COVID-19 Associated Bacteremia with Chryseobacterium indologenes Co-Harboring bla_IND-2, bla_CIA and bla_CcrA

As the COVID-19 pandemic continues, bacterial co-infections are reported globally and attributed to significant mortality. Secondary bacterial infections could occur in more than 50% of fatal COVID-19 patients.¹ Considerable increase in antimicrobial resistance (AMR) in associated with heavy use of broad-spectrum antibiotics in COVID‐19 patients was expected and multidrug‐resistant (MDR) bacterial co-infections were reported.² The prevalence of carbapenem resistance in COVID-19 bacterial co-infection cases was reported higher than 90%.¹ About AMR, different resistant pattern had been classified, including MDR, extensively drug-resistant (XDR), pandrug-resistant (PDR), usual drug-resistant (UDR) and newly difficult-to-treat resistance (DTR).³ The crush of COVID-19 pandemic with increasing AMR deserved close monitor.

Chryseobacterium indologenes, a non-fermenting, non-motile gram-negative bacillus, belongs to the genus Chryseobacterium and was previously named as flavobacterium indologenes. It is distributed in nature, found in soil, plants, and water. C. indologenes has become one of nosocomial pathogens, often associated with immunocompromised and indwelling device in recent decades.⁴ C. indologenes frequently exhibit resistance to penicillin, cephalosporins and carbapenems.⁵ It has been assumed the AMR of C. indologenes is caused by class A β-lactamase bla_CIA and class B carbapenem-hydrolyzing β-lactamase bla_IND. The bla_IND and bla_CIA were the predominant AMR gene in C. indologenes and the bla_IND and bla_CIA co-harboring C. indologenes were also reported.⁶ Although C. indologenes has become one of healthcare-associated infections (HAI) pathogen, there are few reports about C. indologenes infection associated with COVID-19. Here, we reported a COVID-19 patient with superimposed C. indologenes bloodstream infection. Genomic analysis further revealed the C. indologenes co-harboring three β-lactamases gene, bla_IND-2, bla_CIA and bla_CcrA.

A 58-year-old Taiwanese male was admitted due to COVID-19, diagnosed by reverse transcriptase polymerase chain reaction viral nucleic acid test. Bilateral pneumonia complicated with oxygenation failure developed on admission day 1. Recurrent fever to 38.6°C on 10th day after admission. Blood cultures yielded Gram-negative bacilli and was identified as C. indologenes by MALDI-TOF MS (BioMérieux). The susceptibility test, determined by VITEK^®2 (bioMérieux), revealed the C. indologenes isolate was resistant to piperacillin/tazobactam, ceftazidime, ceftriaxone, cefepime, imipenem, amikacin, gentamicin, ciprofloxacin, tigecycline (Table 1). The report was conducted according to the guidelines of the Declaration of Helsinki, and approved by the Institutional Review Board of Taichung Veterans General Hospital (CE20261A).

Table 1 Minimum Inhibitory Concentration (MIC) of the C. indologenes Strain C205

The whole genome of this C. indologenes strain (designated strain as C205) was sequenced using Nanopore sequencing (GridIon, R9.4 flowcells). The genome was assembled by Flye and the errors were corrected by Homopolish. The antibiotic resistant genes were annotated by NCBI AMRFinderPlus and Hidden Markov Models (HMM) search was used. Whole-genome sequencing, assembly, and resistome analysis identified two metallo β-lactamases (bla_IND-2 and bla_CcrA) and one extended-spectrum β-lactamase (bla_CIA) in the chromosome (Figure 1). All the sequencing data have been deposited in GenBank under Accession CP085529. bla_CcrA in Chryseobacterium has not been reported previously. Further investigated did not identify mobile genetic elements at either upstream nor downstream of the bla_CcrA in C. indologenes C205, suggesting a possibility of vertical transmission. Subsequent search of bla_CcrA in the NCBI database confirms it was also presented in the chromosomes of other C. indologenes strains and many species of Chryseobacterium (e.g., C. lactis, C. phosphatilyticum, and C. carnipullorum). No C. indologenes growth in the sputum culture of this case. Indwelling central venous catheter was considered as risk factor and infection source of C. indologenes bacteremia in this case. The patient was treated with trimethoprim-sulfamethoxazole (TMP-SMX) and discharged under clinical stable condition.

Figure 1 Circular maps of the chromosome of C. indologenes. The outermost ring highlights the CDS loci of three beta lactamases: blaIND-2, blaCIA, and blaCcra. The following inner ring depicts the GC content (black). The two remaining inner rings show the GC skew on the forward and reverse strands (purple/green).

To the best of our knowledge, this is the first report COVID-19 associated bacteremia with C. indologenes co-harboring bla_IND-2, bla_CIA and bla_CcrA. Considering secondary bacterial co-infections with AMR attributed to increasing mortality during previous pandemics,² COVID-19 patients superimposed bacterial infection with MDR pathogen deserved more investigation.

The bla_CcrA has not been reported in Chryseobacterium. The CcrA, belonging to metallo-β-lactamase, was initially identified in a clinical isolate of Bacteroides fragilis TAL3636.⁷ CcrA enzyme strongly hydrolyzed cefoxitin and carbapenems, but not the monocyclic β-lactam. CcrA enzyme was inhibited by tazobactam but not clavulanic acid or sulbactam. Our investigation indicated the bla_CcrA is not only found in our strain but also vertically transferred in many species of Chryseobacterium. The presence of bla_CcrA in Chryseobacterium was overlooked in previous studies because of substantial sequence divergence with the original allele in B. fragilis. Therefore, the homology-based search of antibiotic-resistance genes would miss this β-lactamase.

In conclusion, we reported the first case of co-harboring bla_IND-2, bla_CIA and bla_CcrA in a C. indologenes strain isolated from a COVID-19 patient with bacteremia. The interrelationship between SRAS-CoV-2 and AMR represents a public health concern globally.