Enterobacterales Infection after Intestinal Dominance in Hospitalized Patients

Abstract

The Enterobacterales order of Gram-negative bacteria includes the common nosocomial pathogens Klebsiella pneumoniae, Escherichia coli, Serratia marcescens, and Enterobacter species. Intestinal domination by some colonizing bacterial taxa is associated with subsequent infection, but 16S rRNA gene sequencing is too costly and slow to be used in a clinical setting. The objectives of this study were to develop a PCR-based assay that can measure Enterobacterales density, validate it against 16S rRNA gene sequencing, and measure the association between Enterobacterales dominance and subsequent infection. Two quantitative PCR (qPCR) assays that were developed to quantify the absolute and relative abundance of Enterobacterales had good correlation with 16S rRNA sequence analysis (P < 0.0001). Using both PCR assays and 16S sequencing, a matched case-control study was performed comparing rectal swabs from hospitalized patients who later developed bloodstream, urinary tract, or respiratory Enterobacterales infections (n = 95) to swabs from patients who remained uninfected (n = 189). Enterobacterales abundance measured by sequencing was high in both cases and controls (means, 31.1% and 27.5%, respectively; P = 0.322). We observed an increased risk of infection that depended on both the absolute and relative abundance of Enterobacterales as measured by qPCR assay A (P = 0.012). After adjustment for albumin levels, central venous catheter presence, and use of cephalosporins at the time of swab collection, this association still approached significance (P = 0.061). These results demonstrate that using qPCR to measure intestinal colonization dominance is feasible, indicate that hospitalized patients have high levels of Enterobacterales colonization, and suggest that both relative and absolute abundance may be associated with subsequent infection. IMPORTANCE Increasing antibiotic resistance has resulted in infections that are life-threatening and difficult to treat. Interventions that prevent these infections, particularly without using antibiotics, could save lives. Intestinal colonization by pathogens, including vancomycin-resistant Enterococcus and carbapenem-resistant Enterobacteriaceae (part of the order Enterobacterales) is associated with subsequent infection, and increased colonization density is associated with increased infection risk. Therefore, colonization offers a window of opportunity for infection prevention if (i) there are rapid and inexpensive assays to detect colonization, (ii) there are safe and effective interventions, and (iii) the risk of infection outweighs the risk of the treatment. Fecal transplants are proof of principle that manipulating the microbiome can reduce such colonization and prevent infections. This study demonstrates the feasibility of implementing rapid and inexpensive assays to quantify colonization and measures the strength of association between Enterobacterales dominance and subsequent infection. The approach described here could be a valuable tool in the prevention of antibiotic-resistant infections.

Gut microbiome features are associated with sepsis onset and outcomes

“…There is also likely variation in sample collection, which could lead to differences in measured total bacterial abundance. However, this variation is likely to be random, and we have also observed an association between Enterobacterales total abundance and infection (11). Thus, our findings should be confirmed in a study that utilizes stool samples.…”

“…Alternatively, depletion of butyrate-producing taxa are associated with viral respiratory infections, suggesting the microbiome may also play a more indirect immunomodulatory role (9). Most studies of the microbiome measure relative abundance of bacterial taxa, but their absolute abundance individually and as a community are also associated with various disease states (10) (11). Although there is strong evidence that antibiotics that disrupt the microbiome increase sepsis risk, and that dominance of certain microbiome taxa increase the risk of corresponding infections, the specific pattern of microbiome disruption associated with sepsis onset is unclear.…”

Shift in the Dominant Sequence Type of Carbapenem-Resistant Klebsiella pneumoniae Bloodstream Infection from ST11 to ST15 at a Medical Center in Northeast China, 2015–2020

“…Furthermore, the high detection rate of CRKP in BSI coincided with the high percentage of CRKP in all Kpn, which indicated that CRKP-BSI may be associated with CRKP colonization. 12 As the ICU, hematology and respiratory medicine wards were the three departments mainly affected, intensive surveillance as well as effective infection control measures are needed to control the transmission of CRKP, especially among high-risk individuals from high-risk departments. 13,14 Furthermore, molecular epidemiological studies have demonstrated that KPC-2 was the predominant type of carbapenemase in our hospital, followed by NDM-1 and DNM-5.…”

Diversity and prevalence ofClostridium innocuumin the human gut microbiota

“…Fasta sequences of full-length 16S rRNA sequences from C. innocuum genomes were formatted for alignment in mothur (49) and aligned using the SILVA database (v132) (50). Previously published sequences from fecal microbiota samples representing ‘healthy’ (51), hospitalized (52), or antibiotic-exposed (53) individuals were processed in mothur using the Schloss lab SOP, aligning to the SILVA database (54), then classifying to the custom classifier using the ‘classify.seqs’ command in mothur (cutoff=95) or directly to the RDP database (v16) for comparison (56). The log 10 relative abundance of C. innocuum was plotted in R using the Kruskal-Wallis test in R with a pairwise Wilcoxon Rank Sum Test for pairwise comparisons between groups.…”