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...

Descripción completa

Detalles Bibliográficos
Autores principales: Gudra, Dita, Silamikelis, Ivars, Pjalkovskis, Janis, Danenberga, Ilva, Pupola, Darta, Skenders, Girts, Ustinova, Maija, Megnis, Kaspars, Leja, Marcis, Vangravs, Reinis, Fridmanis, Davids
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