Diversity of Achromobacter species recovered from patients with cystic fibrosis, in Argentina

Papalia, Mariana Andrea; Steffanowski, Carla; Traglia, Germán Matías; Almuzara, Marisa; Martina, Pablo; Galanternik, L.; Vay, Carlos; Gutkind, Gabriel; Ramírez, María Soledad; Radice, Marcela

doi:10.1016/j.ram.2019.03.004

“…The Ac-Ax assay also has the advantage of simultaneous detection of both Achromobacter sp. and A. xylosoxidans , unlike most existing methods that only detect A. xylosoxidans , meaning that ∼50% of Achromobacter CF infections are undiagnosed with these methods (4, 10-12).…”

Section: Discussionmentioning

confidence: 99%

“…Although several Achromobacter species can infect CF airways (9), Achromobacter xylosoxidans is the most common, comprising ∼42-65% of all Achromobacter spp. identified in CF respiratory secretions (4, 10-12). Up until recently, the role of Achromobacter spp.…”

Section: Introductionmentioning

confidence: 99%

Duplex real-time PCR assay for the simultaneous detection ofAchromobacter xylosoxidansandAchromobacterspp

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Arango

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23Several members of the Gram-negative environmental bacterial genus, Achromobacter, are 24 associated with serious infections in immunocompromised individuals, of which 25Achromobacter xylosoxidans is the most common. Despite their pathogenic potential, 26comparatively little is understood about these intrinsically drug-resistant bacteria and their role 27 in disease, leading to suboptimal diagnosis and management of Achromobacter infections. 28Here, we performed comparative genomics of 158 Achromobacter spp. genomes to robustly 29 identify species boundaries, to reassign several incorrectly speciated taxa, and to identify 30 genetic sequences specific for the Achromobacter genus and for A. xylosoxidans. Next, we 31 developed a Black Hole Quencher probe-based duplex real-time PCR assay, Ac-Ax, for the 32 rapid and simultaneous detection of Achromobacter spp. and A. xylosoxidans from both 33 purified colonies and polymicrobial clinical specimens. Ac-Ax was tested on 119 isolates 34 identified as Achromobacter spp. using phenotypic or genotypic methods. In comparison to 35 these routine diagnostic methods, the duplex assay showed superior identification of 36 Achromobacter spp. and A. xylosoxidans, with five Achromobacter isolates failing to amplify 37with Ac-Ax confirmed to be different genera according to 16S rRNA gene sequencing. Ac-Ax 38 quantified both Achromobacter spp. and A. xylosoxidans down to ~110 genome equivalents, 39 and detected down to ~12 and ~1 genome equivalent/s, respectively. In silico analysis, and 40 laboratory testing of 34 non-Achromobacter isolates and 38 adult CF sputa, confirmed duplex 41 assay specificity and sensitivity. We demonstrate that the Ac-Ax duplex assay provides a 42 robust, sensitive, and cost-effective method for the simultaneous detection of all 43Achromobacter spp. and A. xylosoxidans, and will facilitate the rapid and accurate diagnosis 44 of this important group of pathogens. 45

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“…Other notable but less abundant CR soil isolates included Enterococcus gallinarum , which is associated with nosocomial‐ and community‐acquired bacteremia and other infections (Narciso‐Schiavon et al, 2015; Quinones, Goni, Rubio, Duran, & Gomez‐Lus, 2005; Reid, Cockerill, & Patel, 2001; Schouten, Voss, & Hoogkamp‐Korstanje, 1999); Enterococcus durans , an infrequent human pathogen mostly associated with diarrhea in piglets and calves (Cheon & Chae, 1996; Quinones et al, 2005; Rogers, Zeman, & Erickson, 1992; Schouten et al, 1999); Achromobacter marplatensis, a soil microbe that has also been found in cystic fibrosis patients (Gomila et al, 2011; Papalia et al, 2019); Bradyrhizobium elkanii, a soil bacterium and legume symbiont used commercially as an inoculant to improve the growth of legume plants (Crovadore et al, 2016; Faruque et al, 2015; Hungria, Delamuta, Ribeiro, & Nogueira, 2019); and Planomicrobium glaciei , an infrequently isolated bacterium, first found in a glacier and later in food (Tshipamba, Lubanza, Adetunji, & Mwanza, 2018; Zhang et al, 2009). Finding these isolates is significant for several reasons.…”

Section: Discussionmentioning

confidence: 99%

Urban and agricultural soils in Southern California are a reservoir of carbapenem‐resistant bacteria

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Farsar

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Harmon

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et al. 2020

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Carbapenems are last‐resort β‐lactam antibiotics used in healthcare facilities to treat multidrug‐resistant infections. Thus, most studies on identifying and characterizing carbapenem‐resistant bacteria (CRB) have focused on clinical settings. Relatively, little is still known about the distribution and characteristics of CRBs in the environment, and the role of soil as a potential reservoir of CRB in the United States remains unknown. Here, we have surveyed 11 soil samples from 9 different urban or agricultural locations in the Los Angeles–Southern California area to determine the prevalence and characteristics of CRB in these soils. All samples tested contained CRB with a frequency of <10 to 1.3 × 104 cfu per gram of soil, with most agricultural soil samples having a much higher relative frequency of CRB than urban soil samples. Identification and characterization of 40 CRB from these soil samples revealed that most of them were members of the genera Cupriavidus, Pseudomonas, and Stenotrophomonas. Other less prevalent genera identified among our isolated CRB, especially from agricultural soils, included the genera Enterococcus, Bradyrhizobium, Achromobacter, and Planomicrobium. Interestingly, all of these carbapenem‐resistant isolates were also intermediate or resistant to at least 1 noncarbapenem antibiotic. Further characterization of our isolated CRB revealed that 11 Stenotrophomonas, 3 Pseudomonas, 1 Enterococcus, and 1 Bradyrhizobium isolates were carbapenemase producers. Our findings show for the first time that both urban and agricultural soils in Southern California are an underappreciated reservoir of bacteria resistant to carbapenems and other antibiotics, including carbapenemase‐producing CRB.

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“…Although several Achromobacter species can infect CF airways [12], Achromobacter xylosoxidans is the most common, comprising ~42-65 % of all Achromobacter spp. identified in CF respiratory secretions [4,[17][18][19]. Until recently, the role of Achromobacter spp.…”

mentioning

confidence: 99%

“…and A. xylosoxidans. In contrast, most existing methods only detect A. xylosoxidans, meaning that ~50% of Achromobacter CF infections remain undiagnosed with these methods[4,[17][18][19].The Ac-Ax assay is highly accurate, with no false-positives or false-negatives identified according to in silico analysis of all microbes present in the NCBI Microbes database, or via laboratory testing of several clinically important species. Indeed, our initial in silico blast analysis of Ac and Ax targets resolved incorrect species assignments in two publicly available genomes: B. bronchiseptica KU1201 (actually Achromobacter sp.)…”

mentioning

confidence: 99%

Duplex real-time PCR assay for the simultaneous detection of Achromobacter xylosoxidans and Achromobacter spp.

Price

¹

,

Arango

²

,

Kidd

³

et al. 2020

View full text Add to dashboard Cite

Several members of the Gram-negative environmental bacterial genus Achromobacter are associated with serious infections, with Achromobacter xylosoxidans being the most common. Despite their pathogenic potential, little is understood about these intrinsically drug-resistant bacteria and their role in disease, leading to suboptimal diagnosis and management. Here, we performed comparative genomics for 158 Achromobacter spp. genomes to robustly identify species boundaries, reassign several incorrectly speciated taxa and identify genetic sequences specific for the genus Achromobacter and for A. xylosoxidans . Next, we developed a Black Hole Quencher probe-based duplex real-time PCR assay, Ac-Ax, for the rapid and simultaneous detection of Achromobacter spp. and A. xylosoxidans from both purified colonies and polymicrobial clinical specimens. Ac-Ax was tested on 119 isolates identified as Achromobacter spp. using phenotypic or genotypic methods. In comparison to these routine diagnostic methods, the duplex assay showed superior identification of Achromobacter spp. and A. xylosoxidans , with five Achromobacter isolates failing to amplify with Ac-Ax confirmed to be different genera according to 16S rRNA gene sequencing. Ac-Ax quantified both Achromobacter spp. and A. xylosoxidans down to ~110 genome equivalents and detected down to ~12 and ~1 genome equivalent(s), respectively. Extensive in silico analysis, and laboratory testing of 34 non- Achromobacter isolates and 38 adult cystic fibrosis sputa, confirmed duplex assay specificity and sensitivity. We demonstrate that the Ac-Ax duplex assay provides a robust, sensitive and cost-effective method for the simultaneous detection of all Achromobacter spp. and A. xylosoxidans and will facilitate the rapid and accurate diagnosis of this important group of pathogens.

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Diversity of Achromobacter species recovered from patients with cystic fibrosis, in Argentina

Cited by 24 publications

References 21 publications

Duplex real-time PCR assay for the simultaneous detection ofAchromobacter xylosoxidansandAchromobacterspp

Duplex real-time PCR assay for the simultaneous detection ofAchromobacter xylosoxidansandAchromobacterspp

Urban and agricultural soils in Southern California are a reservoir of carbapenem‐resistant bacteria

Duplex real-time PCR assay for the simultaneous detection of Achromobacter xylosoxidans and Achromobacter spp.

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