Whole-genome analysis and description of an outbreak due to carbapenem-resistant Ochrobactrum anthropi causing pseudo-bacteraemias

Montaña, Sabrina; Fernandez, Jennifer S.; Barenboim, Maxim; Hernandez, Marlene; Kayriyama, C.; Carulla, Mariana; Iriarte, Andrés; Ramírez, María Soledad; Almuzara, Marisa

doi:10.1016/j.nmni.2018.09.002

Cited by 5 publications

(5 citation statements)

References 29 publications

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“…1; also, see Table S2). The genera Pseudomonas, Stenotrophomonas, Acinetobacter, Algoriphagus, Alteromonas, Brevundimonas, Caulobacter, Chryseobacterium, Empedobacter, Sphingomonas, Sphingopyxis, Pseudoxanthomonas, Flavobacterium, Cupriavidus, Myroides, Ochrobactrum, Pedobacter, Phenylobacterium, and Rhizobium, for which we found isolates with resistance, have already been described to have CR (5,17,(34)(35)(36)(37)(38)(39)(40)(41)(42)(43). In contrast, the genera Chromobacterium, Rheinheimera, Variovorax, Aquiflexum, Chitinophaga, Herbaspirillum, and Xanthobacter were not known to contain CR at the time of isolation.…”

Section: Resultssupporting

confidence: 58%

Diversity and Genetic Basis for Carbapenem Resistance in a Coastal Marine Environment

Dewi

Götz

Thomas

2020

Appl Environ Microbiol

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Resistance to the “last-resort” antibiotics, such as carbapenems, has led to very few antibiotics being left to treat infections by multidrug-resistant bacteria. Spread of carbapenem resistance (CR) has been well characterized for the clinical environment. However, there is a lack of information about its environmental distribution. Our study reveals that CR is present in a wide range of Gram-negative bacteria in the coastal seawater environment, including four phyla, eight classes, and 30 genera. These bacteria were likely introduced into seawater via stormwater flows. Some CR isolates found here, such as Acinetobacter junii, Acinetobacter johnsonii, Brevundimonas vesicularis, Enterococcus durans, Pseudomonas monteilii, Pseudomonas fulva, and Stenotrophomonas maltophilia, are further relevant to human health. We also describe a novel metallo-β-lactamase (MBL) for marine Rheinheimera isolates with CR, which has likely been horizontally transferred to Citrobacter freundii or Enterobacter cloacae. In contrast, another MBL of the New Delhi type was likely acquired by environmental Variovorax isolates from Escherichia coli, Klebsiella pneumoniae, or Acinetobacter baumannii utilizing a plasmid. Our findings add to the growing body of evidence that the aquatic environment is both a reservoir and a vector for novel CR genes. IMPORTANCE Resistance against the “last-resort” antibiotics of the carbapenem family is often based on the production of carbapenemases, and this has been frequently observed in clinical samples. However, the dissemination of carbapenem resistance (CR) in the environment has been less well explored. Our study shows that CR is commonly found in a range of bacterial taxa in the coastal aquatic environment and can involve the exchange of novel metallo-β-lactamases from typical environmental bacteria to potential human pathogens or vice versa. The outcomes of this study contribute to a better understanding of how aquatic and marine bacteria can act as reservoirs and vectors for CR outside the clinical setting.

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Section: Resultssupporting

confidence: 58%

Diversity and Genetic Basis for Carbapenem Resistance in a Coastal Marine Environment

Dewi

Götz

Thomas

2020

Appl Environ Microbiol

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“…[ 13 ] Of note, the increased rate of females in the BLAL group, confirming a sexual dimorphism in antibiotic allergy, also suggests the effect of the genetic background. [ 14 , 15 ] A BLAL was found in only 11% of electronic medical files. This under-reporting could have participated to the low prevalence rate that we found.…”

Section: Discussionmentioning

confidence: 99%

Beta-lactam allergy labeling in intensive care units

et al. 2021

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This retrospective study aimed to describe the association between the “β-lactam allergy” labeling (BLAL) and the outcomes of a cohort of intensive care unit (ICU) patients. Retrospective cohort study. Seven ICU of the Aix Marseille University Hospitals from Marseille in France. We collected the uses of the label “β-lactam allergy” in the electronic medical files of patients aged 18 years or more who required more than 48 hours in the ICU with mechanical ventilation and/or vasopressors admitted to 7 ICUs of a single institution. We retrospectively compared the patients with this labeling (BLAL group) with those without this labeling (control group). The primary outcome was the duration of ICU stay. Among the 7146 patients included in the analysis, 440 and 6706 patients were classified in the BLAL group and the control group, respectively. The prevalence of BLAL was 6.2%. In univariate and multivariate analyses, BLAL was weakly or not associated with the duration of ICU and hospital stays (respectively, 6 [3–14] vs 6 [3–14] days, standardized beta −0.09, P = .046; and 18 [10–29] vs 15 [8–28] days, standardized beta −0.09, P = .344). In multivariate analysis, the ICU and 28-day mortality rates were both lower in the BLAL group than in the control group (aOR 0.79 95% CI [0.64–0.98] P = .032 and 0.79 [0.63–0.99] P = .042). Antibiotic use differed between the 2 groups, but the outcomes were similar in the subgroups of septic patients in the BLAL group and the control group. In our cohort, the labeling of a β-lactam allergy was not associated with prolonged ICU and hospital stays. An association was found between the labeling of a β-lactam allergy and lower ICU and 28-day mortality rates. Trial registration: Retrospectively registered.

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“…This mirrors the nearly universal resistance of these antimicrobial groups reported in the literature; all isolates reviewed were also resistant to the majority of β-lactams as well as β-lactam inhibitors, thus exhibiting an AmpC-like phenotype. Regarding carbapenems, our isolates, as well as the majority of reported isolates, showed low MIC values for this group (100% and 71%, respectively), apart from a unique cluster of carbapenem-resistant isolates in a "pseudo-bacteremia" event described in a single study [20]. Resistance to aminoglycosides appeared variable, with a median MIC value for gentamicin of 4 µg/mL (range 0.256-256) in 104 reported isolates.…”

Section: Phenotypic Datamentioning

confidence: 62%

“…The antimicrobial susceptibility testing results for our five Ochrobactrum isolates are presented in Table 2. We reviewed the literature for studies describing phenotypic susceptibility patterns and found minimal inhibitory concentration (MIC) data for various antimicrobials for a total of 114 isolates [17][18][19][20]22]; the MIC ranges and medians are summarized in Table 2. All five isolates were resistant to both penicillins and cephalosporins (MICs ≥ 32µg/mL).…”

Section: Phenotypic Datamentioning

confidence: 99%

Genomic Characterization of Antimicrobial Resistance, Virulence, and Phylogeny of the Genus Ochrobactrum

et al. 2020

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Ochrobactrum is a ubiquitous Gram-negative microorganism, mostly found in the environment, which can cause opportunistic infections in humans. It is almost uniformly resistant to penicillins and cephalosporins through an AmpC-like β-lactamase enzyme class (OCH). We studied 130 assembled genomes, of which 5 were animal-derived isolates recovered in Israel, and 125 publicly available genomes. Our analysis focused on antimicrobial resistance (AMR) genes, virulence genes, and whole-genome phylogeny. We found that 76% of Ochrobactrum genomes harbored a blaOCH β-lactamase gene variant, while 7% harbored another AmpC-like gene. No virulence genes other than lipopolysaccharide-associated genes were found. Core genome multilocus sequence typing clustered most samples to known species, but neither geographical clustering nor isolation source clustering were evident. When analyzing the distribution of different blaOCH variants as well as of the blaOCH-deficient samples, a clear phylogenomic clustering was apparent for specific species. The current analysis of the largest collection to date of Ochrobactrum genomes sheds light on the resistome, virulome, phylogeny, and species classification of this increasingly reported human pathogen. Our findings also suggest that Ochrobactrum deserves further characterization to underpin its evolution, taxonomy, and antimicrobial resistance.

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Whole-genome analysis and description of an outbreak due to carbapenem-resistant Ochrobactrum anthropi causing pseudo-bacteraemias

Cited by 5 publications

References 29 publications

Diversity and Genetic Basis for Carbapenem Resistance in a Coastal Marine Environment

Diversity and Genetic Basis for Carbapenem Resistance in a Coastal Marine Environment

Beta-lactam allergy labeling in intensive care units

Genomic Characterization of Antimicrobial Resistance, Virulence, and Phylogeny of the Genus Ochrobactrum

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