Цитробактер браакии

Цитробактер браакии

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ABSTRACT

Citrobacter braakii and Citrobacter freundii are Gram-negative opportunistic pathogens associated with many infectious diseases, including septicemia, in humans and animals. Here, we report the draft genome sequences of seven C. braakii strains and one C. freundii strain isolated from Canadian wastewater treatment facilities.

ANNOUNCEMENT

Citrobacter braakii and Citrobacter freundii , two of the 15 species in the genus Citrobacter , are Gram-negative coliform bacteria in the Enterobacteriaceae family (http://www.bacterio.net/citrobacter.html). They can be found in soil, water, sewage, and the intestinal tracts of animals and humans. They are opportunistic pathogens, causing infections of the urinary, gastrointestinal, and pulmonary systems, as well as blood infections, often nosocomial in nature; they are a major cause of neonatal meningitis (1, 2). Citrobacter freundii generally exhibits high antimicrobial resistance to penicillin and third-generation cephalosporins (3), which harbor a β-lactam ring.

This article reports the draft genome sequences of seven C. braakii strains and one C. freundii strain isolated from pre- or posttreated samples collected at three Canadian wastewater treatment facilities. Strains HH1, HH5, HH6, HH8, HH10, and HH11 were isolated using a Compendium of analytical methods of Health Canada method (MFHPB-19) (4) for the isolation of Escherichia coli . Strains HH7 and HH9 were isolated using a Compendium of analytical methods of Health Canada method (MFLP-75) (5) for the isolation of Salmonella species. All isolates were confirmed to be Citrobacter at the genus level by a combination of the API 20E biochemical test (bioMérieux, Canada, Inc.), Biolog (carbohydrate analysis), and Sherlock (fatty acid analysis) (Midi, Inc., Newark, DE, USA) microbial identification systems (Table 1). The isolates were further identified as C. braakii or C. freundii by the API 20E test. Species identifications were confirmed by comparing the draft genome sequences reported here (Table 1) with the reference genome of each species.

Sequencing and assembly metrics for the strains used in this study

Isolates were kept at −80°C in tryptic soy broth with 25% glycerol before sequencing. Genomic DNA was extracted from overnight cultures grown at 37°C on tryptic soy agar using the DNeasy blood and tissue DNA purification kit (catalog number 69504; Qiagen, Inc., Toronto, Ontario, Canada) and quantified using a Qubit 3.0 fluorometer (Life Technologies). Sequencing libraries were constructed using Nextera XT DNA sample preparation kits (Illumina, Inc., San Diego, CA), and the quality of libraries was analyzed using a Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced with a MiSeq platform (Illumina, Inc.) using 300-bp v3 reagent kits.

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Sequencing adapter sequences and low-quality bases were trimmed (BBduk), and overlapping pairs were merged (BBMerge) using the BBTools v37.68 software suite (https://jgi.doe.gov/data-and-tools/bbtools/). The remaining reads were then assembled de novo with Unicycler v0.4.4 (6) running SPAdes v3.11.1 (7) and then polished with Pilon v1.22 (8). Other programs used by Unicycler were BLAST v2.7.1+ (9), Bowtie 2 v2.3.4 (10), and SAMtools v1.6 (11). The parameters used for each step of the assembly pipeline are detailed at https://github.com/duceppemo/bacteria_genome_assembly. Gene predictions and annotations were performed using the NCBI Prokaryotic Genome Annotation Pipeline (12). Sequencing and assembly metrics are summarized in Table 1. Antimicrobial resistance genes were detected using ResFinder v3.1.0 (13), with default parameters.

The median total length, protein count (number of coding sequences [CDS]), and GC content of the C. braakii genome assemblies in the NCBI are 5.1 Mb, 4,822, and 52.1%, respectively. Similarly, the median values of the seven C. braakii strains presented here are 5.1 Mb, 4,672, and 52.0%, respectively. The median total length, protein count (number of CDS), and GC content of the C. freundii genome assemblies on NCBI are 5.3 Mb, 4,991, and 51.7%, respectively, which are similar to those (5.499 Mb, 5,396, and 51.7%, respectively) of the C. freundii strain analyzed in this study (Table 1). All isolates were predicted to be resistant to β-lactam antibiotics.

Data availability. This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers PQWA00000000, SJSJ00000000, SJSI00000000, SJSH00000000, SJSG00000000, SJSF00000000, SJSE00000000, and SJSD00000000 for strains HH1, HH5, HH6, HH7, HH8, HH9, HH10, and HH11, respectively. The versions described in this paper are versions PQWA01000000, SJSJ01000000, SJSI01000000, SJSH01000000, SJSG01000000, SJSF01000000, SJSE01000000, and SJSD01000000, respectively. The Illumina raw sequencing reads are available in the NCBI Sequence Read Archive through the accession numbers found in Table 1.

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ACKNOWLEDGMENTS

This work was funded by the Canadian Food Inspection Agency.

We thank Stephan Brière at the Ottawa Laboratory – Fallowfield, Canadian Food Inspection Agency, for conducting tests using the Biolog and Sherlock microbial identification systems.

FOOTNOTES

    • Received 8 March 2019.
    • Accepted 4 June 2019.
    • Published 3 July 2019.
  • © Crown copyright 2019.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Affiliation

  • 1 Texas Tech University Health Sciences Center and Paul F. Foster School of Medicine, El Paso Texas, 1205 Oregon, El Paso, Texas 79902, TX. United States.
  • PMID: 27658860
  • DOI: 10.2174/1871526516666161005155847
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Authors

Affiliation

  • 1 Texas Tech University Health Sciences Center and Paul F. Foster School of Medicine, El Paso Texas, 1205 Oregon, El Paso, Texas 79902, TX. United States.
  • PMID: 27658860
  • DOI: 10.2174/1871526516666161005155847

Abstract

Bacteremia is frequently caused by gram-positive organisms such as Staphylococcus aureus or β hemolytic streptococci. While there is adequate information for the diagnosis and management of these common bacteria, less information is available to address bacteremia that is caused by uncommon bacteria such as Citrobacter. Citrobacter species are gram-negative bacilli that have been noted to cause infections in immune compromised patients. The re-speciation of Citrobacter by its varied genetic composition has produced 11 distinct species. While C. braakii is part of the genome species 6 of the previous Citrobacter freundii complex, there is a lack of definitive research on the subject of Citrobacter bacteremia caused by lesser- known species. We report an unusual case of Citrobacter braakii bacteremia in a patient with multiple comorbidities that presented to the hospital with cellulitis and pleural effusion. Blood cultures grew Citrobacter braakii. Despite good response to antibiotic treatment, the patient’s infection proved to be persistent and he succumbed to the cirrhosis of the liver and subsequent renal failure. Multiple and fatal underlying disease processes seem to worsen the likelihood of recovery from unusual infections. We believe our case report can add to the limited data available for C. braakii.

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Keywords: Bacteremia; antibiotic treatment; citrobacter braaki; gram-negative; gram-positive organisms; staphylococcus.

Type strain:

Species: Citrobacter braakii

Strain Designation: 167

Culture col. no.: DSM 17596, ATCC 51113, CCUG 30792, CDC 80-58, CIP 104554

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[Ref.: #7079] Sample type/isolated from snake
[Ref.: #7079] Country France
[Ref.: #7079] Country ISO 3 Code FRA
[Ref.: #7079] Continent Europe
[Ref.: #50272] Sample type/isolated from Snake
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[Ref.: #20218] Marker Gene (DDBJ Direct submission) Citrobacter braakii DNA, psp gene cluster, sap gene cluster, partial sequence, strain: ATCC 51113 AB734053
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[Ref.: #7079] Culture collection no. DSM 17596, ATCC 51113, CCUG 30792, CDC 80-58, CIP 104554
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