IJCEMR

Article http://dx.doi.org/10.26855/ijcemr.2024.04.027

Unraveling Citrobacter koseri Infection Outbreaks Using Next-generation Sequencing: A Clinical Case Study

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Suhong Wang1,#, Caiyun Liu2,#, Zhankui Lin3,#, Xue Dong4,#, Mei Tian4,*, Qian Xu5,*

1Clinical Laboratory, Liaocheng Veterans Hospital, Liaocheng, Shandong, China.

2Outpatient Department, Liaocheng Veterans Hospital, Liaocheng, Shandong, China. 

3Neurology Department, Liaocheng Veterans Hospital, Liaocheng, Shandong, China. 

4School of Pharmacy, Jiangsu Ocean University, Lianyungang, Jiangsu, China. 

5Hospital Infection Control Department, Liaocheng Veterans Hospital, Liaocheng, Shandong, China.

#These authors contributed equally to this manuscript.

*Corresponding author: Mei Tian, Qian Xu

Published: May 27,2024

Abstract

Citrobacter koseri (C. koseri) is a normal gut microbe but can cause severe opportunistic infections in immunocompromised individuals and neonates. Due to sudden hospital outbreaks, it has recently gained attention. The lack of adequate environmental surveillance and poor understanding of the epidemiology of its spread warrant the use of more sensitive and superior analysis methods. Next-generation sequencing is a powerful and rapidly emerging tool yet to be validated for routine molecular diagnosis and epidemiology of C. koseri infections. In this study, the next generation sequencing (NGS) was used to investigate the outbreak of 4 cases of C. koseri bloodstream infection in a Neurology setting within a hospital over three days. The blood samples were tested for bacterial culture among the patients with fever (body temperature ≥38°C) and chills. Additionally, the environmental samples were also cultured. A total of 4 patients with chills and fever within three days of admission and cases of sepsis due to C. koseri were identified through routine diagnosis. C. koseri was also found in the sealing fluid of environmental samples. NGS analysis was conducted on four bacterial samples from the patient's blood. The NGS data showed that entire paired-end reads were assembled into a 4.5 Mb genome with an average GC content 54.66%. The phylogram is based on the global pan-genome, suggesting a distinct clade in the identified samples. Phylogenetic analysis of the 16S RNA showed two distinct clusters. Cluster 1 originated from CKB211, while Cluster 2 was isolated from patients in the same ward (CKB212, CKB213, and CKB214). The core-pan evolutionary analysis indicated that CKB211 had a distant evolutionary relationship with other strains and more subtle evolutionary relationships were also analyzed. This analysis is consistent with the physical distance of these patients. It strongly indicates a likely route of infection via shared saline, which was the common operational approach. The study provides unique insights into the rare infection caused by C. koseri, utilizing NGS and phylogenetic analysis. In the present study, although both 16S RNA and the core-pan phylogenetic tree can be used for the evolutionary analysis of C. koseri, the core-pan analysis involves a greater sequence and provides a more nuanced understanding of divergence. The study suggests using core-pan for the evolutionary analysis of C. koseri. However, considering the limited sample size in this study, the applicability of this method remains to be explored.

References

[1] Hirai J, Uechi K, Hagihara M, Sakanashi D, Kinjo T, et al. Bacteremia due to Citrobacter braakii: A case report and literature review. J Infect Chemother, 2016; 22(12):819-821.

[2] Samonis G, Karageorgopoulos DE, Kofteridis DP, Matthaiou DK, Sidiropoulou V, et al. Citrobacter infections in a general hospital: characteristics and outcomes. Eur J Clin Microbiol Infect Dis, 2009; 28(1):61-68.

[3] Lavigne JP, Defez C, Bouziges N, Mahamat A, Sotto A. Clinical and molecular epidemiology of multidrug-resistant Citrobacter spp. infections in a French university hospital. Eur J Clin Microbiol Infect Dis., 2007; 26(6):439-441.

[4] Goold LA, Warrier SK, Wittles NK, Nathan F. Microbial keratitis secondary to infection with Citrobacter koseri. Cornea, 2010; 29(4):479.

[5] Chahrour MA, Hoballah JJ. Citrobacter koseri Surgical Site Infection after Femoropopliteal Vein Bypass for Popliteal Artery Aneurysm Treated with a Graft Preserving Strategy. Surg Infect (Larchmt), 2021; 22(10):1093-1096.

[6] Lim TH, Tai E, Khairy S, Mohtar I. Infective crystalline keratopathy due to Citrobacter koseri. Journal of Acute Disease, 2021; 10:36.

[7] Licata G, De Rosa A, Gambardella A, Calabrese G, Argenziano G, et al. Bullous Erysipelas caused by Citrobacter koseri. J Clin Aesthet Dermatol, 2021;14(5):12.

[8] Tchidjou HK, Romeo B. Infant Case of Co-infection with SARS-CoV-2 and Citrobacter koseri Urinary Infection. J Trop Pediatr, 2021; 67(3).

[9] Kanzawa Y, Ishimaru N, Seto H, Tsutsumi T, Kinami S. Liver abscess with Citrobacter koseri bacteremia. Infez Med, 2018; 26(3):266-269.

[10] Ward HH, Lauber P, Laubach LT, Fishbein J, Greenberg MR. Citrobacter koseri meningitis with cerebral edema and pneumocephalus in a neonate. Radiol Case Rep, 2021; 16(3):528-530.

[11] Ma Xiaoxiao, Mou Gan, Liu Ling, et al. Advances in next-generation sequencing technique for infectious pathogens. Chin J Nosocomiol., 2021, 31(11):1754-1760.

[12] Junie LM, Jeican, II, Matroş L, Pandrea SL. Molecular epidemiology of the community-associated methicillin-resistant staphylococcus aureus clones: a synthetic review. Clujul Med, 2018; 91(1):7-11.

[13] Huang Jing-Jing, Xiao Meng, Xu Ying-chun. Application of Next Generation Sequencing in Clinical Microbiology and Infectious Diseases. Medical Journal of Peking Union Medical College Hospital, 2018, 9(5): 448-452.

[14] Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, 2004; 32(5):1792-1797.

[15] Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol, 2007; 56(4):564-577.

[16] Li Li-Juan, Zhao Dan-Yang, Huang Xue-Min, Guo Qiao-zhi. Analysis of data on nosocomial outbreaks in neonatal worldwide. Chinese Journal of Nosocomiology,  2020; 30(18):2859-2863

[17] Mohanty S, Singhal R, Sood S, Dhawan B, Kapil A, et al. Citrobacter infections in a tertiary care hospital in Northern India. J Infect, 2007; 54(1):58-64.

How to cite this paper

Unraveling Citrobacter koseri Infection Outbreaks Using Next-generation Sequencing: A Clinical Case Study

How to cite this paper: Suhong Wang, Caiyun Liu, Zhankui Lin, Xue Dong, Mei Tian, Qian Xu. (2024) Unraveling Citrobacter koseri Infection Outbreaks Using Next-generation Sequencing: A Clinical Case Study. International Journal of Clinical and Experimental Medicine Research8(2), 338-346.

DOI: http://dx.doi.org/10.26855/ijcemr.2024.04.027