scholarly journals Comparative genomics of Chinese and international isolates of Escherichia albertii: population structure and evolution of virulence and antimicrobial resistance

2021 ◽  
Author(s):  
Lijuan Luo ◽  
Hong Wang ◽  
Michael Payne ◽  
Chelsea Liang ◽  
Li Bai ◽  
...  
Keyword(s):  
Population Structure ◽  
Virulence Genes ◽  
Foodborne Pathogen ◽  
Multidrug Resistant ◽  
Genomic Features ◽  
Drug Classes ◽  
Type Three Secretion System ◽  
Group 5 ◽  
And Control ◽  
Mdr Genes

AbstractEscherichia albertii is a newly recognized species in the genus Escherichia that causes diarrhea. The population structure, genetic diversity and genomic features has not been fully examined. Here, 169 E. albertii isolates from different sources and regions in China were sequenced and combined with 312 publicly available genomes for phylogenetic and genomic analyses. The E. albertii population was divided into 2 clades and 8 lineages, with lineage 3 (L3), L5 and L8 more common in China. Clinical isolates were observed in all clades/lineages. Virulence genes were found to be distributed differently among lineages: subtypes of the intimin encoding gene eae and the cytolethal distending toxin (Cdt) gene cdtB were lineage associated, the second type three secretion system (ETT2) island was truncated in L3 and L6. Seven new eae subtypes and 1 new cdtB subtype (cdtB-VI) were found. Alarmingly, 85.9% of the Chinese E. albertii isolates were predicted to be multidrug resistant (MDR) with 35.9% harboured genes capable of conferring resistance to 10 to 14 different drug classes. By in silico multi-locus sequence typing, majority of the MDR isolates belonged to 4 STs (ST4638, ST4479, ST4633 and ST4488). Thirty-four intact plasmids carrying MDR and virulence genes, and 130 intact prophages were identified from 17 complete E. albertii genomes. Ten plasmid replicon types were found to be significantly associated with MDR. The 130 intact prophages were clustered into 5 groups, with group 5 prophages harbouring more virulence genes. Our findings provided fundamental insights into the population structure, virulence variation and MDR of E. albertii.Impact statementE. albertii is newly recognized foodborne pathogen causing diarrhea. Elucidation of its genomic features is important for surveillance and control of E. albertii infections. In this work, 169 E. albertii genomes from difference sources and regions in China were collected and sequenced, which contributed to the currently limited genomic data pool of E. albertii. In combination with 312 publicly available genomes from 14 additional countries, the population structure of E. albertii was defined. The presence and subtypes of virulence genes in different lineages were significantly different, indicating potential pathogenicity variation. Additionally, the presence of multidrug resistance (MDR) genes was alarmingly high in the Chinese dominated lineages. MDR associated STs and plasmid subtypes were identified, which could be used as sentinels for MDR surveillance. Moreover, the subtypes of plasmids and prophages were distributed differently across lineages, and were found to contribute to the acquisition of virulence and MDR genes of E. albertii. Altogether, this work reveals the diversity of E. albertii and characterized its genomic features in unprecedented detail.Data SummaryAll newly sequenced data in this work were deposited in National Center for Biotechnology Information (NCBI) under the BioProject of PRJNA693666, including 6 complete genomes and raw reads of 164 E. albertii isolates.

scholarly journals Comparative genomics of Chinese and international isolates of Escherichia albertii: population structure and evolution of virulence and antimicrobial resistance

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Lijuan Luo ◽  
Hong Wang ◽  
Michael J. Payne ◽  
Chelsea Liang ◽  
Li Bai ◽  
...  
Keyword(s):  
Population Structure ◽  
Type Species ◽  
Virulence Genes ◽  
Multidrug Resistant ◽  
Toxin Gene ◽  
Content Type ◽  
Link Type ◽  
Drug Classes ◽  
Type Three Secretion System ◽  
Evolution Of Virulence

Escherichia albertii is a recently recognized species in the genus Escherichia that causes diarrhoea. The population structure, genetic diversity and genomic features have not been fully examined. Here, 169 E. albertii isolates from different sources and regions in China were sequenced and combined with 312 publicly available genomes (from additional 14 countries) for genomic analyses. The E. albertii population was divided into two clades and eight lineages, with lineage 3 (L3), L5 and L8 more common in China. Clinical isolates were observed in all clades/lineages. Virulence genes were found to be distributed differently among lineages: subtypes of the intimin encoding gene eae and the cytolethal distending toxin gene cdtB were lineage associated, and the second type three secretion system (ETT2) island was truncated in L3 and L6. Seven new eae subtypes and one new cdtB subtype (cdtB-VI) were identified. Alarmingly, 85.9 % of the Chinese E. albertii isolates were predicted to be multidrug-resistant (MDR) with 35.9 % harbouring genes capable of conferring resistance to 10 to 14 different drug classes. The majority of the MDR isolates were of poultry source from China and belonged to four sequence types (STs) [ST4638, ST4479, ST4633 and ST4488]. Thirty-four plasmids with some carrying MDR and virulence genes, and 130 prophages were identified from 17 complete E. albertii genomes. The 130 intact prophages were clustered into five groups, with group five prophages harbouring more virulence genes. We further identified three E. albertii specific genes as markers for the identification of this species. Our findings provided fundamental insights into the population structure, virulence variation and drug resistance of E. albertii .

scholarly journals Epidemic and molecular characterization of fluoroquinolone-resistant Shigella dysenteriae 1 isolates from calves with diarrhea

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mingze Cao ◽  
Weiwei Wang ◽  
Liwei Zhang ◽  
Guanhui Liu ◽  
Xuzheng Zhou ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Virulence Genes ◽  
Point Mutations ◽  
Multidrug Resistant ◽  
Gansu Province ◽  
Quinolone Resistance ◽  
Shigella Dysenteriae ◽  
Fluoroquinolone Resistance ◽  
And Control

Abstract Background The widespread distribution of antimicrobial-resistant Shigella has become a recurrent challenge in many parts of the developing world. Previous studies indicate that the host of Shigella has expanded from humans to animals. This study aimed to investigate the prevalence of fluoroquinolone resistance and associated molecular characterization of S. dysenteriae 1 isolated from calves. Results All 38 unduplicated S. dysenteriae 1 isolates were collected from calves in Gansu Province from October 2014 to December 2016. According to MLST and PFGE analysis, these isolates were separated into 4 and 28 genotypes, respectively. The most common STs identified were ST228 (34.21%, 13/38) and ST229 (39.47%, 15/38), which were first found in the present study. All isolates harbored virulence genes, and the incidence of the seven virulence genes were ipaH (100%), ipaBCD (92.11%), stx (73.68%), ial (57.89%), sen (28.95%), set1A and set1B (0%). According to the results of antimicrobial susceptibilities, 76.32% (29/38) were resistant to fluoroquinolone and showed multidrug resistance. In a study on the polymorphism of quinolone resistance–determining region (QRDR) of gyrA/B and parC/E genes, we identified two mutations in gyrA (Ser83 → Leu and Asp87 → Asn) and parC (Ser80 → Ile and Ser83 → Leu), respectively. Among them, 55.17% (16/29) of resistant strains had the gyrA point mutations (Ser83 → Leu) and parC point mutation (Ser83 → Leu). Moreover, 41.38% (12/29) of isolates had all five point mutations of gyrA and parC. In addition, the prevalence of the plasmid-mediated quinolone resistance (PMQR) determinant genes was also investigated. All 29 fluoroquinolone-resistant isolates were positive for the aac (6′)-Ib-cr gene but negative for qepA, except for SD001. In addition, only 6 (20.69%, 6/29) isolates harbored the qnr gene, including two with qnrB (6.90%, 2/29) and four with qnrS (13.79%, 4/29). Conclusion Given the increased common emergence of multidrug resistant isolates, uninterrupted surveillance will be necessary to understand the actual epidemic burden and control this infection.

scholarly journals Epidemic and molecular characterization of fluoroquinolone-resistant Shigella dysenteriae 1 isolates from calves with diarrhea

2020 ◽  
Author(s):  
Mingze Cao ◽  
Weiwei Wang ◽  
Liwei Zhang ◽  
Guanhui Liu ◽  
Xuzheng Zhou ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Virulence Genes ◽  
Point Mutations ◽  
Multidrug Resistant ◽  
Gansu Province ◽  
Quinolone Resistance ◽  
Shigella Dysenteriae ◽  
Fluoroquinolone Resistance ◽  
And Control

Abstract Background: The widespread distribution of antimicrobial-resistant Shigella has become a recurrent challenge in many parts of the developing world. Previous studies indicate that the host of Shigella has expanded from humans to animals. This study aimed to investigate the prevalence of fluoroquinolone resistance and associated molecular characterization of S. dysenteriae 1 isolated from calves. Results: All 38 unduplicated S. dysenteriae 1 isolates were collected from calves in Gansu Province from October 2014 to December 2016. According to MLST and PFGE analysis, these isolates were separated into 4 and 28 genotypes, respectively. The most common STs identified were ST228 (34.21%, 13/38) and ST229 (39.47%, 15/38), which were first found in the present study. All isolates harbored virulence genes, and the incidence of the seven virulence genes were ipaH (100%), ipaBCD (92.11%), stx (73.68%), ial (57.89%), sen (28.95%), set1A and set1B (0%). According to the results of antimicrobial susceptibilities, 76.32% (29/38) were resistant to fluoroquinolone and showed multidrug resistance. In a study on the polymorphism of quinolone resistance–determining region (QRDR) of gyrA/B and parC/E genes, we identified two mutations in gyrA (Ser83→Leu and Asp87→Asn) and parC (Ser80→Ile and Ser83→Leu), respectively. Among them, 55.17% (16/29) of resistant strains had the gyrA point mutations (Ser83→Leu) and parC point mutation (Ser83→Leu). Moreover, 41.38% (12/29) of isolates had all five point mutations of gyrA and parC. In addition, the prevalence of the plasmid-mediated quinolone resistance (PMQR) determinant genes was also investigated. All 29 fluoroquinolone-resistant isolates were positive for the aac(6’)-Ib-cr gene but negative for qepA, except for SD001. In addition, only 6 (20.69%, 6/29) isolates harbored the qnr gene, including two with qnrB (6.90%, 2/29) and four with qnrS (13.79%, 4/29). Conclusion: Given the increased common emergence of multidrug resistant isolates, uninterrupted surveillance will be necessary to understand the actual epidemic burden and control this infection.

scholarly journals Epidemic and molecular characterization of fluoroquinolone-resistant Shigella dysenteriae 1 isolates from calves with diarrhea

2020 ◽  
Author(s):  
Zhen Zhu ◽  
Mingze Cao ◽  
Weiwei Wang ◽  
Liwei Zhang ◽  
Guanhui Liu ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Virulence Genes ◽  
Point Mutations ◽  
Multidrug Resistant ◽  
Gansu Province ◽  
Shigella Dysenteriae ◽  
Fluoroquinolone Resistance ◽  
Resistant Strains ◽  
And Control

Abstract Background: The widespread distribution of antimicrobial-resistant Shigella has become a recurrent challenge in many parts of the developing world. Previous studies indicate that the host of Shigella has expanded from humans to animals. This study aimed to investigate the prevalence of fluoroquinolone resistance and associated molecular characterization of S. dysenteriae 1 isolated from calves. Methods and Results: All 38 unduplicated S. dysenteriae 1 isolates were collected from calves in Gansu Province from October 2014 to December 2016. According to MLST and PFGE analysis, these isolates were separated into 4 and 28 genotypes, respectively. The most common STs identified were ST228 (34.21%, 13/38) and ST229 (39.47%, 15/38), which were first found in the present study. All isolates harbored virulence genes, and the incidence of the five virulence genes were ipaH (100%), ipaBCD (92.11%), stx (73.68%), ial (57.89%), and sen (28.95%). According to the results of antimicrobial susceptibilities, 76.32% (29/38) of S. dysenteriae isolates were resistant to fluoroquinolone and showed multidrug resistance. In a study on the polymorphism of QRDR of gyrA/B and parC/E genes, we identified two mutations in gyrA (Ser83→Leu and Asp87→Asn) and parC (Ser80→Ile and Ser83→Leu), respectively. Among them, 55.17% (16/29) of resistant strains had the gyrA point mutations (Ser83→Leu) and parC point mutation (Ser83→Leu). Moreover, 41.38% (12/29) of isolates had all five point mutations of gyrA and parC. In addition, the prevalence of the PMQR determinant genes was also investigated. All 29 fluoroquinolone-resistant isolates were positive for the aac(6’)-Ib-cr gene but negative for qepA, except SD001. In addition, only 6 (20.69%, 6/29) isolates harbored the qnr gene, including two with qnrB (6.90%, 2/29) and four with qnrS (13.79%, 4/29). Conclusion: Given the increased common emergence of multidrug resistant isolates, uninterrupted surveillance will be necessary to understand the actual epidemic burden and control this infection.

Antimicrobial Resistance and Virulence Profiles of Salmonella Isolated from Butcher Shops in Minas Gerais, Brazil

2013 ◽  
Vol 76 (9) ◽  
pp. 1633-1637 ◽  
Author(s):  
MARCUS VINÍCIUS COUTINHO COSSI ◽  
RAQUEL CRISTINA KONRAD BURIN ◽  
DANILO AUGUSTO LOPES ◽  
MARIANE REZENDE DIAS ◽  
NATALIA PARMA AUGUSTO de CASTILHO ◽  
...  
Keyword(s):  
Virulence Genes ◽  
Raw Materials ◽  
Foodborne Pathogen ◽  
Multidrug Resistant ◽  
International Organization ◽  
Surface Samples ◽  
Butcher Shop ◽  
Cutting Boards ◽  
Pcr Targeting ◽  
Butcher Shops

Salmonella can contaminate finished products of butcher shops, mainly through cross-contamination of utensils exposed to raw materials. To identify the main sources of contamination with this foodborne pathogen in four butcher shop environments, surface samples were obtained from employees' hands, cutting boards, knives, floor of the refrigeration room, meat grinders, and meat tenderizers (32 samples per area) and analyzed for Salmonella using the International Organization for Standardization method 6579, with modifications. Suspect isolates were identified by PCR (targeting ompC), and confirmed Salmonella isolates were subjected to pulsed-field gel electrophoresis (after treatment with restriction enzyme XbaI), analyzed for the presence of virulence genes (invA, sefA, and spvC), and screened for resistance to 12 antimicrobials. Salmonella isolates was identified only on cutting boards (five samples) from three butcher shops. Fifteen isolates were confirmed as Salmonella belonging to four pulse types (similarity of 71.1 to 100%). The invA gene was detected in 13 isolates, and the sefA was found in 8 isolates; no isolate carried spvC. All tested isolates were resistant to clindamycin and sensitive to amikacin and cefotaxine, and all isolates were resistant to at least 3 of the 12 antimicrobials tested. The results indicate the importance of cutting boards as a source of Salmonella contamination in butcher shops. The presence of multidrug-resistant Salmonella strains possessing virulence genes highlights the health risks for consumers.

scholarly journals Epidemic and molecular characterization of fluoroquinolone-resistant Shigella dysenteriae 1 isolates from calves with diarrhea

2020 ◽  
Author(s):  
Mingze Cao ◽  
Weiwei Wang ◽  
Liwei Zhang ◽  
Guanhui Liu ◽  
Xuzheng Zhou ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Virulence Genes ◽  
Point Mutations ◽  
Multidrug Resistant ◽  
Gansu Province ◽  
Quinolone Resistance ◽  
Shigella Dysenteriae ◽  
Fluoroquinolone Resistance ◽  
And Control

Abstract Background: The widespread distribution of antimicrobial-resistant Shigella has become a recurrent challenge in many parts of the developing world. Previous studies indicate that the host of Shigella has expanded from humans to animals. This study aimed to investigate the prevalence of fluoroquinolone resistance and associated molecular characterization of S. dysenteriae 1 isolated from calves. Results: All 38 unduplicated S. dysenteriae 1 isolates were collected from calves in Gansu Province from October 2014 to December 2016. According to MLST and PFGE analysis, these isolates were separated into 4 and 28 genotypes, respectively. The most common STs identified were ST228 (34.21%, 13/38) and ST229 (39.47%, 15/38), which were first found in the present study. All isolates harbored virulence genes, and the incidence of the seven virulence genes were ipaH (100%), ipaBCD (92.11%), stx (73.68%), ial (57.89%), sen (28.95%), set1A and set1B (0%). According to the results of antimicrobial susceptibilities, 76.32% (29/38) were resistant to fluoroquinolone and showed multidrug resistance. In a study on the polymorphism of quinolone resistance–determining region (QRDR) of gyrA/B and parC/E genes, we identified two mutations in gyrA (Ser83→Leu and Asp87→Asn) and parC (Ser80→Ile and Ser83→Leu), respectively. Among them, 55.17% (16/29) of resistant strains had the gyrA point mutations (Ser83→Leu) and parC point mutation (Ser83→Leu). Moreover, 41.38% (12/29) of isolates had all five point mutations of gyrA and parC. In addition, the prevalence of the plasmid-mediated quinolone resistance (PMQR) determinant genes was also investigated. All 29 fluoroquinolone-resistant isolates were positive for the aac(6’)-Ib-cr gene but negative for qepA, except for SD001. In addition, only 6 (20.69%, 6/29) isolates harbored the qnr gene, including two with qnrB (6.90%, 2/29) and four with qnrS (13.79%, 4/29). Conclusion: Given the increased common emergence of multidrug resistant isolates, uninterrupted surveillance will be necessary to understand the actual epidemic burden and control this infection.

scholarly journals Epidemic and Molecular Characterization of Fluoroquinolone-Resistant Shigella Dysenteriae 1 Isolates From Calves with Diarrhea

2020 ◽  
Author(s):  
Zhen Zhu ◽  
Mingze Cao ◽  
Weiwei Wang ◽  
Liwei Zhang ◽  
Guanhui Liu ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Virulence Genes ◽  
Point Mutations ◽  
Multidrug Resistant ◽  
Gansu Province ◽  
Shigella Dysenteriae ◽  
Fluoroquinolone Resistance ◽  
Resistant Strains ◽  
And Control

Abstract Background: The widespread distribution of antimicrobial-resistant Shigella has become a recurrent challenge in many parts of the developing world. Previous studies indicate that the host of Shigella has expanded from humans to animals. This study aimed to investigate the prevalence of fluoroquinolone resistance and associated molecular characterization of S. dysenteriae 1 isolated from calves. Results: All 38 unduplicated S. dysenteriae 1 isolates were collected from calves in Gansu Province from October 2014 to December 2016. According to MLST and PFGE analysis, these isolates were separated into 4 and 28 genotypes, respectively. The most common STs identified were ST228 (34.21%, 13/38) and ST229 (39.47%, 15/38), which were first found in the present study. All isolates harbored virulence genes, and the incidence of the five virulence genes were ipaH (100%), ipaBCD (92.11%), stx (73.68%), ial (57.89%), and sen (28.95%). According to the results of antimicrobial susceptibilities, 76.32% (29/38) of S. dysenteriae isolates were resistant to fluoroquinolone and showed multidrug resistance. In a study on the polymorphism of QRDR of gyrA/B and parC/E genes, we identified two mutations in gyrA (Ser83→Leu and Asp87→Asn) and parC (Ser80→Ile and Ser83→Leu), respectively. Among them, 55.17% (16/29) of resistant strains had the gyrA point mutations (Ser83→Leu) and parC point mutation (Ser83→Leu). Moreover, 41.38% (12/29) of isolates had all five point mutations of gyrA and parC. In addition, the prevalence of the PMQR determinant genes was also investigated. All 29 fluoroquinolone-resistant isolates were positive for the aac(6’)-Ib-cr gene but negative for qepA, except SD001. In addition, only 6 (20.69%, 6/29) isolates harbored the qnr gene, including two with qnrB (6.90%, 2/29) and four with qnrS (13.79%, 4/29). Conclusion: Given the increased common emergence of multidrug resistant isolates, uninterrupted surveillance will be necessary to understand the actual epidemic burden and control this infection.

scholarly journals Epidemic and molecular characterization of fluoroquinolone-resistant Shigella dysenteriae 1 isolates from calves with diarrhea

2020 ◽  
Author(s):  
Mingze Cao ◽  
Weiwei Wang ◽  
Liwei Zhang ◽  
Guanhui Liu ◽  
Xuzheng Zhou ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Virulence Genes ◽  
Point Mutations ◽  
Multidrug Resistant ◽  
Gansu Province ◽  
Quinolone Resistance ◽  
Shigella Dysenteriae ◽  
Fluoroquinolone Resistance ◽  
And Control

Abstract Background: The widespread distribution of antimicrobial-resistant Shigella has become a recurrent challenge in many parts of the developing world. Previous studies indicate that the host of Shigella has expanded from humans to animals. This study aimed to investigate the prevalence of fluoroquinolone resistance and associated molecular characterization of S. dysenteriae 1 isolated from calves. Results: All 38 unduplicated S. dysenteriae 1 isolates were collected from calves in Gansu Province from October 2014 to December 2016. According to MLST and PFGE analysis, these isolates were separated into 4 and 28 genotypes, respectively. The most common STs identified were ST228 (34.21%, 13/38) and ST229 (39.47%, 15/38), which were first found in the present study. All isolates harbored virulence genes, and the incidence of the seven virulence genes were ipaH (100%), ipaBCD (92.11%), stx (73.68%), ial (57.89%), sen (28.95%), set1A and set1B. According to the results of antimicrobial susceptibilities, 76.32% (29/38) were resistant to fluoroquinolone and showed multidrug resistance. In a study on the polymorphism of quinolone resistance–determining region (QRDR) of gyrA/B and parC/E genes, we identified two mutations in gyrA (Ser83→Leu and Asp87→Asn) and parC (Ser80→Ile and Ser83→Leu), respectively. Among them, 55.17% (16/29) of resistant strains had the gyrA point mutations (Ser83→Leu) and parC point mutation (Ser83→Leu). Moreover, 41.38% (12/29) of isolates had all five point mutations of gyrA and parC. In addition, the prevalence of the plasmid-mediated quinolone resistance (PMQR) determinant genes was also investigated. All 29 fluoroquinolone-resistant isolates were positive for the aac(6’)-Ib-cr gene but negative for qepA, except SD001. In addition, only 6 (20.69%, 6/29) isolates harbored the qnr gene, including two with qnrB (6.90%, 2/29) and four with qnrS (13.79%, 4/29). Conclusion: Given the increased common emergence of multidrug resistant isolates, uninterrupted surveillance will be necessary to understand the actual epidemic burden and control this infection.

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