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Clustering of Escherichia strains based on small MASH distance (high genetic similarity). Two identical clusterograms surround a heat map showing pair-to-pair comparisons of all Escherichia strains, with dark red denoting close pairwise similarity. Apparent blocks represent clusters that correspond to species, as described to the right. Strain names are given at the bottom.
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Escherichia coli is the most common pathogen found in blood cultures and urine and among the most important pathogenic species in the realm of human health. The notion that some of these isolates are not Es. coli but rather another species within the same genus may have implications for what Es. coli constitutes.
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... accession numbers as well as relevant metadata are provided in Table S1 in the supplemental material. All genomes were clustered based on pairwise distance using MASH (8). The resulting clusterogram agreed well with established clade designations and shows that available Es. marmotae strains constitute a distinct species in the Escherichia genus (Fig. 1). Other former cryptic Escherichia clades recently defined as novel species also cluster by themselves, whereas a selection of diverse Es. coli appear together, albeit with a larger MASH distance distribution than is the case with Es. marmotae. The discrepancy is likely a result of strain selection bias due to a larger available pool of ...
Citations
... E. marmotae isolated from the feces of wild rodents (Marmota himalayana) has been reported as a potential invasive pathogen (Liu et al., 2019). In addition, humaninvasive infections caused by E. marmotae have recently been described, and this Escherichia species has only recently been identified as a new common pathogen because it can be easily misidentified as E. coli in routine diagnostic laboratories (Sivertsen et al., 2022). Like animal isolates from wild rodents (Liu et al., 2019) and clinical isolates from human-invasive infections (Sivertsen et al., 2022), the ESBL-producing isolate of E. marmotae from clams harbored the enterotoxin-encoding gene astA. ...
... In addition, humaninvasive infections caused by E. marmotae have recently been described, and this Escherichia species has only recently been identified as a new common pathogen because it can be easily misidentified as E. coli in routine diagnostic laboratories (Sivertsen et al., 2022). Like animal isolates from wild rodents (Liu et al., 2019) and clinical isolates from human-invasive infections (Sivertsen et al., 2022), the ESBL-producing isolate of E. marmotae from clams harbored the enterotoxin-encoding gene astA. Moreover, the E. coli in silico serotyper evidenced that it contained the fliC-H56 flagellar antigen gene, as did the human clinical isolates (Sivertsen et al., 2022). ...
... Like animal isolates from wild rodents (Liu et al., 2019) and clinical isolates from human-invasive infections (Sivertsen et al., 2022), the ESBL-producing isolate of E. marmotae from clams harbored the enterotoxin-encoding gene astA. Moreover, the E. coli in silico serotyper evidenced that it contained the fliC-H56 flagellar antigen gene, as did the human clinical isolates (Sivertsen et al., 2022). Available data on E. marmotae isolates from different sources showed infrequent occurrences of antimicrobial resistance (Sivertsen et al., 2022); isolates from reported human-invasive infections were phenotypically susceptible to tested antimicrobials, and resistance genes were not identified in their genomes (Sivertsen et al., 2022). ...
The spread of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is a major public health issue. Bivalves are filter-feeder animals capable of bioaccumulating the microorganisms present in water. This physiological characteristic makes them both good indicators of environmental contamination and possible carriers of pathogenic bacteria, including those resistant to antimicrobials. The aim of this study was to investigate the occurrence of ESBL-producing E. coli in clams (n = 308) collected from harvesting areas of the Central Adriatic Sea between 2018 and 2019. ESBL- /class C β-lactamase (AmpC)- producing E. coli and Escherichia spp. were isolated by streaking over the surface of MacConkey agar plates supplemented with cefotaxime enriched broths of the initial shellfish suspension. E. coli and Escherichia spp. resistant to cefotaxime were screened for ESBL production by using the double disk synergy test. Susceptibility to different antimicrobials and confirmation of ESBL-production were determined by the minimum inhibitory concentration (MIC) test. Isolates were further characterized by whole genome sequencing (WGS) and bioinformatic analysis of genomes with different tools. Overall, ESBL-producing E. coli were isolated from 3% of the samples. Of 13 ESBL- and ESBL−/AmpC-producing Escherichia spp. (n = 11 E. coli, n = 1 E. marmotae, n = 1 E. ruysiae) isolates, 13 were resistant to ampicillin and cefotaxime, 9 to sulfamethoxazole, 6 to tetracycline and nalidixic acid, 4 to trimethoprim, and 3 to ceftazidime, cefoxitin, ciprofloxacin, and chloramphenicol. Moreover, the majority (8/11) of the ESBL-producing E. coli isolates were multidrug-resistant. WGS showed that the isolates predominantly carried the blaCTX-M-15 gene (3/11) and blaCTX-M-14 and blaCTX-M-1 (2/11 each). The AmpC β-lactamase CMY-2 was found in two isolates. Phylogroup A was the most prevalent (5/11), followed by phylogroups D (4/11), F (1/11), and B2 (1/11). Ten different sequence types (STs) were identified. Occurrence at sampling sites ranged between 0 and 27%. To identify associations between the occurrence of ESBL-producing E. coli and E. coli levels, samples were divided into two groups, with E. coli at >230 MPN/100 g and E. coli at ≤230 MPN/100 g. ESBL-producing E. coli isolates were significantly more commonly recovered in samples with higher E. coli levels (14%) than in those with lower levels of E. coli (2%). Moreover, the majority (3/4) of the potentially pathogenic strains were isolated in samples with higher E. coli levels. These findings provided evidence for the bacterial indicator of fecal contamination, E. coli, as an index organism for ESBL-producing E. coli isolates in bivalves.
... This new species, which is phenotypically identical to E. coli, has since then been reported as a bla CTX-M-1 carrier from an Alpine marmot in a Belgian zoo (31), and as a bla CTX-M-32 carrier from a red deer in Poland (32); these reports, in addition to the starlings' samples here, suggest that wild animals are preferential hosts of E. marmotae. A recent publication analyzing the genomes of 41 E. marmotae isolates suggested that this species can be pathogenic for humans but is still carrying few resistance determinants, even if sporadic cases of ESBL-and carbapenemase-producing isolates were reported (33). Our study revealed that E. marmotae can be a frequent carrier of AmpC-and ESBL-conferring genes that can be shared with E. coli isolates present in the same niche. ...
European starlings are widespread migratory birds that have already been described as carrying bacteria resistant to extended-spectrum cephalosporins (ESC-R). These birds are well known in Tunisia because they spend the wintertime in this country and are hunted for human consumption. The goal of our study was to estimate the proportion of ESC-R in these birds and to characterize the collected isolates using whole-genome sequencing. Results showed that 21.5% (42/200) of the birds carried either an extended-spectrum beta-lactamase (ESBL) or an acquired AmpC gene. Diverse bla CTX-M genes were responsible for the ESBL phenotype, bla CTX-M-14 being the most prevalent, while only bla CMY-2 and one bla CMY-62 were found in AmpC-positive isolates. Likewise, different genetic determinants carried these resistance genes, including IncHI2, and IncF plasmids for bla CTX-M genes and IncI1 plasmids for bla CMY-2 genes. Three chromosomally encoded bla CTX-M-15 genes were also identified. Surprisingly, species identification revealed a large proportion (32.7%) of Escherichia marmotae isolates. This species is phenotypically indistinguishable from Escherichia coli and has obviously the same capacity to acquire ESC-R genes. Our data also strongly suggest that at least the IncHI2/pST3 plasmid can spread equally between E. coli and E. marmotae . Given the potential transmission routes between humans and animals, either by direct contact with dejections or through meat preparation, it is important to closely monitor antimicrobial resistance in European starlings in Tunisia and to set up further studies to identify the sources of contamination of these birds.
IMPORTANCE
The One Health concept highlighted knowledge gaps in the understanding of the transmission routes of resistant bacteria. A major interest was shown in wild migratory birds since they might spread resistant bacteria over long distances. Our study brings further evidence that wild birds, even though they are not directly submitted to antibiotic treatments, can be heavily contaminated by resistant bacteria. Our results identified numerous combinations of resistance genes, genetic supports, and bacterial clones that can spread vertically or horizontally and maintain a high level of resistance in the bird population. Some of these determinants are widespread in humans or animals (IncHI2/pST3 plasmids and pandemic clones), while some others are less frequent (atypical IncI1 plasmid and minor clones). Consequently, it is essential to be aware of the risks of transmission and to take all necessary measures to prevent the proportions of resistant isolates from increasing uncontrollably.
... E. marmotae was originally isolated from feces of wild Himalayan marmots, but recently also from an alpine marmot. It is reported to be potentially pathogenic and to have zoonotic potential (De Witte et al., 2021;Liu et al., 2019;Sivertsen et al., 2022). Due to the very low human marker concentrations found in this study (at or below the threshold of detection), it could be assumed that human fecal contamination plays a minor role in the catchment studied. ...
The increased occurrence of antibiotic resistant bacteria poses a threat to global public health. Clinically relevant resistances also spread through the environment. Aquatic ecosystems in particular represent important dispersal pathways. In the past, pristine water resources have not been a study focus, although ingestion of resistant bacteria through water consumption constitutes a potentially important transmission route. This study assessed the antibiotic resistances in Escherichia coli populations in two large well-protected and well-managed Austrian karstic spring catchments representing essential groundwater resources for water supply. E. coli were detected seasonally only during the summer period. By screening a representative number of 551 E. coli isolates from 13 sites in two catchments, it could be shown that the prevalence of antibiotic resistance in this study area is low. 3.4 % of the isolates showed resistances to one or two antibiotic classes, 0.5 % were resistant to three antibiotic classes. No resistances to critical and last-line antibiotics were detected. By integrating fecal pollution assessment and microbial source tracking, we could infer that ruminants were the main hosts for antibiotic resistant bacteria in the studied catchment areas. A comparison with other studies on antibiotic resistances in karstic or mountainous springs highlighted the low contamination status of the model catchments studied here, most likely due to the high protection and careful management while other, less pristine catchments showed much higher antibiotic resistances. We demonstrate that studying easily accessible karstic springs allows a holistic view on large catchments concerning the extent and origin of fecal pollution as well as antibiotic resistance. This representative monitoring approach is also in line with the proposed update of the EU Groundwater Directive (GWD).
... Anaplasma capra was first isolated and identified, and then the patients related to this Anaplasma were informed (Li et al., 2015b;Wei et al., 2017). Additionally, Escherichia marmotae was identified as a human pathogen when four infected cases were reported to have been caused by Escherichia marmotae after our team first isolated it in 2015 (Liu et al., 2015;Liu et al., 2019;Sivertsen et al., 2022). ...
The species in the genus Erwinia are Gram-stain-negative, facultatively anaerobic, motile, and rod-shaped. Most species in the genus Erwinia are phytopathogens. Also, Erwinia persicina was involved in several human infections. Based on the reverse microbial etiology principles, it is worth analyzing the pathogenicity of species in this genus. In this study, we isolated and sequenced two species of Erwinia. Phylogenetic, phenotypic, biochemical, and chemotaxonomic analyses were performed to identify its taxonomy position. The virulence tests on plant leaves and pear fruits were used to identify the plant pathogenicity of two species of Erwinia. Bioinformatic methods predicted the possible pathogenic determinants based on the genome sequence. Meanwhile, adhesion, invasion, and cytotoxicity assays on RAW 264.7 cells were applied to identify animal pathogenicity. We isolated two Gram-stain-negative, facultatively anaerobic, motile, and rod-shaped strains from the feces of ruddy shelducks in the Tibet Plateau of China, designated J780T and J316. Distinct phylogenetic, genomic, phenotypic, biochemical, and chemotaxonomic characters of J780T and J316 identified they were novel species and belonged to the genus Erwinia, for which the name Erwinia sorbitola sp. nov. was proposed, the type strain was J780T (= CGMCC 1.17334T = GDMCC 1.1666T = JCM 33839T). Virulence tests showed blight and rot on the leaves and pear fruits confirmed Erwinia sorbitola sp. nov. was a phytopathogen. Predicted gene clusters of motility, biofilm formation, exopolysaccharides, stress survival, siderophores, and Type VI secretion system might be the causes of pathogenicity. In addition, predicted polysaccharide biosynthesis gene clusters on the genome sequence, and the high capacity for adhesion, invasion, and cytotoxicity to animal cells confirmed it has pathogenicity on animals. In conclusion, we isolated and identified a novel phytopathogen Erwinia sorbitola sp. nov. in ruddy shelducks. A predefined pathogen is beneficial for preventing from suffering potential economic losses caused by this new pathogen.
Covering: 1992 up to 2023Since their discovery, lasso peptides went from peculiarities to be recognized as a major family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products that were shown to be spread throughout the bacterial kingdom. Microcin J25 was first described in 1992, making it one of the earliest known lasso peptides. No other lasso peptide has since then been studied to such an extent as microcin J25, yet, previous review articles merely skimmed over all the research done on this exceptional lasso peptide. Therefore, to commemorate the 30th anniversary of its first report, we give a comprehensive overview of all literature related to microcin J25. This review article spans the early work towards the discovery of microcin J25, its biosynthetic gene cluster, and the elucidation of its three-dimensional, threaded lasso structure. Furthermore, the current knowledge about the biosynthesis of microcin J25 and lasso peptides in general is summarized and a detailed overview is given on the biological activities associated with microcin J25, including means of self-immunity, uptake into target bacteria, inhibition of the Gram-negative RNA polymerase, and the effects of microcin J25 on mitochondria. The in vitro and in vivo models used to study the potential utility of microcin J25 in a (veterinary) medicine context are discussed and the efforts that went into employing the microcin J25 scaffold in bioengineering contexts are summed up.
Four yellow-coloured strains (zg-Y815 T /zg-Y108 and zg-Y859 T /zg-Y826) were isolated from the intestinal contents of Marmota himalayana and assigned to the ' Arthrobacter citreus group'. The four strains grew optimally on brain heart infusion agar with 5 % defibrinated sheep blood plate at 30 °C, pH 7.0 and with 0.5 % NaCl (w/v). Comparative analysis of their 16S rRNA genes indicated that the two strain pairs belong to the genus Arthrobacter , showing the highest similarity to Arthrobacter yangruifuii 785 T (99.52 %), which was further confirmed by the 16S rRNA gene and genome-based phylogenetic analysis. The comparative genomic analysis [digital DNA–DNA hybridization, (dDDH) and average nucleotide identity (ANI)] proved that the four strains are two different species (zg-Y815 T /zg-Y108, 71.7 %/96.8 %; zg-Y859 T /zg-Y826, 87.3 %/98.5 %) and differ from other known species within the genus Arthrobacter (zg-Y815 T , 19.6–32.3 %/77.2–88.0 %; zg-Y859 T , 19.5–29.3 %/77.4–86.3 %). Strain pairs zg-Y815 T /zg-Y108 and zg-Y859 T /zg-Y826 had the same major cellular fatty acids (iso-C 16 : 0 and anteiso-C 15 : 0 ), with MK-8(H 2 ) as their dominant respiratory quinone (70.6 and 61.7 %, respectively). The leading polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol. The detected amino acids and cell-wall sugars of the two new species were identical (amino acids: alanine, glutamic acid, and lysine; sugars: rhamnose, galactose, mannose, glucose, and ribose). According to the phylogenetic, phenotypic, and chemotaxonomic analyses, we concluded that the four new strains represented two different novel species in the genus Arthrobacter , for which the names Arthrobacter zhaoxinii sp. nov. (zg-Y815 T = GDMCC 1.3494 T = JCM 35821 T ) and Arthrobacter jinronghuae sp. nov. (zg-Y859 T = GDMCC 1.3493 T = JCM 35822 T ) are proposed.
