Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones
Multi-resistant pathogenic strains of non-lactose fermenting Escherichia coli (NLF E. coli) are responsible for various intestinal and extraintestinal infections. Although several studies have characterised such strains using conventional methods, they have not been comprehensively studied at the ge...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-11-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1027494/full |
| _version_ | 1797990350611021824 |
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| author | Razib Mazumder Arif Hussain Jody E. Phelan Susana Campino S. M. Arefeen Haider Araf Mahmud Dilruba Ahmed Md Asadulghani Taane G. Clark Dinesh Mondal |
| author_facet | Razib Mazumder Arif Hussain Jody E. Phelan Susana Campino S. M. Arefeen Haider Araf Mahmud Dilruba Ahmed Md Asadulghani Taane G. Clark Dinesh Mondal |
| author_sort | Razib Mazumder |
| collection | DOAJ |
| description | Multi-resistant pathogenic strains of non-lactose fermenting Escherichia coli (NLF E. coli) are responsible for various intestinal and extraintestinal infections. Although several studies have characterised such strains using conventional methods, they have not been comprehensively studied at the genomic level. To address this gap, we used whole-genome sequencing (WGS) coupled with detailed microbiological and biochemical testing to investigate 17 NLF E. coli from a diagnostic centre (icddr,b) in Dhaka, Bangladesh. The prevalence of NLF E. coli was 10%, of which 47% (8/17) exhibited multi-drug resistant (MDR) phenotypes. All isolates (17/17) were confirmed as E. coli and could not ferment lactose sugar. WGS data analysis revealed international high-risk clonal lineages. The most prevalent sequence types (STs) were ST131 (23%), ST1193 (18%), ST12 (18%), ST501 (12%), ST167 (6%), ST73 (6%) and ST12 (6%). Phylogenetic analysis corroborated a striking clonal population amongst the studied NLF E. coli isolates. The predominant phylogroup detected was B2 (65%). The blaCTX-M-15 extended-spectrum beta-lactamase gene was present in 53% of isolates (9/17), whilst 64.7% (11/17) isolates were affiliated with pathogenic pathotypes. All extraintestinal pathogenic E. coli pathotypes demonstrated β-hemolysis. Our study underscores the presence of critical pathogens and MDR clones amongst non-lactose fermenting E. coli. We suggest that non-lactose fermenting E. coli be considered equally capable as lactose fermenting forms in causing intestinal and extraintestinal infections. Further, there is a need to undertake systematic, unbiased monitoring of predominant lineages amongst non-lactose fermenting E. coli that would help in better treatment and prevention strategies. |
| first_indexed | 2024-04-11T08:35:05Z |
| format | Article |
| id | doaj.art-03cdd9b0e9a0422f8849ee4ae10444f8 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-11T08:35:05Z |
| publishDate | 2022-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-03cdd9b0e9a0422f8849ee4ae10444f82022-12-22T04:34:22ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-11-011310.3389/fmicb.2022.10274941027494Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clonesRazib Mazumder0Arif Hussain1Jody E. Phelan2Susana Campino3S. M. Arefeen Haider4Araf Mahmud5Dilruba Ahmed6Md Asadulghani7Taane G. Clark8Dinesh Mondal9Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, BangladeshLaboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, BangladeshDepartment of Infection Biology, London School of Hygiene and Tropical Medicine, London, United KingdomDepartment of Infection Biology, London School of Hygiene and Tropical Medicine, London, United KingdomLaboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, BangladeshLaboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, BangladeshClinical Microbiology and Immunology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, BangladeshBiosafety and BSL3 Laboratory, Biosafety Office, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, BangladeshDepartment of Infection Biology, London School of Hygiene and Tropical Medicine, London, United KingdomLaboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, BangladeshMulti-resistant pathogenic strains of non-lactose fermenting Escherichia coli (NLF E. coli) are responsible for various intestinal and extraintestinal infections. Although several studies have characterised such strains using conventional methods, they have not been comprehensively studied at the genomic level. To address this gap, we used whole-genome sequencing (WGS) coupled with detailed microbiological and biochemical testing to investigate 17 NLF E. coli from a diagnostic centre (icddr,b) in Dhaka, Bangladesh. The prevalence of NLF E. coli was 10%, of which 47% (8/17) exhibited multi-drug resistant (MDR) phenotypes. All isolates (17/17) were confirmed as E. coli and could not ferment lactose sugar. WGS data analysis revealed international high-risk clonal lineages. The most prevalent sequence types (STs) were ST131 (23%), ST1193 (18%), ST12 (18%), ST501 (12%), ST167 (6%), ST73 (6%) and ST12 (6%). Phylogenetic analysis corroborated a striking clonal population amongst the studied NLF E. coli isolates. The predominant phylogroup detected was B2 (65%). The blaCTX-M-15 extended-spectrum beta-lactamase gene was present in 53% of isolates (9/17), whilst 64.7% (11/17) isolates were affiliated with pathogenic pathotypes. All extraintestinal pathogenic E. coli pathotypes demonstrated β-hemolysis. Our study underscores the presence of critical pathogens and MDR clones amongst non-lactose fermenting E. coli. We suggest that non-lactose fermenting E. coli be considered equally capable as lactose fermenting forms in causing intestinal and extraintestinal infections. Further, there is a need to undertake systematic, unbiased monitoring of predominant lineages amongst non-lactose fermenting E. coli that would help in better treatment and prevention strategies.https://www.frontiersin.org/articles/10.3389/fmicb.2022.1027494/fullgenomic epidemiologyhigh risk clonecarbapenem resistanceESBL – Escherichia coliST131 and non-ST131 lineagesnon lactose fermenter |
| spellingShingle | Razib Mazumder Arif Hussain Jody E. Phelan Susana Campino S. M. Arefeen Haider Araf Mahmud Dilruba Ahmed Md Asadulghani Taane G. Clark Dinesh Mondal Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones Frontiers in Microbiology genomic epidemiology high risk clone carbapenem resistance ESBL – Escherichia coli ST131 and non-ST131 lineages non lactose fermenter |
| title | Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones |
| title_full | Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones |
| title_fullStr | Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones |
| title_full_unstemmed | Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones |
| title_short | Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones |
| title_sort | non lactose fermenting escherichia coli following in the footsteps of lactose fermenting e coli high risk clones |
| topic | genomic epidemiology high risk clone carbapenem resistance ESBL – Escherichia coli ST131 and non-ST131 lineages non lactose fermenter |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1027494/full |
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