Molecular epidemiology of extraintestinal pathogenic (uropathogenic) Escherichia coli

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

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

Antimicrobial resistance, serogroups, virulence gene profiles and MLST of Escherichia coli from giant panda

Escherichia coli is a major bacterial pathogen which causes diarrhea in the giant panda. This study investigated the biological characteristics of 100 E. coli strains isolated from fecal samples collected from 100 captive giant pandas of different age groups and sexes. A standard Kirby-Bauer disk diffusion antimicrobial susceptibility test was performed with the isolates and we then further evaluated the antibiotic resistance genes (ARGs) by high-throughput quantitative PCR. Additionally, we then analyzed O serogroups through a slide agglutination test, virulence genes and the multi-locus sequence typing (MLST) by PCR. Antimicrobial susceptibility testing demonstrated that the 100 E. coli strains were mainly resistant to ENR (68%), AM (56%), IPM (55%), AMX (54%) and CA (52%), but were susceptible to MEM and FOX. The resistance to TZP, AK, FEP, CAZ, AMS, AZM, AT and IPM was significantly related to age (p < 0.05); the resistance rate of E. coli isolated from female giant pandas to N was significantly higher than in males (p < 0.05). Forty-five different types of ARGs were found, which included a total of 2,258 ARGs, in the 100 E. coli isolates. The top 10 of detection rate of ARGs were: acrA-04, acrA-05, aacC, blaCTX-M-04, ampC-04, blaSHV-01, blaTEM, sul2, blaOXY, tetA-02. ARGs aac (6')I1, blaCTX-M-03, tetD-02, blaSHV-02 and blaOXY were significantly related to age (p < 0.05), blaSHV-02, blaNDM and ampC-04 were related to sex (p < 0.05). Twelve different O serogroups from 32 E. coli isolates were distinguished, including O4, O8, O9, O15, O18, O20, O55, O88, O112, O157, O158, and O167. The most prevalent O serotype was O20, but O28, O45, O101, O149, and O152 were not detected. Fourteen different types of virulence genes were detected in the 100 E. coli isolates, of which papA (99%) were highly detected, while hlyA, elt and estA were not detected. MLST showed that 41 STs, which had one CCs and six groups with SLVs, in the 100 E. coli strains were identified, the main type was ST37. Our results advocate the need of strict biosecurity and surveillance programs in order to prevent the spread of pathogenic bacteria in the captive giant panda population.

Genotypic Characterization of Uropathogenic Escherichia coli from Companion Animals: Predominance of ST372 in Dogs and Human-Related ST73 in Cats

Extraintestinal pathogenic Escherichia coli (ExPEC) account for over 80% and 60% of bacterial urinary tract infections (UTIs) in humans and animals, respectively. As shared uropathogenic E. coli (UPEC) strains have been previously reported among humans and pets, our study aimed to characterize E. coli lineages among UTI isolates from dogs and cats and to assess their overlaps with human UPEC lineages. We analysed 315 non-duplicate E. coli isolates from the UT of dogs (198) and cats (117) collected in central Germany in 2019 and 2020 utilizing whole genome sequencing and in silico methods. Phylogroup B2 (77.8%), dog-associated sequence type (ST) 372 (18.1%), and human-associated ST73 (16.6%), were predominant. Other STs included ST12 (8.6%), ST141 (5.1%), ST127 (4.8%), and ST131 (3.5%). Among these, 58.4% were assigned to the ExPEC group and 51.1% to the UPEC group based on their virulence associated gene (VAG) profile (ExPEC, presence of ≥VAGs: papAH and/or papC, sfa/focG, afaD/draBC, kpsMTII, and iutA; UPEC, additionally cnf1 or hlyD). Extended-spectrum cephalosporin (ESC) resistance mediated by extended-spectrum β-lactamases (ESBL) and AmpC-β-lactamase was identified in 1.9% of the isolates, along with one carbapenemase-producing isolate and one isolate carrying a mcr gene. Low occurrence of ESC-resistant or multidrug-resistant (MDR) isolates (2.9%) in the two most frequently detected STs implies that E. coli isolated from UTIs of companion animals are to a lesser extent associated with resistance, but possess virulence-associated genes enabling efficient UT colonization and carriage. Detection of human-related pandemic lineages suggests interspecies transmission and underscores the importance of monitoring companion animals.

Baicalin Weakens the Porcine ExPEC-Induced Inflammatory Response in 3D4/21 Cells by Inhibiting the Expression of NF-κB/MAPK Signaling Pathways and Reducing NLRP3 Inflammasome Activation

Porcine extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of death in pigs and has led to considerable economic losses for the pig industry. Porcine ExPEC infections often cause systemic inflammatory responses in pigs, characterized by meningitis, arthritis, pneumonia, and septicemia. Baicalin has been reported to possess potent anti-inflammatory activity, but its function in porcine ExPEC remains unknown. The aim of this study was to explore the protective effect and mechanism of baicalin against the porcine ExPEC-induced inflammatory responses in 3D4/21 cells. After treatment with baicalin, the effects on cell damage, the level of pro-inflammatory cytokines, the expression of nuclear factor-κB (NF-κB)/mitogen-activated protein kinase (MAPK) signaling pathways, and the activation of NOD-like receptor protein 3 (NLRP3) inflammasomes were examined. Our results show that baicalin significantly reduced the damage to 3D4/21 cells infected with porcine ExPEC PCN033. Further study showed that baicalin significantly reduced the transcription and expression of pro-inflammatory cytokines such as interleukin-1β (IL-1β), interleukin-6 (IL-6), and interleukin-8 (IL-8). Furthermore, baicalin inhibited the phosphorylation of proteins such as P65, nuclear factor κB inhibitor α (IκBα), extracellular regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and P38 and reduced the expression levels of proteins such as NLRP3, apoptosis-associated speck-like protein containing a CARD (ASC), and caspase-1. These results reveal that baicalin reduced the damage to 3D4/21 cells by inhibiting the expression of NF-κB/MAPK signaling pathways and blocking NLRP3 inflammasome activation in 3D4/21 cells infected with porcine ExPEC. Taken together, these results suggest that baicalin may have potential as a medicine for the treatment of porcine ExPEC-infected pigs by regulating inflammatory responses. This study provides a novel potential pharmaco-therapeutic approach to preventing porcine ExPEC infection.

Distribution of virulence determinants among Escherichia coli ST131 and its H30/H30-Rx subclones in Turkey

Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading pathogen in urinary tract infection. In recent years multidrug-resistant B2-ST131 E. coli clonal group has disseminated worldwide. The ST131 and its subclones H30 and H30-Rx have been identified only in a few studies from Turkey. The aim of this study is to investigate the presence of ST131 and its subclones and to analyze their adhesin virulence genes and antimicrobial resistance. A total of 250 urinary ExPEC isolates were included in the study. Resistance rates of 16 antimicrobial agents were determined by disk-diffusion. Multidrug-resistance and ESBL production were analyzed. Altogether 8 adhesin genes were investigated namely, papAH, fimH, sfa/focDE, focG, afa/draBC, iha, bmaE and gafD. A total of 39 ST131 isolate were determined and 33 (84.6%) were multidrug-resistant. ESBL production was detected in 34 (87.2%) ST131 and 61 (28.9%) of non-ST131 strains. In our study, we found a strong correlation between ST131 strains and fimH, iha, afa/draBC, papAH virulence determinants. Twenty-nine (85.3%) of 34 ST131-O25b-H30 isolates were identified as H30-Rx. All the papAH gene positive isolates were identified within ST131-O25b-H30-Rx lineage. Non-H30-Rx isolates within H30 isolates were identified as pattern 2. Almost 16% of the isolates were identified as ST131 regardless of clinical syndrome and approximately 34% of the multidrug-resistant isolates were H30-Rx subclone. We report H30-Rx as the dominant subclone of ST131 in our study. Imipenem, fosfomycin and nitrofurantoin proved to be the most effective agents according to antibiotic resistance patterns of both ST131 and non-ST131 E. coli strains.

The shared NDM-positive strains in the hospital and connecting aquatic environments

The spread of antibiotic-resistant priority pathogens outside hospital settings is, both, a significant public health concern and an environmental problem. In recent years, New Delhi Metallo-β-lactamase (NDM)-positive strains have caused nosocomial infections with high mortality and poor prognosis worldwide. Our study investigated the links of NDM-positive strains between the hospital and the connecting river system in Jinan city, Eastern China by using NDM-producing Escherichia coli (NDM-EC) as an indicator via whole genome sequencing. Thirteen NDM-EC isolates were detected from 187 river water and sediment samples, while 9 isolates were identified from patients at the local hospital. All NDM-EC isolates were resistant to imipenem, meropenem, cefotaxime, cefoxitin, ampicillin, tetracycline, fosfomycin, piperacillin-tazobactam. The bla_NDM-5 (n = 20) and bla_NDM-9 (n = 2) genes were identified, which were predominantly on IncX3 plasmids (n = 13), followed by IncFII plasmids (n = 5) and IncFIA plasmids (n = 2). Conjugation experiments showed that 21 isolates could transfer NDM-harboring plasmids. The well-conserved bla_NDM-5 genetic environment (ISAba125-bla_NDM-5/9-ble_MBL-trpF-dsbD-IS26) of these plasmids suggested a common genetic origin. Nine sequence types (STs) were detected, including three international high-risk clones ST167 (n = 8), ST410 (n = 1), and ST617 (n = 1). Phylogenetic analysis showed ST167 E. coli from the river was genotypically related to clinical isolates recovered from patients. Furthermore, ST167 isolates showed high genetic similarities with other clinical strains from geographically distinct regions. The genetic concordance between isolates from different sampling sites in the same river (ST218 clone), and different rivers (ST448 clone) raises concerns regarding the rapid dissemination of NDM-EC in the aquatic environment. The emergence and spread of the clinically relevant NDM-positive strains, especially for E. coli ST167 clone, an international high-risk clone associated with multi-resistance and virulence capacity, within and between the hospital and aquatic environments were elucidated, highlighting the need for attention and action.

Genes mcr improve the intestinal fitness of pathogenic E. coli and balance their lifestyle to commensalism

BACKGROUND

The plasmid-mediated resistance gene mcr-1 confers colistin resistance in Escherichia coli and paves the way for the evolution to pan-drug resistance. We investigated the impact of mcr-1 in gut colonization in the absence of antibiotics using isogenic E. coli strains transformed with a plasmid encoding or devoid of mcr-1.

RESULTS

In gnotobiotic and conventional mice, mcr-1 significantly enhanced intestinal anchoring of E. coli but impaired their lethal effect. This improvement of intestinal fitness was associated with a downregulation of intestinal inflammatory markers and the preservation of intestinal microbiota composition. The mcr-1 gene mediated a cross-resistance to antimicrobial peptides secreted by the microbiota and intestinal epithelial cells (IECs), enhanced E. coli adhesion to IECs, and decreased the proinflammatory activity of both E. coli and its lipopolysaccharides.

CONCLUSION

Overall, mcr-1 changed multiple facets of bacterial behaviour and appeared as a factor enhancing commensal lifestyle and persistence in the gut even in the absence of antibiotics. Video Abstract.

Characterization of cephalosporin and fluoroquinolone resistant Enterobacterales from Irish farm waste by whole genome sequencing

Background

The Enterobacterales are a group of Gram-negative bacteria frequently exhibiting extended antimicrobial resistance (AMR) and involved in the transmission of resistance genes to other bacterial species present in the same environment. Due to their impact on human health and the paucity of new antibiotics, the World Health Organization (WHO) categorized carbapenem resistant and ESBL-producing as critical. Enterobacterales are ubiquitous and the role of the environment in the transmission of AMR organisms or antimicrobial resistance genes (ARGs) must be examined in tackling AMR in both humans and animals under the one health approach. Animal manure is recognized as an important source of AMR bacteria entering the environment, in which resistant genes can accumulate.

Methods

To gain a better understanding of the dissemination of third generation cephalosporin and fluoroquinolone resistance genes between isolates in the environment, we applied whole genome sequencing (WGS) to Enterobacterales (79 E. coli, 1 Enterobacter cloacae, 1 Klebsiella pneumoniae, and 1 Citrobacter gillenii) isolated from farm effluents in Ireland before (n = 72) and after (n = 10) treatment by integrated constructed wetlands (ICWs). DNA was extracted using the MagNA Pure 96 system (Roche Diagnostics, Rotkreuz, Switzerland) followed by WGS on a MiSeq platform (Illumina, Eindhoven, Netherlands) using v3 chemistry as 300-cycle paired-end runs. AMR genes and point mutations were identified and compared to the phenotypic results for better understanding of the mechanisms of resistance and resistance transmission.

Results

A wide variety of cephalosporin and fluoroquinolone resistance genes (mobile genetic elements (MGEs) and chromosomal mutations) were identified among isolates that mostly explained the phenotypic AMR patterns. A total of 31 plasmid replicon types were identified among the 82 isolates, with a subset of them (n = 24), identified in E. coli isolates. Five plasmid replicons were confined to the Enterobacter cloacae isolate and two were confined to the Klebsiella pneumoniae isolate. Virulence genes associated with functions including stress, survival, regulation, iron uptake secretion systems, invasion, adherence and toxin production were identified.

Conclusion

Our study showed that antimicrobial resistant organisms (AROs) can persist even following wastewater treatment and could transmit AMR of clinical relevance to the environment and ultimately pose a risk to human or animal health.

Distribution of papG alleles among uropathogenic Escherichia coli from reproductive age women

BACKGROUND

Extraintestinal Escherichia coli (E. coli) causing urinary tract infections (UTIs), and often referred to as uropathogenic E. coli (UPEC), are a major contributor to the morbidity of UTIs and associated healthcare costs. UPEC possess several virulence factors (VFs) for infecting and injuring the host. We studied the papG allele distribution, and its association with other VF genes and phylogenetic groups, amongst 836 UPEC and fecal isolates from reproductive age women.

RESULTS

The papGII gene was highly prevalent amongst pyelonephritis isolates (68%), whilst the majority, albeit smaller proportion, of cystitis isolates (31%) harboured the papGIII gene. Among the pyelonephritis and cystitis isolates, papG positive isolates on average had higher VF gene scores, and were more likely to belong to phylogenetic group B2, than their negative counterparts. This was mostly due to the contribution of papGII isolates, which on average contained more VF genes than their papGIII counterparts, irrespective of the uro-clinical syndrome. However, the papGII isolates from the pyelonephritis cohort had higher VF gene scores than the cystitis ones, suggesting presence of possible papGII clones with differing inferred virulence potential. Furthermore, papGII isolates were more likely to possess an intact pap gene operon than their papGIII counterparts. Also of note was the high proportion of isolates with the papGI allele which was not associated with other pap operon genes; and this finding has not been described before.

CONCLUSIONS

The association of the papGII gene with several VF genes compared to the papGIII gene, appears to explain the abundance of these genes in pyelonephritis and cystitis isolates, respectively.

Virulence potential of faecal <i>Escherichia coli</i> strains isolated from healthy cows and calves on farms in Perm Krai

Cattle are a reservoir of pathogenic and potentially pathogenic Escherichia coli (E. coli) strains, which can pose a threat to human and animal health. The aim of the study was to evaluate the occurrence of 22 virulence-associated genes (VAGs), as well as the prevalence of antimicrobial drug resistance and three different bla-genes among 49 E. coli strains isolated from healthy cattle. The presence of VAGs that are common among diarrheagenic E. coli (DEC) strains and/or extraintestinal pathogenic E. coli (ExPEC) strains was determined by amplifying specific gene sequences by PCR. The following VAGs associated with DEC were found: east1 in 24.5 % of the studied E. coli strains, estI in 10.2 %, ehxA in 8.2 %, stx2 in 6.1 %, eltA in 4.1 %, estII and stx1 in 2.0 % of the studied strains. The prevalence of ExPEC VAGs was: fimH – 91.8 %, afa/draBC – 61.2 %, iutA – 44.9 %, flu – 32.7 %, sfaDE and hlyF – 30.6 %, iroN – 22.4 %, ompT and papC – 20.4 %, kpsMTII and hlyA – 18.4 %, iss – 14.3 %, usp – 2.0 %, cnf1 and iha were not detected among the studied strains. Based on the found co-occurrence of VAGs “classical”, hetero-pathogenic and hybrid-pathogenic E. coli strains were found. E. coli strains isolated from cows had a higher diarrheagenic potential, whereas E. coli strains isolated from calves more frequently contained genes associated with the ExPEC pathotype. Among the studied E. coli strains, 77.6 % were resistant to ampicillin, 49.0 % to tetracycline, 20.4 % to chloramphenicol, 16.3 % to cefoperazone, 16.3 % to ceftriaxone, 16.3 % to aztreonam, 14.3 % to cefepime, 10.2 % to norfloxacin, 10.2 % to ciprofloxacin, 6.1 % to levofloxacin and 2.0 % to gentamicin. All strains were sensitive to meropenem and amikacin. 32.7 % of the studied E. coli strains were found to be multidrug resistant, as they were resistant to at least three groups of antibiotics. With PCR, the blaTEM, blaSHV, and blaCTX-M genes were detected in 100, 31.6, and 26.3 %, respectively, of strains resistant to at least one of the beta-lactam antibiotics. Thus, it was shown that the studied faecal E. coli of healthy cows and calves had a high hetero-pathogenic potential, therefore in the future molecular genetic characterization of these bacteria shall be an important part of the epizootic monitoring.

Effects of TolC on the pathogenicity of porcine extraintestinal pathogenic Escherichia coli

Extraintestinal pathogenic Escherichia coli (ExPEC) is a well-known critical pathogenic zoonosis that causes extraintestinal infections in humans and animals by affecting their immune organs. Recently, research on the outer membrane protein of E. coli, tolerant colicin (TolC), a virulent protein in the formation of the ExPEC efflux pump, has been an attractive subject. However, the pathogenic mechanisms remain unclear. This study aimed to explore the role of TolC in the pathogenesis of the ExPEC strain PPECC42; a complementation strain (Cm-TolC) and an isogenic mutant (ΔTolC) were constructed. Loss of TolC drastically impaired the virulence of ExPEC in an experimental mouse model. ΔTolC showed a substantial decrease in the porcine aortic vascular endothelial cell (PAVEC) adherence, invasion, and pro-inflammatory response, in contrast to that of the wild type, with a reduced survival ratio in both the bacterial load and whole blood in mice. ΔTolC also showed decreased expression of necroptosis signals such as receptor-interacting protein kinase 1, phosphorylated mixed-lineage kinase domain-like protein, and mitochondrial proteins such as phosphoglycerate mutase family member 5. Our data suggest that TolC is closely associated with ExPEC pathogenesis. These results provide scientific grounds for exploring the potential of TolC as an effective drug target for controlling ExPEC infection, screening new inhibitors, and developing new drugs. This will allow for further prevention and control of ExPEC infection.

Association between Escherichia coli with NotI-restriction resistance and urinary tract infections

BACKGROUND

Escherichia coli is the most common cause of urinary tract infections (UTIs). It is widely accepted that uropathogenic E. coli (UPEC) mainly emerge from the distal gut microbiota. Identification of bacterial characteristics that are able to differentiate UPEC from fecal commensal strains will facilitate the development of novel strategies to detect and monitor the spread of UPEC.

METHODS

Fifty fecal commensal, 83 UTI-associated and 40 biliary tract infection (BTI)-associated E. coli isolates were analyzed. The NotI restriction patterns of chromosomal DNA in the isolates were determined by pulse-field gel electrophoresis. The phylogenetic types and the presence of 9 known virulence genes of each isolate were determined by PCR analyses. Additionally, the susceptibilities of the isolates to antibiotics were revealed. Then the associations of NotI resistance with UTI-associated isolates, phylotypes, and antibiotic resistance were assessed.

RESULTS

NotI resistance was correlated with UTI-associated isolates, compared to the fecal isolates. Consistently, NotI-resistant isolates harbored a greater number of virulence factors and mainly belonged to phylotype B2. Additionally NotI resistance was correlated with chloramphenicol resistance among the bacteria. Among the fecal, UTI-associated and BTI-associated groups, the distribution of NotI-resistant group B2 isolates was correlated with UTI-associated bacteria.

CONCLUSION

NotI resistance alone is a potential marker for distinguishing fecal strains and UPEC, while the combination of NotI resistance and B2 phylogeny is a candidate marker to differentiate UPEC from fecal and other extraintestinal pathogenic E. coli. Additionally, NotI resistance may be valuable for assessing the potential of chloramphenicol resistance of E. coli.

Molecular Epidemiology and Presence of Hybrid Pathogenic Escherichia coli among Isolates from Community-Acquired Urinary Tract Infection

Urinary tract infections (UTI) affect community and healthcare patients worldwide and may have different clinical outcomes. We assessed the phylogenetic origin, the presence of 43 virulence factors (VFs) of diarrheagenic and extraintestinal pathogenic Escherichia coli, and the occurrence of hybrid strains among E. coli isolates from 172 outpatients with different types of UTI. Isolates from phylogroup B2 (46%) prevailed, followed by phylogroups A (15.7%) and B1 (12.2%), with similar phylogenetic distribution in symptomatic and asymptomatic patients. The most frequent VFs according to their functional category were fimA (94.8%), ompA (83.1%), ompT (63.3%), chuA (57.6%), and vat (22%). Using published molecular criteria, 34.3% and 18.0% of the isolates showed intrinsic virulence and uropathogenic potential, respectively. Two strains carried the eae and escV genes and one the aggR gene, which classified them as hybrid strains. These hybrid strains interacted with renal and bladder cells, reinforcing their uropathogenic potential. The frequency of UPEC strains bearing a more pathogenic potential in the outpatients studied was smaller than reported in other regions. Our data contribute to deepening current knowledge about the mechanisms involved in UTI pathogenesis, especially among hybrid UPEC strains, as these could colonize the host’s intestine, leading to intestinal infections followed by UTI.

High levels of gut carriage of antimicrobial-resistant Escherichia coli in community settings in Rio de Janeiro, Brazil

The prevalence and risk factors for gut carriage of antimicrobial-resistant Escherichia coli among individuals living in the community in Rio de Janeiro, Brazil, are unknown. The aim of this study was to determine the prevalence of colonization with antimicrobial-resistant E. coli, including isolates producing ESBL and harboring plasmid-mediated quinolone resistant (PMQR) genes in this community. We performed a cross-sectional study and analyzed fecal specimens of individuals attending outpatient clinics in the city from January 2015 to July 2019. We investigated susceptibility to antimicrobial agents by disc diffusion tests and used PCR to determine ESBL types, PMQR, and the virulence genes that characterize an isolate as extraintestinal pathogenic E. coli (ExPEC). Among the 623 subjects, 212 (34%) carried an isolate resistant to at least one of the tested antimicrobial agents, with the highest frequencies of resistance to ampicillin (26%), trimethoprim-sulfamethoxazole (19%), cefazolin (14%), and ciprofloxacin (CIP, 9%). In addition, 13% (81) of subjects carried a multidrug-resistant-E.coli (MDR-E), including 47 (8% of all isolates) ESBL-producing E. coli (ESBL-E), mainly of CTX-M-8 (15, 32%) and CTX-M-15 (9, 20%) types. PMQR genes were present in 7% (42) of all isolates, including 60% (32) of the 53 resistant to CIP. Previous use of antimicrobial agents, particularly fluoroquinolones, was a risk factor for colonization with MDR-E (25%, 20/81 vs 13%, 70/542, p = 0.01), ESBL-E (28%, 13/47, vs 13%, 77/576, p = 0.01), and resistance to CIP (26%, 14/53, vs 12%, 70/570, p = 0.01). The most pathogenic phylogroups B2, C, and D were 37% of the MDR-E, 30% of the ESBL-E, 38% of the CIP-resistant, and 31% of PMQR gene carrying E. coli isolates. We show that carriage of MDR-E (mostly ESBL-E) reached high levels in the community in Rio de Janeiro, increased by the selection of antimicrobial agents. Much of the resistant E. coli isolates are potential pathogenic strains. The widespread use of antimicrobial agents during the COVID-19 pandemic in Brazil may have worsened this picture.

An Integrated Perspective on Virulence-Associated Genes (VAGs), Antimicrobial Resistance (AMR), and Phylogenetic Clusters of Pathogenic and Non-pathogenic Avian Escherichia coli

Avian pathogenic Escherichia coli (APEC) is an important bacterial pathogen that causes avian colibacillosis and leads to huge economic losses in the poultry industry. Different virulence traits contribute to pathogenesis of APEC infections, and antimicrobial resistance (AMR) has also been an overwhelming issue in poultry worldwide. In the present study, we aimed to investigate and compare the presence of virulence-associated genes (VAGs), AMR, and phylogenetic group's distribution among APEC and avian fecal E. coli (AFEC) strains. E. coli from birds with colisepticemia and yolk sac infection (YSI) (APEC) plus E. coli strains from the feces of healthy birds (AFEC) were compared by the aforementioned traits. In addition, the clonal relatedness was compared using Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Although all strains were susceptible to fosfomycin, ceftriaxone, and cefixime, almost all strains (98%) were multi-drug resistant (MDR). All strains (except two) harbored at least three or more VAGs, and the virulence scores tended to be higher in pathogenic strains especially in the colisepticemic group. All phylogenetic groups were found in isolates from YSI, colisepticemia, and the feces of healthy birds; however, the frequency of phylogroups varied according to the source of the isolate. B1 and C phylogroups were statistically more likely to be found among APEC from YSI and colisepticemic E. coli groups, respectively, while phylogroup A was the most frequently occurring phylogroup among AFEC strains. Our findings also revealed that AMR and VAGs are not essentially co-evolved traits as in some instances AMR strains were more prevalent among AFEC. This reflects the divergent evolutionary pathways of resistance acquisition in pathogenic or non-pathogenic avian E. coli strains. Importantly, strains related to phylogenetic group C showed higher virulence score and AMR that requires further attention. To some extent, ERIC-PCR was able to group strains by isolation source, phylogroup, or virulence genes. Further integrated studies along with assessment of more detailed genotypic and phenotypic features could potentially lead to better understanding of virulence, resistance, and evolution of ExPEC.

Structural and functional characterization of the FimH adhesin of uropathogenic Escherichia coli and its novel applications

Type 1 fimbriae are responsible for bacterial pathogenicity and biofilm production, which are important virulence factors in uropathogenic Escherichia coli strains. Many articles are published on fimH, but each examined a specific aspect of this protein. The current review study aimed at focusing on structure and conformational changes and describing efforts to use this protein in novel potential treatments for urinary tract infections, typing methods, and expression systems. The current study was the first review that briefly and effectively examined issues related to fimH adhesin.

Transcription Regulator YgeK Affects the Virulence of Avian Pathogenic Escherichia coli

Simple Summary

Avian pathogenic Escherichia coli (APEC) is the responsible pathogen for colibacillosis in poultry. Transcriptional regulator YgeK was a transcriptional regulator locating at E. coli type three secretion system 2 (ETT2) in APEC. However, the role of YgeK in APEC has not been reported. In this study, we found that the inactivation of YgeK in APEC decreased the flagellar formation ability, bacterial motility ability, serum sensitivity, adhesion ability, and virulence. Results suggested that the transcriptional regulator YgeK plays a crucial role in APEC virulence.

Abstract

Avian pathogenic Escherichia coli (APEC) is the responsible pathogen for colibacillosis in poultry, and is a potential gene source for human extraintestinal pathogenic Escherichia coli. Escherichia coli type III secretion system 2 (ETT2) is widely distributed in human and animal ExPEC isolates, and is crucial for the virulence of ExPEC. Transcriptional regulator YgeK, located in the ETT2 gene cluster, was identified as an important regulator of gene expression in enterohemorrhagic E. coli (EHEC). However, the role of YgeK in APEC has not been reported. In this study, we performed amino acid alignment analysis of YgeK among different E. coli strains and generated ygeK mutant strain AE81ΔygeK from clinical APEC strain AE81. Flagellar formation, bacterial motility, serum sensitivity, adhesion, and virulence were all significantly reduced following the inactivation of YgeK in APEC. Then, we performed transcriptome sequencing to analyze the functional pathways involved in the biological processes. Results suggested that ETT2 transcriptional regulator YgeK plays a crucial role in APEC virulence. These findings thus contribute to our understanding of the function of the ETT2 cluster, and clarify the pathogenic mechanism of APEC.

D-Mannoside FimH Inhibitors as Non-Antibiotic Alternatives for Uropathogenic Escherichia coli

FimH is a type I fimbria of uropathogenic Escherichia coli (UPEC), recognized for its ability to adhere and infect epithelial urinary tissue. Due to its role in the virulence of UPEC, several therapeutic strategies have focused on the study of FimH, including vaccines, mannosides, and molecules that inhibit their assembly. This work has focused on the ability of a set of monosubstituted and disubstituted phenyl mannosides to inhibit FimH. To determine the 3D structure of FimH for our in silico studies, we obtained fifteen sequences by PCR amplification of the fimH gene from 102 UPEC isolates. The fimH sequences in BLAST had a high homology (97–100%) to our UPEC fimH sequences. A search for the three-dimensional crystallographic structure of FimH proteins in the PDB server showed that proteins 4X5P and 4XO9 were found in 10 of the 15 isolates, presenting a 67% influx among our UPEC isolates. We focused on these two proteins to study the stability, free energy, and the interactions with different mannoside ligands. We found that the interactions with the residues of aspartic acid (ASP 54) and glutamine (GLN 133) were significant to the binding stability. The ligands assessed demonstrated high binding affinity and stability with the lectin domain of FimH proteins during the molecular dynamic simulations, based on MM-PBSA analysis. Therefore, our results suggest the potential utility of phenyl mannoside derivatives as FimH inhibitors to mitigate urinary tract infections produced by UPEC; thus, decreasing colonization, disease burden, and the costs of medical care.

The causal relationship between O2:K7:H6 extra-intestinal pathogenic Escherichia coli (ExPEC) and native valve endocarditis: a case report

Background

Native valves infective endocarditis due to Escherichia coli is still a rare disease and a particular virulence of some E.coli isolate may be suspected.

Case presentation

A 79-year-old woman presented during the post-operative period of an orthopedic surgery a urinary tract infection following obstructive ureteral lithiasis. E. coli was isolated from a pure culture of urine and blood sampled simultaneously. After evidence of sustained E.coli septicemia, further investigations revealed acute cholecystitis with the same micro-organism in biliary drainage and a native valve mitral endocarditis. E.coli was identified as O2:K7:H6, phylogenetic group B2, ST141, and presented several putative and proven virulence genes. The present isolate can be classified as both extra-intestinal pathogenic E.coli (ExPEC_JJ) and uropathogenic E. coli (UPEC_HM).

Conclusions

The relationship between the virulent factors present in ExPEC strains and some serotypes of E. coli that could facilitate the adherence to cardiac valves warrants further investigation.

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

Background

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

Methods

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

Results

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

Conclusion

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

Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Escherichia coli Strains From Healthy Food Animals Across Europe

The role of livestock animals as a putative source of ESBL/pAmpC E. coli for humans is a central issue of research. In a large-scale pan-European surveillance, 2,993 commensal Escherichia spp. isolates were recovered from randomly collected fecal samples of healthy cattle, pigs and chickens in various abattoirs. One-hundred Escherichia spp. isolates (0.5% from cattle, 1.3% pigs, 8.0% chickens) fulfilled the criteria for cefotaxime and ceftazidime non-wildtype (EUCAST). In silico screening of WGS data of 99 isolates (98 E. coli and 1 E. fergusonii) revealed bla_SHV–12 (32.3%), bla_CTX–M–1 (24.2%), and bla_CMY–2 (22.2%) as predominant ESBL/pAmpC types. Other types were bla_SHV–2 (1.0%), bla_{CTX–M–2/–14/–15} (1.0/6.1/1.0%), and bla_TEM–52 (5.1%). Six isolates revealed AmpC-promoter mutations (position −42 (C > T) and one carried mcr-1. The majority (91.3%) of ESBL/pAmpC genes were located on plasmids. SHV-12 was mainly (50%) encoded on IncI1α plasmids (pST-3/-26/-95), followed by IncX3 (12.5%) and IncK2 (3.1%). The bla_TEM–52 genes were located on IncI1α-pST-36 (60%) and IncX1 plasmids (20%). The dominant plasmid lineage among CTX-M-1 isolates was IncI1α (pST-3/-295/-317) (87.5%), followed by IncN-pST-1 (8.3%). CMY-2 was mostly identified on IncI1α (pST-12/-2) (54.5%) and IncK2 (31.8%) plasmids. Several plasmids revealed high similarity to published plasmids from human and animal Enterobacteriaceae. The isolates were assigned to phylogroups A/C (34.7/7.1%), B1 (27.6%), B2 (3.1%), D/F (9.2/10.2%), E (5.1%), and to E. clades (3.0%). With 51 known and 2 novel MLST types, a wide variety of STs was found, including STs previously observed in human isolates (ST10/38/117/131/648). ESBL/AmpC types or STs were rarely correlated with the geographic origin of the isolates or animal species. Virulence gene typing identified extraintestinal pathogenic E. coli (ExPEC; 2.0%), avian pathogenic E. coli (APEC; 51.5%), and atypical enteropathogenic E. coli (EPEC; 6.1%). In conclusion, the high diversity of STs and phylogenetic groups provides hardly any hint for clonal spread of single lineages but hints toward the dissemination of cephalosporin resistance genes in livestock via distinct, globally successful plasmid lineages. Even though a number of isolates could not be assigned to a distinct pathotype, our finding of combined multidrug-resistance and virulence in this facultative pathogen should be considered an additional threat to public health.

Population structure and uropathogenic potential of extended-spectrum cephalosporin-resistant Escherichia coli from retail chicken meat

Background

Food-producing animals and their products are considered a source for human acquisition of antimicrobial resistant (AMR) bacteria, and poultry are suggested to be a reservoir for Escherichia coli resistant to extended-spectrum cephalosporins (ESC), a group of antimicrobials used to treat community-onset urinary tract infections in humans. However, the zoonotic potential of ESC-resistant E. coli from poultry and their role as extraintestinal pathogens, including uropathogens, have been debated. The aim of this study was to characterize ESC-resistant E. coli isolated from domestically produced retail chicken meat regarding their population genetic structure, the presence of virulence-associated geno- and phenotypes as well as their carriage of antimicrobial resistance genes, in order to evaluate their uropathogenic potential.

Results

A collection of 141 ESC-resistant E. coli isolates from retail chicken in the Norwegian monitoring program for antimicrobial resistance in bacteria from food, feed and animals (NORM-VET) in 2012, 2014 and 2016 (n = 141) were whole genome sequenced and analyzed. The 141 isolates, all containing the beta-lactamase encoding gene bla_CMY-2, were genetically diverse, grouping into 19 different sequence types (STs), and temporal variations in the distribution of STs were observed. Generally, a limited number of virulence-associated genes were identified in the isolates. Eighteen isolates were selected for further analysis of uropathogen-associated virulence traits including expression of type 1 fimbriae, motility, ability to form biofilm, serum resistance, adhesion- and invasion of eukaryotic cells and colicin production. These isolates demonstrated a high diversity in virulence-associated phenotypes suggesting that the uropathogenicity of ESC-resistant E. coli from chicken meat is correspondingly highly variable. For some isolates, there was a discrepancy between the presence of virulence-associated genes and corresponding expected phenotype, suggesting that mutations or regulatory mechanisms could influence their pathogenic potential.

Conclusion

Our results indicate that the ESC-resistant E. coli from chicken meat have a low uropathogenic potential to humans, which is important knowledge for improvement of future risk assessments of AMR in the food chains.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02160-y.

Non-lactose-fermenting uropathogenic Escherichia coli from dogs: virulence profile characterization

Non-lactose-fermenting Escherichia coli (NLFEC) has a few descriptive studies restricted to human infections. In the present study, isolates of NLFEC obtained from urine samples of dogs with hyperadrenocorticism were characterized regarding their virulence ability, biofilm formation capacity and antimicrobial susceptibility profile. Escherichia coli lactose-fermenting strains from urinary infection in dogs with the same conditions were analysed to provide comparisons. The non-lactose-fermenting E. coli strains were classified as belonging to clade I E. coli, whereas the lactose-fermenting strains were classified in phylogroup B2. All strains presented virulence markers to adhesion, iron acquisition, toxins, colicin and cytotoxin production, and biofilm regulation. Components of the extracellular matrix in addition to the in vitro biofilm formation ability were observed in the strains. Multidrug resistance (MDR) profiles were observed by in vitro susceptibility tests to all NLFEC strains. In summary, non-lactose-fermenting uropathogenic E. coli from dogs behaves similar to lactose-fermenting E. coli, exhibiting MDR profile, and pathogenic potential of promote animal infections.

Distinguishing Pathovars from Nonpathovars: Escherichia coli

Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.

A Toxic Environment: a Growing Understanding of How Microbial Communities Affect Escherichia coli O157:H7 Shiga Toxin Expression

Enterohemorrhagic Escherichia coli (EHEC) strains, including E. coli O157:H7, cause severe illness in humans due to the production of Shiga toxin (Stx) and other virulence factors. Because Stx is coregulated with lambdoid prophage induction, its expression is especially susceptible to environmental cues. Infections with Stx-producing E. coli can be difficult to model due to the wide range of disease outcomes: some infections are relatively mild, while others have serious complications. Probiotic organisms, members of the gut microbiome, and organic acids can depress Stx production, in many cases by inhibiting the growth of EHEC strains. On the other hand, the factors currently known to amplify Stx act via their effect on the stx-converting phage. Here, we characterize two interactive mechanisms that increase Stx production by O157:H7 strains: first, direct interactions with phage-susceptible E. coli, and second, indirect amplification by secreted factors. Infection of susceptible strains by the stx-converting phage can expand the Stx-producing population in a human or animal host, and phage infection has been shown to modulate virulence in vitro and in vivo Acellular factors, particularly colicins and microcins, can kill O157:H7 cells but may also trigger Stx expression in the process. Colicins, microcins, and other bacteriocins have diverse cellular targets, and many such molecules remain uncharacterized. The identification of additional Stx-amplifying microbial interactions will improve our understanding of E. coli O157:H7 infections and help elucidate the intricate regulation of pathogenicity in EHEC strains.

A complex approach to a complex problem: the use of whole-genome sequencing in monitoring avian-pathogenic Escherichia coli – a review

Infections associated with Escherichia coli are responsible for immense losses in poultry production; moreover, poultry products may serve as a source of pathogenic and/or resistant strains for humans. As early as during the first hours of life, commercially hatched chickens are colonized with potentially pathogenic E. coli from the environment of hatcheries. The source of contamination has not been quite elucidated and the possibility of vertical spread of several avian pathogenic E. coli (APEC) lineages has been suggested, making the hatcheries an important node where cross-contamination of chicken of different origin can take place. The recent technological progress makes the method of whole-genome sequencing (WGS) widely accessible, allowing high-throughput analysis of a large amount of isolates. Whole-genome sequencing offers an opportunity to trace APEC and extended-spectrum/plasmid-encoded AmpC beta-lactamases-producing E. coli (ESBL/pAmpC-E.coli) along the poultry processing chain and to recognize the potential pathways of “epidemicˮ sequence types. Data from WGS may be used in monitoring antimicrobial resistance, comparative pathogenomic studies describing new virulence traits and their role in pathogenesis and, above all, epidemiologic monitoring of clonal outbreaks and description of different transmission routes and their significance. This review attempts to outline the complexity of poultry-associated E. coli issues and the possibility to employ WGS in elucidating them.

Clinical and molecular characteristics of carbapenem non-susceptible Escherichia coli: A nationwide survey from Oman

The prevalence of carbapenem-resistant Enterobacterales (CRE) in the Arabian Peninsula is predicted to be high, as suggested from published case reports. Of particular concern, is carbapenem-resistant E. coli (CR-EC), due to the importance of this species as a community pathogen. Herein, we conducted a comprehensive molecular characterization of putative CR-EC strains from Oman. We aim to establish a baseline for future molecular monitoring. We performed whole-genome sequencing (WGS) for 35 putative CR-EC. Isolates were obtained from patients at multiple centers in 2015. Genetic relatedness was investigated using several typing approaches such as MLST, SNP calling, phylogroup and CRISPR typing. Maxiuium likelihood SNP-tree was performed by RAxML after variant calling and removal of recombination regions with Snippy and Gubbins, respectively. Resistance genes, plasmid replicon types, virulence genes, and prophage were also characterised. The online databases CGE, CRISPRcasFinder, Phaster and EnteroBase were used for the in silico analyses. Screening for mutations in genes regulating the expression of porins and efflux pump as well as mutations lead to fluoroquinolones resistance were performed with CLC Genomics Workbench. The genetic diversity suggests a polyclonal population structure with 21 sequence types (ST), of which ST38 being the most prevalent (11%). SNPs analysis revealed possible transmission episodes. Whereas, CRISPR typing helped to spot outlier strains belonged to phylogroups other than B2 which was CRISPR-free. The virulent phylogroups B2 and D were detected in 4 and 9 isolates, respectively. In some strains bacteriophages acted as vectors for virulence genes. Regarding resistance to β-lactam, 22 were carbapenemase producers, 3 carbapenem non-susceptible but carbapenemase-negative, 9 resistant to expanded-spectrum cephalosporins, and one isolate with susceptibility to cephalosporins and carbapenems. Thirteen out of the 22 (59%) carbapenemase-producing isolates were NDM and 7 (23%) were OXA-48-like which mirrors the situation in Indian subcontinent. Two isolates co-produced NDM and OXA-48-like enzymes. In total, 80% (28/35) were CTX-M-15 producers and 23% (8/35) featured AmpC. The high-risk subclones ST131-H30Rx/C2, ST410-H24RxC and ST1193-H64RxC were detected, the latter associated with NDM. To our knowledge, this is the first report of ST1193-H64Rx subclone with NDM. In conclusion, strains showed polyclonal population structure with OXA-48 and NDM as the only carbapenemases in CR-EC from Oman. We detected the high-risk subclone ST131-H30Rx/C2, ST410-H24RxC and ST1193-H64RxC. The latter was reported with carbapenemase gene for the first time here.

In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data

Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause in humans of urinary tract infection and bacteremia. The previously published web tool VirulenceFinder (http://cge.cbs.dtu.dk/services/VirulenceFinder/) uses whole-genome sequencing (WGS) data for in silico characterization of E. coli isolates and enables researchers and clinical health personnel to quickly extract and interpret virulence-relevant information from WGS data. In this study, 38 ExPEC-associated virulence genes were added to the existing E. coli VirulenceFinder database. In total, 14,441 alleles were downloaded. A total of 1,890 distinct alleles were added to the database after removal of redundant sequences and analysis of the remaining alleles for open reading frames (ORFs). The database now contains 139 genes-of which 44 are related to ExPEC-and 2,826 corresponding alleles. Construction of the database included validation against 27 primer pairs from previous studies, a search for serotype-specific P fimbriae papA alleles, and a BLASTn confirmation of seven genes (etsC, iucC, kpsE, neuC, sitA, tcpC, and terC) not covered by the primers. The augmented database was evaluated using (i) a panel of nine control strains and (ii) 288 human-source E. coli strains classified by PCR as ExPEC and non-ExPEC. We observed very high concordance (average, 93.4%) between PCR and WGS findings, but WGS identified more alleles. In conclusion, the addition of 38 ExPEC-associated genes and the associated alleles to the E. coli VirulenceFinder database allows for a more complete characterization of E. coli isolates based on WGS data, which has become increasingly important considering the plasticity of the E. coli genome.

Transcriptional Regulator YqeI, Locating at ETT2 Locus, Affects the Pathogenicity of Avian Pathogenic Escherichia coli

Simple Summary

Avian pathogenic Escherichia coli (APEC) is the causative agent of colibacillosis, threatening the development of the poultry industry. The study on APEC’s pathogenic mechanism is of great importance. In this study, we investigated the role of YqeI, a transcriptional regulator locating at E. coli type three secretion system 2 in APEC. The transcriptional results revealed that YqeI affected the expression of the genes involving in bacterial localization, locomotion and biological adhesion. A series experiments also demonstrated that the absence of yqeI decreased the bacterial flagella formation ability, motility ability, antiserum bactericidal ability, adhesion ability and colonization ability. Our data suggested that the transcriptional regulator YqeI indeed participates in the pathogenicity of APEC.

Abstract

Avian pathogenic Escherichia coli (APEC) is the leading cause of systemic infections in poultry worldwide and has a hidden threat to public health. Escherichia coli type three secretion system 2 (ETT2), similar to the Salmonella pathogenicity island SPI1, is widely distributed in APEC and associated with virulence. The function of YqeI, which is one of the hypothetical transcriptional regulators locating at the ETT2 locus of APEC, is unknown. In this study, we successfully obtained the mutant strain AE81ΔyqeI of the wild type strain AE81 and performed the transcriptional profiling assays. Additionally, the transcriptional sequencing results revealed that YqeI influenced localization, locomotion and biological adhesion and so on. The transmission electron microscope observation showed that the wild type strain AE81 possessed long curved flagella, whereas the mutant strain AE81ΔyqeI hardly had any. The strain AE81ΔyqeI exhibited lower motility than AE81 after culturing the dilute bacterial suspension on a semisolid medium. It was also found that the survival ability of AE81ΔyqeI weakened significantly when AE81ΔyqeI was cultured with 0%, 10%, 20%, 30%, 40% and 50% SPF serum in PBS, and AE81ΔyqeI had decreased adherence to DF-1 cells compared with AE81 in the bacterial adhesion assay. The bacterial colonization assay indicated that the virulence of AE81ΔyqeI was reduced in the heart, liver, spleen, and lung. These results confirmed that the transcription regulator YqeI is involved in APEC’s pathogenicity, and this study provides clues for future research.

SMART Antimicrobial Resistance Goals to Drive Meat Safety Improvement

Concerns that food-animal production significantly contributes to antibiotic-resistant human infections have persisted for more than 20 years. Most antibiotic resistance concerns are generalized, not specific. By their nature, non- specific concerns are unfalsifiable and can never be scientifically alleviated or remediated. Therefore, antibiotic resistance meat safety improvement begins with defining SMART (Specific, Measurable, Attainable, Relevant, and Time bound) antibiotic resistance goals. Two SMART goals related to high-priority antibiotic resistance in beef production are described as an example to facilitate scientific goal attainment

Extended-Spectrum-β-Lactamase- and Plasmid AmpC-Producing Escherichia coli Causing Community-Onset Bloodstream Infection: Association of Bacterial Clones and Virulence Genes with Septic Shock, Source of Infection, and Recurrence

Invasive infections due to extended-spectrum-β-lactamase- and pAmpC-producing Escherichia coli (ESBL/pAmpC-EC) are an important cause of morbidity, often caused by the high-risk clone sequence type (ST131) and isolates classified as extraintestinal pathogenic E. coli (ExPEC). The relative influence of host immunocompetence versus microbiological virulence factors in the acquisition and outcome of bloodstream infections (BSI) is poorly understood. Herein, we used whole-genome sequencing on 278 blood culture isolates of ESBL/pAmpC-EC from 260 patients with community-onset BSI collected from 2012 to 2015 in Stockholm to study the association of virulence genes, sequence types, and antimicrobial resistance with severity of disease, infection source, ESBL/pAmpC-EC BSI low-risk patients, and patients with repeated episodes. ST131 subclade C2 comprised 29% of all patients. Factors associated with septic shock in multivariable analysis were patient host factors (hematologic cancer or transplantation and reduced daily living activity), presence of the E. coli virulence factor iss (increased serum survival), absence of phenotypic multidrug resistance, and absence of the genes pap and hsp Adhesins, particularly pap, were associated with urinary tract infection (UTI) source, while isolates from post-prostate biopsy sepsis had a low overall number of virulence operons, including adhesins, and commonly belonged to ST131 clades A, B, and subclade C1, ST1193, and ST648. ST131 was associated with recurrent episodes. In conclusion, the most interesting finding is the association of iss with septic shock. Adhesins are important for UTI pathogenesis, while otherwise low-pathogenic isolates from the microbiota can cause post-prostate biopsy sepsis.

Broad-Spectrum Cephalosporin-Resistant and/or Fluoroquinolone-Resistant Enterobacterales Associated with Canine and Feline Urogenital Infections

The aim of the present study was to characterize Enterobacterales resistant to 3rd and 4th generation cephalosporins, carbapenems and/or fluoroquinolones, isolated from dogs and cats with urogenital infections. In total, 36 strains (Escherichia coli (n = 28), Klebsiella pneumoniae (n = 3), Serratia marcescens, Raoultella ornithinolytica, Proteus mirabilis, Citrobacter portucalensis and Enterobacter cloacae (each n = 1)) were included in the present study, 28 from Austria and 8 from Serbia. Isolates were characterized by a polyphasic approach including susceptibility pheno- and genotyping and microarray-based assays. Escherichia (E.) coli isolates were additionally characterized by two-locus (fumC and fimH) sequence phylotyping and multi-locus sequence typing (MLST) of selected isolates. MLST of carbapenem-resistant Enterobacter cloacae isolates was also performed. Among E. coli, the most dominant phylogenetic group was B1 (27.8%), followed by C, (16.6%), A and Clade II (5.5% each), B2 and F (2.77% each). The most predominant β-lactam resistance genes were blaTEM (70%) and blaCTX-M (38.8%), blaCMY (25%). blaNDM was detected in one carbapenem-resistant Enterobacter cloacae ST114. The most common ST among selected E. coli was 744 (10.7% isolates). The pandemic clones ST131 and ST648 carrying CTX-M-15 were also detected. Remaining STs belonged to 469, 1287, 1463 and 1642. E. coli clonotyping revealed 20 CH types. Based on the presence of certain virulence genes, three isolates were categorized as ExPEC/UPEC. The most prevalent virulence factors were fimH detected in 61%, iucD and iss both in 55%, iroN in 27.8%, papC in 13.8% and sat in 8.3% isolates.

Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring

Intensive pig production systems often rely on the use of antimicrobials and heavy metal feed additives to maintain animal health and welfare. To gain insight into the carriage of antimicrobial resistance genes (ARGs) in the faecal flora of commercially reared healthy swine, we characterised the genome sequences of 117 porcine commensal E. coli that carried the class 1 integrase gene (intI1⁺). Isolates were sourced from 42 healthy sows and 126 of their offspring from a commercial breeding operation in Australia in 2017. intI1⁺ E. coli was detected in 28/42 (67%) sows and 90/126 (71%) piglets. Phylogroup A, particularly clonal complex 10, and phylogroup B1 featured prominently in the study collection. ST10, ST20, ST48 and ST361 were the dominant sequence types. Notably, 113/117 isolates (96%) carried three or more ARGs. Genes encoding resistance to -lactams, aminoglycosides, trimethoprim, sulphonamides, tetracyclines and heavy metals were dominant. ARGs encoding resistance to last-line agents, such as carbapenems and third generation cephalosporins, were not detected. IS26, an insertion sequence noted for its ability to capture and mobilise ARGs, was present in 108/117 (92%) intI1⁺ isolates, and it played a role in determining class 1 integron structure. Our data shows that healthy Australian pig faeces are an important reservoir of multidrug resistant E. coli that carry genes encoding resistance to multiple first-generation antibiotics and virulence-associated genes.

Pathogenic Escherichia coli in Dogs Reveals the Predominance of ST372 and the Human-Associated ST73 Extra-Intestinal Lineages

Escherichia coli is a ubiquitous commensal and pathogen that has also been recognized as a multi-sectoral indicator of antimicrobial resistance (AMR). Given that latter focus, such as on resistances to extended-spectrum cephalosporins (ESC) and carbapenems, the reported population structure of E. coli is generally biased toward resistant isolates, with sequence type (ST)131 being widely reported in humans, and ST410 and ST648 being reported in animals. In this study, we characterized 618 non-duplicate E. coli isolates collected throughout France independently of their resistance phenotype. The B2 phylogroup was over-represented (79.6%) and positively associated with the presence of numerous virulence factors (VFs), including those defining the extra-intestinal pathogenic E. coli isolates (presence of ≥2 VFs: papA, sfaS, focG, afaD, iutA, and kpsMTII) and those more specifically related to uropathogenic E. coli (cnf1, hlyD). The major STs associated with clinical isolates from dogs were by far the dog-associated ST372 (20.7%) and ST73 (20.1%), a lineage that had commonly been considered until now as human-associated. Resistance to ESC was found in 33 isolates (5.3%), along with one carbapenemase-producing isolate, and was mostly restricted to non-B2 isolates. In conclusion, the presence of virulent E. coli lineages may be the issue, rather than the presence of ESC-resistant isolates, and the risk of transmission of such virulent isolates to humans needs to be further studied.

E. coli diversity: low in colorectal cancer

BACKGROUND

Escherichia coli are mostly commensals but also contain pathogenic lineages. It is largely unclear whether the commensal E. coli as the potential origins of pathogenic lineages may consist of monophyletic or polyphyletic populations, elucidation of which is expected to lead to novel insights into the associations of E. coli diversity with human health and diseases.

METHODS

Using genomic sequencing and pulsed field gel electrophoresis (PFGE) techniques, we analyzed E. coli from the intestinal microbiota of three groups of healthy individuals, including preschool children, university students, and seniors of a longevity village, as well as colorectal cancer (CRC) patients, to probe the commensal E. coli populations for their diversity.

RESULTS

We delineated the 2280 fresh E. coli isolates from 185 subjects into distinct genome types (genotypes) by PFGE. The genomic diversity of the sampled E. coli populations was so high that a given subject may have multiple genotypes of E. coli, with the general diversity within a host going up from preschool children through university students to seniors. Compared to the healthy subjects, the CRC patients had the lowest diversity level among their E. coli isolates. Notably, E. coli isolates from CRC patients could suppress the growth of E. coli bacteria isolated from healthy controls under nutrient-limited culture conditions.

CONCLUSIONS

The coexistence of multiple E. coli lineages in a host may help create and maintain a microbial environment that is beneficial to the host. As such, the low diversity of E. coli bacteria may be associated with unhealthy microenvironment in the intestine and hence facilitate the pathogenesis of diseases such as CRC.

Extraintestinal Foodborne Pathogens

In general, foodborne diseases present themselves with gastrointestinal symptoms caused by bacterial, viral, and parasitic pathogens well established to be foodborne. These pathogens are also associated with extraintestinal clinical manifestations. Recent studies have suggested that Escherichia coli and Klebsiella pneumoniae, which both cause common extraintestinal infections such as urinary tract and bloodstream infections, may also be foodborne. The resolution and separation of these organisms into pathotypes versus commensals by modern genotyping methods have led to the identification of key lineages of these organisms causing outbreaks of extraintestinal infections. These epidemiologic observations suggested common- or point-source exposures, such as contaminated food. Here, we describe the spectrum of extraintestinal illnesses caused by recognized enteric pathogens and then review studies that demonstrate the potential role of extraintestinal pathogenic E. coli (ExPEC) and K. pneumoniae as foodborne pathogens. The impact of global food production and distribution systems on the possible foodborne spread of these pathogens is discussed.

The KdpD/KdpE two-component system contributes to the motility and virulence of avian pathogenic Escherichia coli

Two-component systems (TCSs) are widespread regulatory systems which can help bacteria to control their cellular functions and respond to a diverse range of stimuli. The KdpD/KdpE system had been well studied for regulating potassium transport and identified as an adaptive regulator involved in the virulence of some pathogenic bacteria, but its role in avian pathogenic Escherichia coli (APEC) was still unknown. In this study, the mutant strain AE17ΔKdpDE was obtained successfully of a clinical APEC isolation AE17 using the lambda Red recombinase system and performed the transcriptional sequencing of the wild type strain AE17 and the mutant strain AE17ΔKdpDE. The transcriptional sequencing results revealed that the KdpD/KdpE two-component system mainly influenced the expression of the genes covering metabolic pathways, flagellar assembly, global transcription regulator. The expression of some flagellar-related genes detecting by quantitative real-time PCR was consistent with the results of transcriptional sequencing. Importantly, fewer flagellum of the mutant strain AE17ΔKdpDE was observed than AE17 using the transmission electron microscope and a decreased motility circle of AE17ΔKdpDE appeared in the semisolid medium. In addition, the serum bactericidal assay was carried out with the specific-pathogen-free chicken in different dilution and the survival ability in the serum of AE17ΔKdpDE was also obviously lower than that of AE17. These results suggested that in APEC, the KdpD/KdpE two-component system mainly influenced the expression of flagella-related genes, the flagellum formation, the motility and antiserum bactericidal activity.

Extended Phylogeny and Extraintestinal Virulence Potential of Commensal Escherichia coli from Piglets and Sows

Commensal Escherichia coli, naturally occurring in the intestinal tract, can be the origin of extraintestinal pathogenic E. coli (ExPEC) strains. ExPEC causes high mortality and significant economic losses in the swine industry in several countries and poses a serious threat to public health worldwide. The aim of this study was to analyze the extended phylogenetic structure and extraintestinal virulence potential in two groups of commensal E. coli isolates from post-weaning piglets and sows. The phylogenetic assignment to eight groups was determined using the revised Clermont phylogenetic typing method in quadruplex PCR. Identification of extraintestinal virulence genes (VGs) and adhesin operon genes was performed using multiplex or simplex PCR. The revised phylogenetic assignment allowed us to distinguish E. coli with significantly higher (groups C and F) or lower (group E) virulence potential in isolates from piglets. The majority of the tested VGs occurred more frequently in isolates from piglets than from sows, with statistically significant differences for seven genes: fimH, papAH, iutA, iroN, ompT, traT, and iss. Complete operons for type I and P fimbriae significantly prevailed among E. coli from piglets. This study provides insight into the extended phylogenetic structure of porcine commensal E. coli and showed that these strains, particularly from piglets, constitute a considerable reservoir of extraintestinal VGs and may increase the potential risk of extraintestinal infections.

Multidrug-Resistant and Clinically Relevant Gram-Negative Bacteria Are Present in German Surface Waters

Water is considered to play a role in the dissemination of antibiotic-resistant Gram-negative bacteria including those encoding Extended-spectrum beta-lactamases (ESBL) and carbapenemases. To investigate the role of water for their spread in more detail, we characterized ESBL/Carbapenemase-producing bacteria from surface water and sediment samples using phenotypic and genotypic approaches. ESBL/Carbapenemase-producing isolates were obtained from water/sediment samples. Species and antibiotic resistance were determined. A subset of these isolates (n = 33) was whole-genome-sequenced and analyzed for the presence of antibiotic resistance genes and virulence determinants. Their relatedness to isolates associated with human infections was investigated using multilocus sequence type and cgMLST-based analysis. Eighty-nine percent of the isolates comprised of clinically relevant species. Fifty-eight percent exhibited a multidrug-resistance phenotype. Two isolates harbored the mobile colistin resistance gene mcr-1. One carbapenemase-producing isolate identified as Enterobacter kobei harbored bla VIM- 1. Two Escherichia coli isolates had sequence types (ST) associated with human infections (ST131 and ST1485) and a Klebsiella pneumoniae isolate was classified as hypervirulent. A multidrug-resistant (MDR) Pseudomonas aeruginosa isolate encoding known virulence genes associated with severe lung infections in cystic fibrosis patients was also detected. The presence of MDR and clinically relevant isolates in recreational and surface water underlines the role of aquatic environments as both reservoirs and hot spots for MDR bacteria. Future assessment of water quality should include the examination of the multidrug resistance of clinically relevant bacterial species and thus provide an important link regarding the spread of MDR bacteria in a One Health context.

Virulence-associated traits and in vitro biofilm-forming ability of Escherichia coli isolated from a major river traversing Northern India

Several strains of Escherichia coli harbor virulence traits, resulting in E. coli-related intestinal and extra-intestinal infections. Various studies have reported that extra-intestinal pathogenic E. coli (ExPEC) strains were prevalent in nonhuman reservoirs, including environmental waterways. It is therefore important to identify the pathogenic potential and/or ExPEC status of E. coli strains inhabiting the aquatic environments associated with anthropogenic activities. Besides virulence-associated genes, biofilm production also helps in the survival of E. coli in environmental waterbodies. Thus, the aim of the current study was to assess the virulence potential, ExPEC status, and biofilm-producing capability of E. coli isolated from the River Yamuna, a major river traversing the National Capital Region of Delhi, India. We also tried to discern a co-relation, if any, between virulence, biofilm formation, and antimicrobial resistance in these strains. Our results indicated that virulence-associated genes were scarce and none of the strain qualified the molecular criteria essential for ExPEC. This suggested that E. coli strains which can presumably cause human extra-intestinal infections were not prominent in the River Yamuna. However, the fact that more than 80% of the aquatic E. coli isolates were moderate and strong biofilm producers suggests that E. coli in these environments might serve as opportunistic pathogens. Also, no unequivocal association was observed between biofilm production, virulence, and β-lactamase genes in E. coli strains. As per the best of our knowledge, this is the first study where the relationship between virulence, biofilms, and antimicrobials has been examined in E. coli, isolated from an Indian urban aquatic waterbody.

Numerical interpretation of TRS-PCR profiling results for Escherichia coli strains isolated from patients with bacteriuria in Lodz region, Poland

With the multiplicity of existing methods to track E. coli infections, it still seems necessary to seek new, better and/or complementary ways for epidemiological investigations. Particularly, fast, cheap, effective and reproducible methods providing easily comparable results are needed. Our previous studies showed that the use of TRS-PCR is an effective molecular tool in E. coli epidemiology. In this paper, we have developed a unique classification scheme in which an individual TRS-PCR pattern is assigned a numerical value. This approach allows for rapid interpretation of the results obtained from several similarity dendrograms. Using this approach, based on CAC-PCR, GTG-PCR and CGG-PCR, we obtained 52, 86 and 99 different numerical types for the 124 analyzed uropathogenic E. coli strains, respectively. This allowed for the identification of 121 unique isolates differing in at least one TRS-PCR class. In this approach, we got numerical results, easy to sort and interpret, allowing easier analysis of these strains.

Diversity, Virulence, and Clinical Significance of Extended-Spectrum β-Lactamase- and pAmpC-Producing Escherichia coli From Companion Animals

Escherichia coli are opportunistic pathogens with the potential to cause a variety of infections in both humans and animals and in many cases have developed antimicrobial resistance. In this study, we characterized extended-spectrum cephalosporin resistant (ESCR) E. coli isolates from diseased companion animals (dogs, cats, and horses) and related the results to clinical findings. ESCR E. coli clinical isolates obtained over a 6-year period were screened for extended-spectrum β-lactamase (ESBL) and/or plasmid mediated AmpC (pAmpC) and virulence markers likely to be associated with extraintestinal pathogenic E. coli (ExPEC). ESBL and/or pAmpC genetic determinants were identified in 79.9% of the ESCR E. coli isolates with bla CTX-M genes being the most common ESBL genotype of which bla CTX-M-15, bla CTX-M-14, and bla CTX-M-55 were the most prevalent. In addition, bla CMY -2 was the most common genotype identified amongst pAmpC producing isolates. Phylogenetic group typing showed that B2 was the most prevalent phylogroup among the ESCR E. coli isolates, followed by the closely related phylogroups D and F which are also associated with extra-intestinal infections. ESCR was also identified in phylogroups commonly regarded as commensals (B1, A, and C). Virulence factor (VF) scores >2 were mostly present amongst isolates in phylogroup B2. Higher virulence scores were found in isolates lacking ESBL/pAmpC resistance genes compared with those carrying both genes (p < 0.05). Five of phylogroup B2 isolates, were typed to the pandemic virulent O25b-ST131 clone and three ST131 isolates carrying bla CTX-M-15 belonged to the subclade C2/H30Rx whilst one isolate carrying bla CTX-M-27 typed to the recently described sub-clade C1-M27. MLST typing also identified other sequence types commonly associated with infections in humans (ST410, ST10, and ST648). Most ESCR E. coli isolates obtained in pure growth were cultured from normally sterile body sites (mostly from urinary tract infections, UTIs) whilst only a small proportion were obtained from body sites populated with commensal flora (p < 0.0001). Our study has shown that ExPEC ESBL/pAmpC producing E. coli isolates are common amongst companion animal isolates and are associated with colonization and infection. In addition, their isolation from a normally sterile site is likely to be clinically significant and warrants antimicrobial treatment.

Characterization of multiple type-VI secretion system (T6SS) VgrG proteins in the pathogenicity and antibacterial activity of porcine extra-intestinal pathogenic Escherichia coli

Porcine extra-intestinal pathogenic Escherichia coli (ExPEC) causes great economic losses to the pig industry and poses a serious threat to public health worldwide. Some secreted virulence factors have been reported to be involved in the pathogenicity of the infection caused by ExPEC. Type-VI secretion system (T6SS) is discovered in many Gram-negative bacteria and contributes to the virulence of pathogenic bacteria. Valine-glycine repeat protein G (VgrG) has been reported as an important component of the functional T6SS. In our previous studies, a functional T6SS was identified in porcine ExPEC strain PCN033. Further analysis of the PCN033 genome identified two putative vgrGs genes (vgrG1 and 0248) located inside T6SS cluster and another two (vgrG2 and 1588) outside it. This study determined the function of the four putative VgrG proteins by constructing a series of mutants and complemented strains. In vitro, the VgrG1 protein was observed to be involved in the antibacterial ability and the interactions with cells. The animal model experiment showed that the deletion of vgrG1 significantly led to the decrease in the multiplication capacity of PCN033. However, the deletion of 0248 and/or the deletion of vgrG2 and 1588 had no effect on the pathogenicity of PCN033. The study of four putative VgrGs in PCN033 indicated that only VgrG1 plays an important role in the interaction between PCN033 and other bacteria or host cells. This study can provide a novel perspective to the pathogenesis of PCN033 and lay the foundation for discovering potential T6SS effectors.

Escherichia coli Pathobionts Associated with Inflammatory Bowel Disease

Gut bacteria play a key role in initiating and maintaining the inflammatory process in the gut tissues of inflammatory bowel disease (IBD) patients, by supplying antigens or other stimulatory factors that trigger immune cell activation. Changes in the composition of the intestinal microbiota in IBD patients compared to that in healthy controls and a reduced diversity of intestinal microbial species are linked to the pathogenesis of IBD. Adherent invasive Escherichia coli (AIEC) has been linked to Crohn's disease (CD) patients, while diffusely adherent E. coli (DAEC) has been associated with ulcerative colitis (UC). Bacteriological analysis of intestinal biopsy specimens and fecal samples from IBD patients shows an increased number of E. coli strains belonging to the B2 phylogenetic group, which are typically known as extraintestinal pathogenic E. coli (ExPEC). Results from studies of both cell cultures and animal models reveal pathogenic features of these E. coli pathobionts, which may link them to IBD pathogenesis. This suggests that IBD-associated E. coli strains play a facilitative role during IBD flares. In this review, we explain IBD-associated E. coli and its role in IBD pathogenesis.

Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26

Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.

Antimicrobial Resistance in Escherichia coli

Multidrug resistance in Escherichia coli has become a worrying issue that is increasingly observed in human but also in veterinary medicine worldwide. E. coli is intrinsically susceptible to almost all clinically relevant antimicrobial agents, but this bacterial species has a great capacity to accumulate resistance genes, mostly through horizontal gene transfer. The most problematic mechanisms in E. coli correspond to the acquisition of genes coding for extended-spectrum β-lactamases (conferring resistance to broad-spectrum cephalosporins), carbapenemases (conferring resistance to carbapenems), 16S rRNA methylases (conferring pan-resistance to aminoglycosides), plasmid-mediated quinolone resistance (PMQR) genes (conferring resistance to [fluoro]quinolones), and mcr genes (conferring resistance to polymyxins). Although the spread of carbapenemase genes has been mainly recognized in the human sector but poorly recognized in animals, colistin resistance in E. coli seems rather to be related to the use of colistin in veterinary medicine on a global scale. For the other resistance traits, their cross-transfer between the human and animal sectors still remains controversial even though genomic investigations indicate that extended-spectrum β-lactamase producers encountered in animals are distinct from those affecting humans. In addition, E. coli of animal origin often also show resistances to other-mostly older-antimicrobial agents, including tetracyclines, phenicols, sulfonamides, trimethoprim, and fosfomycin. Plasmids, especially multiresistance plasmids, but also other mobile genetic elements, such as transposons and gene cassettes in class 1 and class 2 integrons, seem to play a major role in the dissemination of resistance genes. Of note, coselection and persistence of resistances to critically important antimicrobial agents in human medicine also occurs through the massive use of antimicrobial agents in veterinary medicine, such as tetracyclines or sulfonamides, as long as all those determinants are located on the same genetic elements.

Putrescine biosynthesis and export genes are essential for normal growth of avian pathogenic Escherichia coli

BACKGROUND

Avian pathogenic Escherichia coli (APEC) is the infectious agent of a wide variety of avian diseases, which causes substantial economic losses to the poultry industry worldwide. Polyamines contribute to the optimal synthesis of nucleic acids and proteins in bacteria. The objectives of this study were to investigate; i) whether APEC E. coli encodes the same systems for biosynthesis and uptake as described for E. coli K12 and ii) the role of polyamines during in vitro growth of an avian pathogenic E. coli strain (WT-ST117- O83:H4T).

RESULTS

Following whole genome sequencing, polyamine biosynthesis and export genes present in E. coli MG1655 (K-12) were found to be identical in WT-ST117. Defined mutants were constructed in putrescine and spermidine biosynthesis pathways (ΔspeB, ΔspeC, ΔspeF, ΔspeB/C and ΔspeD/E), and in polyamines transport systems (ΔpotE, ΔyeeF, ΔpotABCD and ΔpotFGHI). Contrary to what was observed for MG1655, the ΔpotE-ST117 mutant was growth attenuated, regardless of putrescine supplementation. The addition of spermidine or orthinine restored the growth to the level of WT-ST117. Growth attenuation after induction of membrane stress by SDS suggested that PotE is involved in protection against this stress. The ΔspeB/C-ST117 mutant was also growth attenuated in minimal medium. The addition of putrescine or spermidine to the media restored growth rate to the wild type level. The remaining biosynthesis and transport mutants showed a growth similar to that of WT-ST117. Analysis by Ultra-High Performance Liquid Chromatography revealed that the ΔspeB/C mutant was putrescine-deficient, despite that the gene speF, which is also involved in the synthesis of putrescine, was expressed.

CONCLUSIONS

Deletion of the putrescine transport system, PotE, or the putrescine biosynthesis pathway genes speB/C affected in vitro growth of APEC (ST117- O83:H4) strain, but not E. coli MG1655, despite the high similarity of the genetic make-up of biosynthesis and transport genes. Therefore, blocking these metabolic reactions may be a suitable way to prevent APEC growth in the host without disturbing the commensal E. coli population.

Genetic diversity, virulence genotype and antimicrobial resistance of uropathogenic Escherichia coli (UPEC) isolated from sows

Background: Urinary tract infections (UTI) cause severe losses to the swine industry worldwide and uropathogenic Escherichia coli (UPEC) are the main agent isolated from UTI in sows.

Objective: The aim of this study was to investigate the virulence genes, assess the phylogenetic background, clonal diversity, and the pattern of resistance to antimicrobials in 186 isolates of UPEC isolated from sows in Brazil.

Materials and methods: Urine samples from 300 sows of three herds with clinical signs from São Paulo State (Brazil) were screened for UTI; samples with suggestive results were submitted to bacterial isolation. E. coli strains isolated were characterized using disk diffusion technique, polymerase chain reaction and Single-enzyme amplification fragment length polymorphism (SE-AFLP).

Results: Virulence genes focH and papC were present in 78.5% and 58% of strains, respectively, followed by cnf1 (23.2%), afa (13.4%), sfa (11.3%), iucD (6.9%), and hlyA (1.6%). No clonal relatedness was found by SE-AFLP. A total of 98% of isolates (182/186) were multidrug resistant, and the highest levels of resistance were to sulfonamides, tetracycline, florfenicol, and ampicillin. Isolates were classified in phylogenetic group B1 (34.4%), followed by D (33.9%), E (30.1%) and A (1.6%).

Conclusions: The data obtained suggest that pigs from clinically affected herds may serve as a reservoir of uropathogenic and multidrug-resistant E. coli strains.