Biology subjects

von Mentzer, A.

Publications and source records attributed to von Mentzer, A..

3 recordsLinked to original sources

bioRxiv2023

Construction of the ETECFinder database for the characterisation of enterotoxigenic Escherichia coli (ETEC) and revision of the VirulenceFinder webtool at the CGE website

The identification of pathogens is essential for effective surveillance and outbreak detection, which has been facilitated by the decreasing cost of whole-genome sequencing (WGS). However, extracting relevant virulence genes from WGS data remains a challenge. In this study, we developed a web-based tool to predict virulence-associated genes in enterotoxigenic Escherichia coli (ETEC), including heat-labile toxin (LT) genes (eltA and eltB), heat-stable enterotoxin (ST) genes (est) for both human and animal, enterotoxin (espC), colonization factors CS1 through 30, F4, F5, F6, F17, F18, and F41, and toxigenic invasion and adherence loci (tia, tibAC, etpBAC, eatA, yghJ, and tleA). To construct the database, we revised the existing ETEC nomenclature and used the VirulenceFinder webtool at the CGE website (https://cge.cbs.dtu.dk/services/VirulenceFinder/). The database was tested on 1,083 preassembled ETEC genomes and the ETEC reference sequence for strain H10407. We added 455 new alleles, replaced or renamed 50 alleles, and removed two. Overall, our tool has the potential to greatly facilitate ETEC identification and improve the accuracy of WGS analysis. The revised nomenclature and expanded gene repertoire provide a better understanding of the genetic diversity of ETEC. Additionally, the user-friendly interface makes it accessible to users with limited bioinformatics experience.

microbiology↗

bioRxiv2023

Circulation of enterotoxigenic Escherichia coli (ETEC) isolates expressing CS23 from the environment to clinical settings

Enterotoxigenic Escherichia coli (ETEC) is one of the leading causes of infant diarrhea in low- and middle-income countries (LMICs). Diarrheal pathogens are transmitted through environmental reservoirs; however, the bacterial clones that spread across the human-environment interphases remind unexplored. We aimed to determine the relationship and clonal dissemination of ETEC between children with diarrhea (> 5 years of age) and polluted water samples from local river in La Paz, Bolivia. Our study used whole genome sequencing and phenotypic fingerprinting system (PhenePlates) to analyze ETEC strains. We showed that ST218 and ST410 LT+STh CS23 ETEC were found with high frequency in both samples. The CS23 ETEC isolates were found within several STs, E. coli phylogroups A, B1, C, and D, and across ETEC lineages. Our comparative genomic analysis and PhenePlate screening of globally distributed clinical ETEC strains suggested that virulent CS23 plasmids acquisition occurs independently of the bacterial chromosomal background. Environmental strains were more often multidrug-resistant (MDR) than clinical isolates and harbored the class 1 integron-integrase gene intI1 next to the MDR cassettes. Retrospective analysis of antibiotic resistance in ETEC revealed a high frequency of MDR in clinical isolates. The LT+STh CS23 ETEC isolates showed an increased biofilm ability at environmental temperature, equal cytotoxicity, and significantly lower adherence to human epithelial cells compared to ETEC expressing other CFs. Together, our findings suggest that CS23 is more prevalent in ETEC than previously estimated, and the Choqueyapu River is a reservoir for LT+STh CS23 ETEC containing strains capable of causing diarrheal cases in children. ImportanceThe importance of clean water cannot be overstated. It is a vital resource for maintaining health and well-being. Unfortunately, water sources contaminated with fecal discharges from animal and human origin due to a lack of wastewater management poses a significant risk to communities, as they can become a means of transmission pathogenic bacteria like enterotoxigenic E. coli (ETEC). ETEC is frequently found in polluted water in countries with a high prevalence of diarrheal diseases, such as Bolivia. This study provides novel insights into the circulation of ETEC between diarrheal cases and polluted water sources in areas with high rates of diarrheal disease. The findings highlight the Choqueyapu River as a potential reservoir for emerging pathogens carrying antibiotic-resistance genes, making it a crucial area for monitoring and intervention. Furthermore, the results demonstrate the feasibility of a low-cost, high-throughput method for tracking bacterial pathogens in low- and middle-income countries, making it a valuable tool for One Health monitoring efforts.

microbiology↗

bioRxiv2020

Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time

BackgroundEnterotoxigenic Escherichia coli (ETEC) is an enteric pathogen responsible for the majority of diarrheal cases worldwide. ETEC infections are estimated to cause 80,000 fatalities per year, with the highest rates of burden, ca 75 million cases per year, amongst children under five years of age in resource-poor countries. It is also the leading cause of diarrhoea in travellers. Previous large-scale sequencing studies have found seven major ETEC lineages currently in circulation worldwide. ResultsWe used PacBio long-read sequencing combined with Illumina sequencing to create high-quality complete reference genomes for each of the major lineages with manually curated chromosomes and plasmids. The plasmids carrying ETEC virulence genes were compared to other available long-read sequenced ETEC strains using blastn. The ETEC reference strains harbour between two and five plasmids, including virulence, antibiotic resistance and phage-plasmids. The virulence plasmids carrying the colonisation factors are highly conserved as shown by comparison with plasmids with other ETEC strains and confirm that the plasmids and chromosomes of ETEC are both crucial for ETEC virulence and success as pathogens. ConclusionWe confirm that the major ETEC lineages all harbour conserved plasmids that have been associated with their respective background genomes for decades. The in-depth analysis of gene content, synteny and correct annotations of plasmids will elucidate other plasmids with and without virulence factors in related bacterial species. These reference genomes allow for fast and accurate comparison between different ETEC strains, and these data will form the foundation of ETEC genomics research for years to come.

genomics↗