Characterization of a Multidrug-Resistant, Novel Bacteroides Genomospecies

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Technical Appendix

Stephen J. Salipante1, Aley Kalapila1, Paul S. Pottinger, Daniel R. Hoogestraat, Lisa Cummings, Jeffrey S. Duchin, Dhruba J. Sengupta, Steven A. Pergam, Brad T. Cookson, and Susan M. Butler-Wu

Author affiliations: University of Washington, Seattle, Washington, USA (S.J. Salipante, A. Kalapila, P.S. Pottinger, D.R. Hoogestraat, L. Cummings, J.S. Duchin, D.J. Sengupta, S.A. Pergam, B.T. Cookson, S.M. Butler-Wu); Fred Hutchinson Cancer Research Center, Seattle (A. Kalapila, S.A. Pergam)

Abstract

Metronidazole- and carbapenem-resistant Bacteroides fragilis are rare in the United States. We isolated a multidrug-resistant anaerobe from the bloodstream and intraabdominal abscesses of a patient who had traveled to India. Whole-genome sequencing identified the organism as a novel Bacteroides genomospecies. Physicians should be aware of the possibility for concomitant carbapenem- and metronidazole-resistantBacteroides infections.

We previously reported a 2013 case of intraabdominal abscesses and bacteremia caused by a multidrug-resistant anaerobe identified as Bacteroides fragilis (1). In brief, unremitting abdominal pain developed in a 71-year-old man who had been traveling in India for 1 month. The man was hospitalized locally and subsequently received a diagnosis of metastatic colon adenocarcinoma. He returned to Seattle, Washington, USA, for treatment consisting of 5 cycles of chemotherapy, followed by right hemicolectomy and right hepatectomy. On postoperative day 4, the patient showed marked leukocytosis, and abdominal abscesses were noted on computed tomographic scan images. Cultured percutaneous drainage fluid grew Escherichia coli that was resistant to ampicillin, trimethoprim/sulfamethoxazole, and fluoroquinolones. Therapy was then limited to ceftriaxone, and the patient’s leukocyte count continued to rise and fever returned. Blood cultures grew anaerobic gram-negative rods identified as B. fragilis by MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) mass spectrometry and 16S rRNA sequencing. New rim-enhancing fluid collections in the abdomen and pelvis were noted on computed tomographic scan images, and percutaneous drainage fluid from these collections grew 3+ (moderate) quantities of B. fragilis. Isolates from blood culture and abscess fluid were resistant to multiple classes of antimicrobial drugs, including metronidazole and imipenem (Table). The abscesses ultimately resolved after treatment for 60 days with linezolid and empiric ertapenem.

Thumbnail of Characterization of circular plot of genome diversity between the clinical isolate of a multidrug-resistant, novel Bacteroides genomospecies and other Bacteroides spp. isolates. Reading from the center outwards, the map, GC content, and GC skew of the B. fragilis reference strain 638R are depicted. The white and colored regions of the following outer rings indicate regions absent and present, respectively, in genomes of the indicated organism compared with the genome of B. fragilis

Figure. Characterization of circular plot of genome diversity between the clinical isolate of a multidrug-resistant, novel Bacteroidesgenomospecies and otherBacteroides spp. isolates. Reading from the center outwards, the map, GC content,...

Dr. Salipante is a laboratory medicine practitioner at the University of Washington, Seattle. His research interests are in the application of genomic technologies to clinical practice. Dr. Kalapila is an Infectious Diseases fellow at the University of Washington. Her research interests are in the management of HIV–hepatitis C virus co-infection

Acknowledgments

We thank Sue Swanzy for excellent technical assistance.

This work was supported in part by the National Center for Advancing Translational Sciences of the National Institutes of Health (grant no. UL1TR000423).

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Suggested citation for this article: Salipante SJ, Kalapila A, Pottinger PS, Hoogestraat DR, Cummings L, Duchin JS, et al. Characterization of a multidrug-resistant, novel Bacteroides genomospecies. Emerg Infect Dis. 2015 Jan [date cited]. http://dx.doi.org/10.3201/eid2101.140662

DOI: 10.3201/eid2101.140662

1These first authors contributed equally to this article.