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Pan-genome and resistome analysis of extended-spectrum ß-lactamase-producing Escherichia coli: A multi-setting epidemiological surveillance study from Malaysia. PLoS One 2022; 17:e0265142. [PMID: 35271656 PMCID: PMC8912130 DOI: 10.1371/journal.pone.0265142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/23/2022] [Indexed: 11/19/2022] Open
Abstract
Objectives
This study profiled the prevalence of extended-spectrum ß-lactamase-producing Escherichia coli (ESBL-EC) in the community and compared their resistome and genomic profiles with isolates from clinical patients through whole-genome sequencing.
Methods
Fecal samples from 233 community dwellers from Segamat, a town in southern Malaysia, were obtained between May through August 2018. Putative ESBL strains were screened and tested using antibiotic susceptibility tests. Additionally, eight clinical ESBL-EC were obtained from a hospital in the same district between June through October 2020. Whole-genome sequencing was then conducted on selected ESBL-EC from both settings (n = 40) for pan-genome comparison, cluster analysis, and resistome profiling.
Results
A mean ESBL-EC carriage rate of 17.82% (95% CI: 10.48%– 24.11%) was observed in the community and was consistent across demographic factors. Whole-genome sequences of the ESBL-EC (n = 40) enabled the detection of multiple plasmid replicon groups (n = 28), resistance genes (n = 34) and virulence factors (n = 335), with no significant difference in the number of genes carried between the community and clinical isolates (plasmid replicon groups, p = 0.13; resistance genes, p = 0.47; virulence factors, p = 0.94). Virulence gene marker analysis detected the presence of extraintestinal pathogenic E. coli (ExPEC), uropathogenic E. coli (UPEC), and enteroaggregative E. coli (EAEC) in both the community and clinical isolates. Multiple blaCTX-M variants were observed, dominated by blaCTX-M-27 (n = 12), blaCTX-M-65 (n = 10), and blaCTX-M-15 (n = 9). The clinical and community isolates did not cluster together based on the pan-genome comparison, suggesting isolates from the two settings were clonally unrelated. However, cluster analysis based on carried plasmids, resistance genes and phenotypic susceptibility profiles identified four distinct clusters, with similar patterns between the community and clinical isolates.
Conclusion
ESBL-EC from the clinical and community settings shared similar resistome profiles, suggesting the frequent exchange of genetic materials through horizontal gene transfer.
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Tajbakhsh M, Avini MY, Alikhajeh J, Tajeddin E, Rahbar M, Eslami P, Alebouyeh M, Zali MR. Emergence of blaCTX-M-15, blaTEM-169 and blaPER-1 extended-spectrum β-lactamase genes among different Salmonella enterica serovars from human faecal samples. Infect Dis (Lond) 2016; 48:550-6. [PMID: 27117981 DOI: 10.3109/23744235.2016.1166260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Broad-spectrum β-lactams are used for empirical therapy of severe infections with non-typhoid Salmonella serotypes; however, activities of these drugs against the strains producing different β-lactamase is not so clear. This study investigated the prevalence of β-lactamase genes among isolates of S. enterica serovars from human faecal samples and determined their diversity in activity against different β-lactams. METHODS Antimicrobial resistance of faecal isolates of S. enterica to extended-spectrum cephalosporins was analysed and MIC values were determined for the strains presenting extended-spectrum β-lactamases (ESBLs) phenotypes. The β-lactamase genes were identified by PCR and sequencing. β-lactamase activity of the Salmonella strains exhibiting ESBL phenotype was detected by biological, iodometric, spectrophotometry and nitrocefin assays. RESULTS Out of 202 S. enterica isolates, ESBLs phenotype was detected among 3.4% (7/202) of the strains. blaTEM-1 and blaCTX-M-15 were among the frequent β-lactamase genes. Detection of blaTEM-169 in S. enterica serovar Typhimurium and S. enterica serovar Bredeney and blaPER-1 in S. enterica serovar Infantis was a new finding in this experiment. Location of blaCTX-M-15/blaTEM-169/blaPER-1 genes on plasmid was confirmed in a transformation experiment. While crude extracts of the enzymes from each strain showed higher activity against cephalothin and cefotaxime, the lowest activity was detected against ceftazidime. The greatest synergistic activity was seen in a strain of S. enterica that carried blaCTX-M-15 and blaPER-1 genes compared with those presenting blaCTX-M-15/blaTEM-169 or blaCTX-M-15/blaTEM-1 genotypes. CONCLUSIONS The results show dissemination of ESBLs encoding genes and their combined activity among different serovars of S. enterica that are a threat for future treatment options.
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Affiliation(s)
- Mercedeh Tajbakhsh
- a Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences , Tehran , Iran ;,b Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Mohammad Yaghoobi Avini
- a Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Jahan Alikhajeh
- c Department of Physiology and Cellular Biophysics , Columbia University Medical Center , New York , NY , USA
| | - Elahe Tajeddin
- a Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Mohammad Rahbar
- d Department of Microbiology , Iranian Reference Health Laboratory Research Center, Ministry of Health and Medical Education , Tehran , Iran ;,e Department of Microbiology , Central Laboratory, Milad Hospital , Tehran , Iran
| | - Parisa Eslami
- e Department of Microbiology , Central Laboratory, Milad Hospital , Tehran , Iran
| | - Masoud Alebouyeh
- a Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences , Tehran , Iran ;,b Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Mohammad Reza Zali
- a Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences , Tehran , Iran ;,b Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences , Tehran , Iran
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