Cargando…
Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori
The spread of extended-spectrum beta-lactamases (ESBLs) in nosocomial and community-acquired enterobacteria is an important challenge for clinicians due to the limited therapeutic options for infections that are caused by these organisms. Here, we developed a panel of ESBL coding genes, evaluated th...
Autores principales: | , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10414638/ https://www.ncbi.nlm.nih.gov/pubmed/37561723 http://dx.doi.org/10.1371/journal.pone.0289879 |
_version_ | 1785087384328601600 |
---|---|
author | Gudra, Dita Silamikelis, Ivars Pjalkovskis, Janis Danenberga, Ilva Pupola, Darta Skenders, Girts Ustinova, Maija Megnis, Kaspars Leja, Marcis Vangravs, Reinis Fridmanis, Davids |
author_facet | Gudra, Dita Silamikelis, Ivars Pjalkovskis, Janis Danenberga, Ilva Pupola, Darta Skenders, Girts Ustinova, Maija Megnis, Kaspars Leja, Marcis Vangravs, Reinis Fridmanis, Davids |
author_sort | Gudra, Dita |
collection | PubMed |
description | The spread of extended-spectrum beta-lactamases (ESBLs) in nosocomial and community-acquired enterobacteria is an important challenge for clinicians due to the limited therapeutic options for infections that are caused by these organisms. Here, we developed a panel of ESBL coding genes, evaluated the abundance and prevalence of ESBL encoding genes in patients undergoing H. pylori eradication therapy, and summarized the effects of eradication therapy on functional profiles of the gut microbiome. To assess the repertoire of known beta lactamase (BL) genes, they were divided into clusters according to their evolutionary relation. Primers were designed for amplification of cluster marker regions, and the efficiency of this amplification panel was assessed in 120 fecal samples acquired from 60 patients undergoing H. pylori eradication therapy. In addition, fecal samples from an additional 30 patients were used to validate the detection efficiency of the developed ESBL panel. The presence for majority of targeted clusters was confirmed by NGS of amplification products. Metagenomic sequencing revealed that the abundance of ESBL genes within the pool of microorganisms was very low. The global relative abundances of the ESBL-coding gene clusters did not differ significantly among treatment states. However, at the level of each cluster, classical ESBL producers such as Klebsiella sp. for bla(OXY) (p = 0.0076), Acinetobacter sp. for bla(ADC) (p = 0.02297) and others, differed significantly with a tendency to decrease compared to the pre- and post-eradication states. Only 13 clusters were common across all three datasets, suggesting a patient-specific distribution profile of ESBL-coding genes. The number of AMR genes detected in the post-eradication state was higher than that in the pre-eradication state, which could be attributed, at least in part, to the therapy. This study demonstrated that the ESBL screening panel was effective in targeting ESBL-coding gene clusters from bacterial DNA and that minor differences exist in the abundance and prevalence of ESBL-coding gene levels before and after eradication therapy. |
format | Online Article Text |
id | pubmed-10414638 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-104146382023-08-11 Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori Gudra, Dita Silamikelis, Ivars Pjalkovskis, Janis Danenberga, Ilva Pupola, Darta Skenders, Girts Ustinova, Maija Megnis, Kaspars Leja, Marcis Vangravs, Reinis Fridmanis, Davids PLoS One Research Article The spread of extended-spectrum beta-lactamases (ESBLs) in nosocomial and community-acquired enterobacteria is an important challenge for clinicians due to the limited therapeutic options for infections that are caused by these organisms. Here, we developed a panel of ESBL coding genes, evaluated the abundance and prevalence of ESBL encoding genes in patients undergoing H. pylori eradication therapy, and summarized the effects of eradication therapy on functional profiles of the gut microbiome. To assess the repertoire of known beta lactamase (BL) genes, they were divided into clusters according to their evolutionary relation. Primers were designed for amplification of cluster marker regions, and the efficiency of this amplification panel was assessed in 120 fecal samples acquired from 60 patients undergoing H. pylori eradication therapy. In addition, fecal samples from an additional 30 patients were used to validate the detection efficiency of the developed ESBL panel. The presence for majority of targeted clusters was confirmed by NGS of amplification products. Metagenomic sequencing revealed that the abundance of ESBL genes within the pool of microorganisms was very low. The global relative abundances of the ESBL-coding gene clusters did not differ significantly among treatment states. However, at the level of each cluster, classical ESBL producers such as Klebsiella sp. for bla(OXY) (p = 0.0076), Acinetobacter sp. for bla(ADC) (p = 0.02297) and others, differed significantly with a tendency to decrease compared to the pre- and post-eradication states. Only 13 clusters were common across all three datasets, suggesting a patient-specific distribution profile of ESBL-coding genes. The number of AMR genes detected in the post-eradication state was higher than that in the pre-eradication state, which could be attributed, at least in part, to the therapy. This study demonstrated that the ESBL screening panel was effective in targeting ESBL-coding gene clusters from bacterial DNA and that minor differences exist in the abundance and prevalence of ESBL-coding gene levels before and after eradication therapy. Public Library of Science 2023-08-10 /pmc/articles/PMC10414638/ /pubmed/37561723 http://dx.doi.org/10.1371/journal.pone.0289879 Text en © 2023 Gudra et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Gudra, Dita Silamikelis, Ivars Pjalkovskis, Janis Danenberga, Ilva Pupola, Darta Skenders, Girts Ustinova, Maija Megnis, Kaspars Leja, Marcis Vangravs, Reinis Fridmanis, Davids Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori |
title | Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori |
title_full | Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori |
title_fullStr | Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori |
title_full_unstemmed | Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori |
title_short | Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori |
title_sort | abundance and prevalence of esbl coding genes in patients undergoing first line eradication therapy for helicobacter pylori |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10414638/ https://www.ncbi.nlm.nih.gov/pubmed/37561723 http://dx.doi.org/10.1371/journal.pone.0289879 |
work_keys_str_mv | AT gudradita abundanceandprevalenceofesblcodinggenesinpatientsundergoingfirstlineeradicationtherapyforhelicobacterpylori AT silamikelisivars abundanceandprevalenceofesblcodinggenesinpatientsundergoingfirstlineeradicationtherapyforhelicobacterpylori AT pjalkovskisjanis abundanceandprevalenceofesblcodinggenesinpatientsundergoingfirstlineeradicationtherapyforhelicobacterpylori AT danenbergailva abundanceandprevalenceofesblcodinggenesinpatientsundergoingfirstlineeradicationtherapyforhelicobacterpylori AT pupoladarta abundanceandprevalenceofesblcodinggenesinpatientsundergoingfirstlineeradicationtherapyforhelicobacterpylori AT skendersgirts abundanceandprevalenceofesblcodinggenesinpatientsundergoingfirstlineeradicationtherapyforhelicobacterpylori AT ustinovamaija abundanceandprevalenceofesblcodinggenesinpatientsundergoingfirstlineeradicationtherapyforhelicobacterpylori AT megniskaspars abundanceandprevalenceofesblcodinggenesinpatientsundergoingfirstlineeradicationtherapyforhelicobacterpylori AT lejamarcis abundanceandprevalenceofesblcodinggenesinpatientsundergoingfirstlineeradicationtherapyforhelicobacterpylori AT vangravsreinis abundanceandprevalenceofesblcodinggenesinpatientsundergoingfirstlineeradicationtherapyforhelicobacterpylori AT fridmanisdavids abundanceandprevalenceofesblcodinggenesinpatientsundergoingfirstlineeradicationtherapyforhelicobacterpylori |