Identification of Gram negative non-fermentative bacteria: How hard can it be?
INTRODUCTION:The prevalence of bacteremia caused by Gram negative non-fermentative (GNNF) bacteria has been increasing globally over the past decade. Many studies have investigated their epidemiology but focus on the common GNNF including Pseudomonas aeruginosa and Acinetobacter baumannii. Knowledge...
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ftdoajarticles:oai:doaj.org/article:eb5c4f05083740dbb37fc01c68611f2b 2023-05-15T15:11:58+02:00 Identification of Gram negative non-fermentative bacteria: How hard can it be? Toni Whistler Ornuma Sangwichian Possawat Jorakate Pongpun Sawatwong Uraiwan Surin Barameht Piralam Somsak Thamthitiwat Chidchanok Promkong Leonard Peruski 2019-09-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0007729 https://doaj.org/article/eb5c4f05083740dbb37fc01c68611f2b EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pntd.0007729 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0007729 https://doaj.org/article/eb5c4f05083740dbb37fc01c68611f2b PLoS Neglected Tropical Diseases, Vol 13, Iss 9, p e0007729 (2019) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2019 ftdoajarticles https://doi.org/10.1371/journal.pntd.0007729 2022-12-31T11:56:29Z INTRODUCTION:The prevalence of bacteremia caused by Gram negative non-fermentative (GNNF) bacteria has been increasing globally over the past decade. Many studies have investigated their epidemiology but focus on the common GNNF including Pseudomonas aeruginosa and Acinetobacter baumannii. Knowledge of the uncommon GNNF bacteremias is very limited. This study explores invasive bloodstream infection GNNF isolates that were initially unidentified after testing with standard microbiological techniques. All isolations were made during laboratory-based surveillance activities in two rural provinces of Thailand between 2006 and 2014. METHODS:A subset of GNNF clinical isolates (204/947), not identified by standard manual biochemical methodologies were run on the BD Phoenix automated identification and susceptibility testing system. If an organism was not identified (12/204) DNA was extracted for whole genome sequencing (WGS) on a MiSeq platform and data analysis performed using 3 web-based platforms: Taxonomer, CGE KmerFinder and One Codex. RESULTS:The BD Phoenix automated identification system recognized 92% (187/204) of the GNNF isolates, and because of their taxonomic complexity and high phenotypic similarity 37% (69/187) were only identified to the genus level. Five isolates grew too slowly for identification. Antimicrobial sensitivity (AST) data was not obtained for 93/187 (50%) identified isolates either because of their slow growth or their taxa were not in the AST database associated with the instrument. WGS identified the 12 remaining unknowns, four to genus level only. CONCLUSION:The GNNF bacteria are of increasing concern in the clinical setting, and our inability to identify these organisms and determine their AST profiles will impede treatment. Databases for automated identification systems and sequencing annotation need to be improved so that opportunistic organisms are better covered. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 13 9 e0007729 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
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Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Toni Whistler Ornuma Sangwichian Possawat Jorakate Pongpun Sawatwong Uraiwan Surin Barameht Piralam Somsak Thamthitiwat Chidchanok Promkong Leonard Peruski Identification of Gram negative non-fermentative bacteria: How hard can it be? |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
INTRODUCTION:The prevalence of bacteremia caused by Gram negative non-fermentative (GNNF) bacteria has been increasing globally over the past decade. Many studies have investigated their epidemiology but focus on the common GNNF including Pseudomonas aeruginosa and Acinetobacter baumannii. Knowledge of the uncommon GNNF bacteremias is very limited. This study explores invasive bloodstream infection GNNF isolates that were initially unidentified after testing with standard microbiological techniques. All isolations were made during laboratory-based surveillance activities in two rural provinces of Thailand between 2006 and 2014. METHODS:A subset of GNNF clinical isolates (204/947), not identified by standard manual biochemical methodologies were run on the BD Phoenix automated identification and susceptibility testing system. If an organism was not identified (12/204) DNA was extracted for whole genome sequencing (WGS) on a MiSeq platform and data analysis performed using 3 web-based platforms: Taxonomer, CGE KmerFinder and One Codex. RESULTS:The BD Phoenix automated identification system recognized 92% (187/204) of the GNNF isolates, and because of their taxonomic complexity and high phenotypic similarity 37% (69/187) were only identified to the genus level. Five isolates grew too slowly for identification. Antimicrobial sensitivity (AST) data was not obtained for 93/187 (50%) identified isolates either because of their slow growth or their taxa were not in the AST database associated with the instrument. WGS identified the 12 remaining unknowns, four to genus level only. CONCLUSION:The GNNF bacteria are of increasing concern in the clinical setting, and our inability to identify these organisms and determine their AST profiles will impede treatment. Databases for automated identification systems and sequencing annotation need to be improved so that opportunistic organisms are better covered. |
format |
Article in Journal/Newspaper |
author |
Toni Whistler Ornuma Sangwichian Possawat Jorakate Pongpun Sawatwong Uraiwan Surin Barameht Piralam Somsak Thamthitiwat Chidchanok Promkong Leonard Peruski |
author_facet |
Toni Whistler Ornuma Sangwichian Possawat Jorakate Pongpun Sawatwong Uraiwan Surin Barameht Piralam Somsak Thamthitiwat Chidchanok Promkong Leonard Peruski |
author_sort |
Toni Whistler |
title |
Identification of Gram negative non-fermentative bacteria: How hard can it be? |
title_short |
Identification of Gram negative non-fermentative bacteria: How hard can it be? |
title_full |
Identification of Gram negative non-fermentative bacteria: How hard can it be? |
title_fullStr |
Identification of Gram negative non-fermentative bacteria: How hard can it be? |
title_full_unstemmed |
Identification of Gram negative non-fermentative bacteria: How hard can it be? |
title_sort |
identification of gram negative non-fermentative bacteria: how hard can it be? |
publisher |
Public Library of Science (PLoS) |
publishDate |
2019 |
url |
https://doi.org/10.1371/journal.pntd.0007729 https://doaj.org/article/eb5c4f05083740dbb37fc01c68611f2b |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 13, Iss 9, p e0007729 (2019) |
op_relation |
https://doi.org/10.1371/journal.pntd.0007729 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0007729 https://doaj.org/article/eb5c4f05083740dbb37fc01c68611f2b |
op_doi |
https://doi.org/10.1371/journal.pntd.0007729 |
container_title |
PLOS Neglected Tropical Diseases |
container_volume |
13 |
container_issue |
9 |
container_start_page |
e0007729 |
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1766342738347819008 |