Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167
            <i>Escherichia coli</i>
            Strain Sanji with Novel
            <i>In Silico</i>
            Serotype O89b:H9

Zhang, Xiancheng; Chi, Xuelin; Ho, Brian T.; Moon, Damee; Lambert, Christine; Hall, Richard J.; Baybayan, Primo; Wang, Shihua; Wilson, Brenda A.; Ho, Mengfei

doi:10.1128/msystems.00242-18

Cited by 16 publications

(15 citation statements)

References 81 publications

(77 reference statements)

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“…Moreover, the O antigen gene cluster, O89 was found to be present in all ST167 E. coli strains as recently reported (37). The co-occurrence of the bla NDM-5 gene in serotype O89 harboring ST167 clone with fitness and virulence factors such the capsule synthesis clusters could explain its global dissemination as a high-risk clone.…”

Section: Ndm-encodingsupporting

confidence: 76%

Cross-Border Emergence of Escherichia coli Producing the Carbapenemase NDM-5 in Switzerland and Germany

et al. 2021

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A series of clinical NDM-5-producing E. coli isolates obtained from two surveillance networks of carbapenem-producing Enterobacterales from 2018-2019, namely Switzerland (NARA) and Germany (SurvCARE), were analyzed. The 33 NDM-5-producing E. coli isolates were highly resistant to β-lactams including the novel ß-lactam/ß-lactamase inhibitor combinations (ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam), and remained susceptible to fosfomycin, colistin, and tigecycline. Those isolates were assigned to different sequence types (STs) and indicated a predominance of isolates exhibiting the sequence type (ST) ST167 in Switzerland and in Germany (n=10, phylogenetic group C), followed by ST405 (n=4, phylogenetic group E), ST1284 (n=4, phylogenetic group C) and ST361 (n=4, phylogenetic group C). The blaNDM-5 gene was predominantly present on an IncF-type plasmid (n=29), and to a lesser extent on the narrow-host range IncX3 plasmid (n=4). Sequence analyses of eight NDM-5 plasmids indicated that NDM-5-encoding F-type plasmids varied in size between 86 to 132 kb. The two IncX3 plasmids pCH8NDM5 and pD12NDM5 were 46 and 45 kb in size, respectively. The highly conserved blaNDM-5 genetic surrounding structures [ΔISAba125-blaNDM-5-bleMBL-trpT-dsbD-IS26] of both the F-type and IncX3 plasmids suggested a common genetic origin. The emergence of the NDM-5 carbapenemase was evidenced in particular for the E. coli ST167 clone, which is a successful epidemic clone, known to be associated to both multi-resistance and virulence traits and is therefore of high public health concern. The occurrence of clonally related NDM-5-producing E. coli isolates in Switzerland and Germany further indicates the international spread of this multidrug-resistant superbug at least throughout Europe.

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Section: Ndm-encodingsupporting

confidence: 76%

Cross-Border Emergence of Escherichia coli Producing the Carbapenemase NDM-5 in Switzerland and Germany

et al. 2021

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“…In a previously performed genomic analysis of ST167 strains, it was hypothesized that ST167 and its related ST617 lineage emerged from clone ST10 by the complete loss of the wca operon, encoding colanic acid biosynthesis in the lipopolysaccharide (LPS) biosynthesis pathway (12). Furthermore, a recent study proposed the O89b name for the novel variant of O89 antigen identified in ST167 detected in all strains of the clone (9). Both studies evidenced that the ST167 lineage has peculiar virulence and surface antigen features that could justify its worldwide spread as a high-risk clone.…”

Section: Discussionmentioning

confidence: 99%

Novel Insights and Features of the NDM-5-Producing Escherichia coli Sequence Type 167 High-Risk Clone

García-Fernández

Villa

Bibbolino

et al. 2020

mSphere

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Escherichia coli sequence type 167 (ST167), producing the metallo beta-lactamase NDM-5, has been isolated as a colonizer of patients recovered at the University Hospital Policlinico Umberto I of Rome. Phylogenesis and comparative analysis of the genomes of these strains were performed against 343 ST167 genomes available from the EnteroBase database. These analyses revealed that resistance plasmids, integrative conjugative elements (ICEs), carrying the yersiniabactin virulence trait and capsular synthesis gene clusters had variable compositions and distributions within different strains of the ST167 clone. A novel capsular synthesis gene cluster, highly similar to the K48 cluster previously described only for Klebsiella pneumoniae, was identified in phylogenetically related strains of the ST167 clone. IMPORTANCE Global dissemination of some E. coli high-risk clones has been described in the last decades. The most widespread was the ST131 clone, associated with extended-spectrum-beta-lactamase (ESBL) production. Genomics of ST131 demonstrated that one clade within the ST emerged in the early 2000s, followed by a rapid, global expansion. The E. coli ST167 clone is emerging throughout the world, being frequently reported for its association with carbapenem resistance. Our study shows that virulence features are differently represented within the ST167 population. One clade shows the K48 capsular synthesis gene cluster of K. pneumoniae, not previously described for E. coli, and is populated by NDM-5-producing strains. The combination of resistance and virulence may sustain the global expansion of this specific ST167 clade.

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“…Community sources for the OXA-244-producing E. coli isolates seem possible since many of the patients had not been hospitalised and the E. coli isolates belonged to STs that are present in the community [23][24][25][26][27][28][29][30][31][32]. The ECDC RRA identified one main geographically dispersed ST38 OXA-244-producing E. coli cluster with chromosomal-encoded bla OXA-244 present in all 10 countries, including Denmark, that submitted data for the RRA [10].…”

Section: Discussionmentioning

confidence: 99%

Surveillance of OXA-244-producing Escherichia coli and epidemiologic investigation of cases, Denmark, January 2016 to August 2019

et al. 2020

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Background: Carbapenemase-producing Escherichia coli are increasing worldwide. In recent years, an increase in OXA-244-producing E. coli isolates has been seen in the national surveillance of carbapenemase-producing organisms in Denmark. Aim: Molecular characterisation and epidemiological investigation of OXA-244-producing E. coli isolates from January 2016 to August 2019. Methods: For the epidemiological investigation, data from the Danish National Patient Registry and the Danish register of civil registration were used together with data from phone interviews with patients. Isolates were characterised by analysing whole genome sequences for resistance genes, MLST and core genome MLST (cgMLST). Results: In total, 24 OXA-244-producing E. coli isolates were obtained from 23 patients. Among the 23 patients, 13 reported travelling before detection of the E. coli isolates, with seven having visited countries in Northern Africa. Fifteen isolates also carried an extended-spectrum beta-lactamase gene and one had a plasmid-encoded AmpC gene. The most common detected sequence type (ST) was ST38, followed by ST69, ST167, ST10, ST361 and ST3268. Three clonal clusters were detected by cgMLST, but none of these clusters seemed to reflect nosocomial transmission in Denmark. Conclusion: Import of OXA-244 E. coli isolates from travelling abroad seems likely for the majority of cases. Community sources were also possible, as many of the patients had no history of hospitalisation and many of the E. coli isolates belonged to STs that are present in the community. It was not possible to point at a single country or a community source as risk factor for acquiring OXA-244-producing E. coli.

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Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 Escherichia coli Strain Sanji with Novel In Silico Serotype O89b:H9

Cited by 16 publications

References 81 publications

Cross-Border Emergence of Escherichia coli Producing the Carbapenemase NDM-5 in Switzerland and Germany

Cross-Border Emergence of Escherichia coli Producing the Carbapenemase NDM-5 in Switzerland and Germany

Novel Insights and Features of the NDM-5-Producing Escherichia coli Sequence Type 167 High-Risk Clone

Surveillance of OXA-244-producing Escherichia coli and epidemiologic investigation of cases, Denmark, January 2016 to August 2019

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