, kidneys, bladder, and urinary tract. However, adhesins, a virulence protein of ExPEC, promote the initial bacterial attachment and invasion of host cells. In addition to adhesion proteins, ExPEC contains iron acquisition systems and toxins to evade the host immune system, acquire essential nutrients, and gain antibiotic resistance. The presence of antibiotic-resistant genes makes treating ExPEC in urinary tract infections (UTIs) more complicated. Therefore, screening for the presence of ExPEC among other uropathogens in UTI patients is essential, as it can potentially aid in the effective treatment and mitigation of ExPEC pathogens. Several diagnostic techniques are available for detecting ExPEC, including urine culture, polymerase chain reaction, serological testing, loop-mediated isothermal amplification, and biochemical tests. This review addresses strain-specific diagnostic techniques for screening ExPEC in UTI patients.

Escherichia coli induced matrix metalloproteinase-9 activity and type IV collagen degradation is regulated by progesterone in human maternal decidual

BACKGROUND

Escherichia coli (E. coli) is one of the main bacteria associated with preterm premature rupture of membranes by increasing pro-matrix metalloproteinase 9 (proMMP-9) and degradation of type IV collagen in human feto-maternal interface (HFMi). proMMP-9 is regulated by progesterone (P4) but it is unclear whether P4 inhibits proMMP in human maternal decidual (MDec). This study aimed to determine a role of P4 on proMMP-2 and - 9 and type IV collagen induced by E. coli infection in MDec.

METHODS

Nine HFMi were mounted in a Transwell system. MDec was stimulated with P4 or E. coli for 3-, 6-, or 24-hours. proMMP-2, -9 and type IV collagen were assessed.

RESULTS

Gelatin zymography revealed an increase in proMMP-9 after 3, 6, and 24 h of stimulating MDec with E. coli. Using immunofluorescence, it was confirmed the increase in the HFMi tissue and a reduction on the amount of type IV collagen leading to the separation of fetal amniochorion and MDEc. The degradative activity of proMMP-9 was reduced by 20% by coincubation with P4.

CONCLUSIONS

P4 modulates the activity of proMMP-9 induced by E. coli stimulation but it was unable to completely reverse the degradation of type IV collagen in human MDec tissue.

Selective colonization of microplastics, wood and glass by antimicrobial-resistant and pathogenic bacteria

The Plastisphere is a novel niche whereby microbial communities attach to plastic debris, including microplastics. These communities can be distinct from those found in the surrounding environment or those attached to natural substrates and may serve as a reservoir of both pathogenic and antimicrobial-resistant (AMR) bacteria. Owing to the frequent omission of appropriate comparator particles (e.g. natural substrates) in previous studies, there is a lack of empirical evidence supporting the unique risks posed by microplastics in terms of enrichment and spread of AMR pathogens. This study investigated selective colonization by a sewage community on environmentally sampled microplastics with three different polymers, sources and morphologies, alongside natural substrate (wood), inert substrate (glass) and free-living/planktonic community controls. Culture and molecular methods (quantitative polymerase chain reaction (qPCR)) were used to ascertain phenotypic and genotypic AMR prevalence, respectively, and multiplex colony PCR was used to identify extra-intestinal pathogenic Escherichia coli (ExPECs). From this, polystyrene and wood particles were found to significantly enrich AMR bacteria, whereas sewage-sourced bio-beads significantly enriched ExPECs. Polystyrene and wood were the least smooth particles, and so the importance of particle roughness on AMR prevalence was then directly investigated by comparing the colonization of virgin vs artificially weathered polyethylene particles. Surface weathering did not have a significant effect on the AMR prevalence of colonized particles. Our results suggest that the colonization of plastic and non-plastic particles by AMR and pathogenic bacteria may be enhanced by substrate-specific traits.

The prevalent dynamic and genetic characterization of mcr-1 encoding multidrug resistant Escherichia coli strains recovered from poultry in Hebei, China

OBJECTIVES

Colistin is known as the last resort antibiotic to treat the infections caused by multidrug resistant foodborne pathogens. The emergence and widespread dissemination of plasmid-mediated colistin resistance gene mcr-1 in the Escherichia coli (E. coli) incurs potential threat to public health. Here, we investigated the epidemiology, transmission dynamics, and genetic characterization of mcr-1 harbouring E. coli isolates from poultry originated in Hebei Province, China.

METHODS

A total of 297 faecal samples were collected from the two large poultry farms in Hebei Province, China. The samples were processed for E. coli identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry and 16S rDNA sequencing. Then, the mcr-1 gene harbouring E. coli strains were identified by polymerase chain reaction and subjected to antimicrobial susceptibility testing by broth microdilution assay. The genomic characterization of the isolates was done by whole genome sequencing using the various bioinformatics tools, and multi-locus sequence typing was done by sequence analysis of the seven housekeeping genes. The conjugation experiment was done to check the transferability of mcr-1 along with the plasmid stability testing.

RESULTS

A total of six mcr-1 E. coli isolates with minimum inhibitory concentration of 4 μg/mL were identified from 297 samples (2.02%). The mcr-1 harbouring E. coli were identified as multidrug resistant and belonged to ST101 (n = 4) and ST410 (n = 2). The genetic environment of mcr-1 presented its position on IncHI2 plasmid in 4 isolates and p0111 in 2 isolates, which is a rarely reported plasmid type for mcr-1. Moreover, both type of plasmids was transferable to recipient J53, and mcr-1 was flanked by 3 mobile elements ISApl1, Tn3, and IS26 forming a novel backbone Tn3-IS26-mcr-1- pap2-ISApl1 on the p0111 plasmid. The phylogenetic analysis shared a common lineage with mcr-1 harbouring isolates from the environment, humans, and animals, which indicate its horizontal spread among the diverse sources, species, and hosts.

CONCLUSION

This study recommends the one health approach for future surveillance across multiple sources and bacterial species to adopt relevant measures and reduce global resistance crises.

Prevalence of specific serogroups, antibiotic resistance and virulence factors of avian pathogenic Escherichia coli (APEC) isolated from clinical cases: A systematic review and meta-analysis

Pathogenic strains of Escherichia coli infecting poultry, commonly called avian pathogenic E. coli (APEC) present significant risks, to the health of both poultry and the general public. This systematic review aimed to examine the prevalence of APEC serotypes, sequence types (ST), phylogenetic groups, virulence factors and antibiotic resistance patterns based on 189 research papers sourced from PubMed, Web of Science, and ProQuest. Then, data were extracted from the selected studies and analyzed to assess the global distribution and characteristics of APEC strains. The metaprop codes in the Meta and Metafor packages of R as implemented in RStudio were then used to conduct meta-analysis. Among APEC strains identified from these different research reports serogroup O78 had the highest overall prevalence (16 %), followed by serogroups O2 (10 %), and O117 (8 %). The most common ST profiles were ST117 (20 %), ST140 (15 %), ST95 (12 %), and ST131 (9 %). ST117 and ST140 are known reservoirs for pathogenic E. coli in humans. Moreover, phylogenetic assessment highlighted the prevalence of phylogroups A, A1, F, D, and B2 among APEC strains indicating diversity in phylogenetic origin within poultry populations. The presence of antimicrobial resistance was notable among APEC strains against antibiotics such as tetracyclines, penicillins, and cephalosporins. This resistance may be linked to use of antimicrobials in poultry production in certain regions presenting challenges for both animal health management and human infection control. Analysis of sequences linked to adherence or virulence indicated that genes encoding adhesins (csg, fimC), iron/metal uptake (sitB, sitC, iroD) and cytotoxicity (estB, hlyF), and serum resistance (traT, iss) were highly prevalent. These factors have been reported to contribute to APEC host colonization and virulence in poultry. In summary, this overview of the characteristics of APEC highlights the pressing importance of monitoring and implementing management approaches to reduce antimicrobial resistance considering that a phylogenetic diversity of E. coli strains causes infections in both poultry and humans and represents a risk to both animal and public health. Further, determining the major conserved aspects and predominant mechanisms of virulence of APEC is critical for improving diagnostics and developing preventative measures to reduce the burden of infection caused by pathogenic E. coli in poultry and lower risks associated with foodborne transmission of E. coli to humans through poultry and poultry products.

Extended-Spectrum Beta-Lactamase- and Plasmidic AmpC-Producing Enterobacterales among the Faecal Samples in the Bulgarian Community

The aim of the present work was to genetically characterise cefotaxime-resistant enterobacteria isolated from community carriers in Bulgaria. In total, 717 faecal samples from children and adults in five medical centres in Sofia, Pleven and Burgas were examined. Antimicrobial susceptibility was evaluated by the disk diffusion method. blaESBL or plasmidic AmpC (pAmpC) genes were detected by PCR and sequencing. MLST and ERIC-PCR were used to detect clonal relatedness. Among the faecal samples, 140 cefotaxime-resistant enterobacteria were found. The most frequently detected species was Escherichia coli (77.9%, 109/140 samples), followed by Klebsiella pneumoniae (7.9%, 11/140). Among the isolates, blaCTX-M-15 (37.1%) was predominant, followed by blaCTX-M-3 (19.2%), blaCTX-M-14 (10%), and blaCTX-M-27 (4.3 %). Genes encoding pAmpC were observed in 11.4% (blaDHA-1, 16/140) and in 1.4% (blaCMY-2, 2/140). The frequency of ESBL and pAmpC producers among the subjects was 14.6% and 2.5%, respectively. No carbapenem-resistant isolates were found. Four main clonal complexes (CC131, CC10, CC38, and CC155) were detected among E. coli isolates. The most common type was ST131, phylogroup B2 (16.5%). The increased frequency of ESBL- and pAmpC-producing enterobacteria in the community is a prerequisite for treatment failures of the associated infections and a good background for further studies.

Increasing Fluroquinolone Susceptibility and Genetic Diversity of ESBL-Producing E. coli from the Lower Respiratory Tract during the COVID-19 Pandemic

Lower respiratory tract infections (LRTIs) are the fourth leading cause of death worldwide, among which Escherichia coli (E. coli) pneumonia is considered a rare phenomenon. Treatment options for LRTIs have become limited, especially for extended-spectrum β-lactamase-producing E. coli (ESBL-EC), which are usually resistant to other groups of antimicrobials as well. The aim of our study was to compare the phenotypic resistance profiles and genotypes of ESBL-EC isolates associated with LRTIs before (pre-COVID-19) and during (COVID-19) the COVID-19 pandemic. All isolates were screened for antimicrobial resistance genes (ARGs) and virulence-associated genes (VAGs) and assigned to phylogenetic groups, sequence types and clonal groups by PCR. During the pandemic, a significantly lower proportion of ciprofloxacin-, levofloxacin- and trimethoprim-sulfamethoxazole-resistant ESBL-EC isolates was retrieved from lower respiratory tract (LRT) samples. PCR-based genotypization revealed greater clonal diversity and a significantly lower proportion of isolates with blaTEM, aac(6')-Ib-cr and qacEΔ1 genes. In addition, a higher proportion of isolates with the integrase gene int1 and virulence genes sat and tsh was confirmed. The lower prevalence of fluoroquinolone resistance and greater genetic diversity of ESBL-EC isolated during the COVID-19 period may have been due to the introduction of new bacterial strains into the hospital environment, along with changes in clinical establishment guidelines and practices.

A Novel Dhillonvirus Phage against Escherichia coli Bearing a Unique Gene of Intergeneric Origin

Antibiotics resistance is expanding amongst pathogenic bacteria. Phage therapy is a revived concept for targeting bacteria with multiple antibiotics resistances. In the present study, we isolated and characterized a novel phage from hospital treatment plant input, using Escherichia coli (E. coli) as host bacterium. Phage lytic activity was detected by using soft agar assay. Whole-genome sequencing of the phage was performed by using Next-Generation Sequencing (NGS). Host range was determined using other species of bacteria and representative genogroups of E. coli. Whole-genome sequencing of the phage revealed that Escherichia phage Ioannina is a novel phage within the Dhillonvirus genus, but significantly diverged from other Dhillonviruses. Its genome is a 45,270 bp linear double-stranded DNA molecule that encodes 61 coding sequences (CDSs). The coding sequence of CDS28, a putative tail fiber protein, presented higher similarity to representatives of other phage families, signifying a possible recombination event. Escherichia phage Ioannina lytic activity was broad amongst the E. coli genogroups of clinical and environmental origin with multiple resistances. This phage may present in the future an important therapeutic tool against bacterial strains with multiple antibiotic resistances.