Difei Academic | mNGS analyzes hemodialysis catheter tip microbiota

Introduction

Recently, the team of Director Miao Yun of the Transplantation Department of Nanfang Hospital collaborated with Diffei Medical to prospectively collect clinical samples from 40 perioperative kidney transplant patients who underwent hemodialysis catheter removal for mNGS detection and culture.mNGSThe positive detection rates of bacteria by traditional culture were 97.09% (200/206) and 2.65% (3/113) respectively.At the same time, the study describes the microbial structure and diversity at the tip of hemodialysis catheters in dialysis patients during the perioperative period of kidney transplantation, filling the gap in the colonization microbial database in hemodialysis catheters.The research results were published inRenal Failure。

Research Background

Catheter-related infection (CRI) is one of the major clinical complications of indwelling hemodialysis catheters and the second leading cause of death in hemodialysis patients after cardiovascular events.Prevention and early diagnosis of CRI are particularly important in patients with indwelling hemodialysis catheters during the perioperative period of kidney transplantation (KTx) due to intensive use of immunosuppressants.mNGS has the characteristics of short detection cycle, wide coverage and high sensitivity.

This study uses mNGS to detect hemodialysis catheter samples and other body fluid samples to improve diagnostic specificity and provide new insights into preventing CRI.

Enrolled patients

Forty patients who underwent hemodialysis catheter removal during hospitalization participated in this study, including 21 males.Eighteen patients had catheter replacement before kidney transplantation, 4 of whom had suspected CRI; 22 patients had hemodialysis catheter removal after kidney transplantation, and 2 of them had suspected CRI.A total of 206 clinical samples were collected, including 40 catheter tip samples, 40 peripheral blood samples, 33 catheter blood samples, 33 catheter exit skin swabs (30 from the neck, 3 from the groin), 32 oral Throat swabs and 28 mid-segments of urine (Figure 1).All the above samples were tested using mNGS.Catheter tip, peripheral blood, and catheter blood samples were cultured simultaneously.

Figure 1 A. Analysis flow chart of 206 samples; B. Pie chart of the proportion of bacteria, fungi, and viruses in 206 samples

Research result

Composition of core bacterial groups at different sampling points

mNGSThe positive rate of detection was 97.09% (200/206), and the positive rate of traditional culture was 2.65% (3/113).1,545 species of bacteria, 226 species of fungi and 57 species of viruses were identified in 206 samples.Figure 2 shows the phylogenetic composition, detection frequency and read number of dominant bacterial species in the six samples.

There is a significant difference in the number of reads between oropharyngeal swabs and other types of samples (p<0.001).Bacteria were most frequently detected in catheter tip and catheter exit skin swab samples, and lowest in catheter blood and peripheral blood samples.The frequency of bacterial detection at the catheter tip was associated with catheter blood (p<0.001), peripheral blood (p<0.001), oropharyngeal swab (p=0.009) and mid-section urine (p<0.001) are significantly different.The frequency of bacterial detection in catheter exit skin swabs is related to the frequency of catheter blood (p=0.007) and peripheral blood (p=0.005) are significantly different.Except for urine samples, the detection rate of Gram-negative bacteria in other samples was higher (43.73%).

Figure 2 Phylogenetic composition of microbiota at six different sampling sites

Effects of immunosuppressants and antibiotics on catheter tip microbiota

1,298 bacterial species, 194 fungal species, and 24 viral species were detected at the catheter tip.Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were the most frequently detected microorganisms in both groups before and after kidney transplantation (Fig. 2).A total of 60 dominant bacterial species were detected in both groups, most of which were Gram-negative bacteria (55.00%, 33/60).Predominant bacteria with a detection frequency higher than 50.00% in both groups included Micrococcus luteus, Brevibacterium casei, Moraxella osloi and Pseudomonas aeruginosa.Patients were routinely treated with cefoperazone sodium, sulbactam sodium, caspofungin, and metronidazole for infection prevention within 7 days after kidney transplantation.The coverage of these antibiotics against dominant bacteria in the catheter tip and blood was only 23.33%.

Furthermore, microorganisms within the antimicrobial spectrum were still detected at the catheter tip.There was no statistical difference in the diversity of bacterial flora between the two groups before and after kidney transplantation (p>0.050) (Figure 3A,B).

Microbiota composition associated with clinical features

The alpha diversity of the catheter tip microbiota in the diabetic group was significantly higher than that in the non-diabetic group (p<0.010) (Figure 3C).The abundance of Pseudomonas azoospermum, Corynebacterium tuberculosis stearic acid, and Escherichia coli in the diabetic group was significantly higher than that in the non-diabetic group (Figure 3D).In the post-renal transplantation group, serum creatinine levels were inversely correlated with Stenotrophomonas maltophilia and Ralstonia pitii.

In both groups before and after kidney transplantation, hemoglobin levels were negatively correlated with Stenotrophomonas maltophilia and Ralstonia piti, and positively correlated with Gordonia terrestrial; C-reactive protein levels were associated with Ralstonia piti. bacteria was negatively correlated; the dialysis catheter placement time was negatively correlated with Staphylococcus hominis; the white blood cell count was negatively correlated with Gordonia terrestrialis (Figure 3E).

Figure 3 Correlation between microbiota composition and clinical characteristics

Analysis of microbial sources at catheter tip

Bayesian algorithm was used to trace the possible sources of microorganisms at the catheter tip.Catheter exit skin swabs were found to be predicted to be the main source of catheter tip microorganisms (32.51%), followed by peripheral blood (20.95%) and catheter blood (6.64%) (Figure 4).In addition, about 35.03% of microorganisms do not belong to these sources.

Figure 4 Microbes tracking catheter tips in other samples

in conclusion

The database of microorganisms colonizing hemodialysis catheters in renal transplant patients is almost blank, making it difficult to quickly and accurately distinguish microbial colonization from infection.As the first study to use mNGS technology to detect perioperative hemodialysis catheter tip microbiota in kidney transplantation, the results of this study can serve as a supplement to the database and provide new insights into the prevention of CRI in the perioperative period of kidney transplantation.

references:

Yan Z, Wang Y, Zeng W, et al. Microbiota of long-term indwelling hemodialysis catheters during renal transplantation perioperative period: a cross-sectional metagenomic microbial community analysis[J]. Renal Failure, 2023, 45(2): 2256421.

Compiler: Lily Reviewer: Jia, Xiaoyang Typesetting: Lin