Clinical Profile, Prognostic Factors, and Outcome Prediction in Hospitalized Patients With Bloodstream Infection: Results From a 10-Year Prospective Multicenter Study

Relationship of C-reactive Protein/Serum Albumin Ratio and qPitt Bacteremia Score With An All-Cause In-Hospital Mortality in Patients With Bloodstream Infections

BACKGROUND

Bloodstream infections remain a major cause of morbidity and mortality despite notable advances in their diagnosis and treatment. C-reactive protein/serum albumin ratio and the quick Pitt bacteremia score are two useful tools for clinicians to assess severity and predict mortality risk in patients with sepsis attributable to bloodstream infections. This study examined the relationship between C-reactive protein/serum albumin ratio and Q Pitt bacteremia score with all-cause in-hospital mortality in patients with bloodstream infections.

METHODS

Hospitalized adult patients with bacteremic bloodstream infections between January 1, 2020, and December 31, 2021, were retrospectively reviewed. Patients' demographics and clinical and laboratory data were retrieved from patient electronic records. C-reactive protein/albumin ratio was calculated using CRP (mg/L) and serum albumin (g/L) values obtained within 24 hours of blood culture collection and quick Pitt bacteremia score was calculated for each patient with each of the five variables of the score determined within 24 hours of blood culture collection and each patient was assigned a numerical score of 0-5 accordingly. The relationship between C-reactive protein/albumin ratio and quick Pitt bacteremia score with all-cause in-hospital mortality was determined.

RESULTS

A total of 187 hospitalized adult patients with non-repeat bacteremic bloodstream infections were identified. Escherichia coli was the most common Gram-negative blood isolate while Staphylococcus aureus was the predominant Gram-positive isolate. One hundred and five (56.1%) patients were male with a cohort mean age of 56.9 ± 2.7 years. All-cause in-hospital mortality was 27.3%. The mean CRP/albumin ratio (8.6 ±1.7) and mean quick Pitt bacteremia score (2.8 ±0.4) were significantly higher in patients with bloodstream infections who died during their hospitalization compared to those who survived. The all-cause in-hospital mortality was 8%, 12%, 22%, 46%, 93%, and 100% for patients with quick Pitt scores of 0, 1, 2, 3, 4, and 5, respectively.

CONCLUSION

In hospitalized patients with bacteremic bloodstream infections, an incremental increase in quick Pitt bacteremia score and mean C-reactive protein/albumin ratio of >8 was associated with higher mortality.

Clinical impacts of the rapid diagnostic method on positive blood cultures

OBJECTIVE

This study aimed to evaluate the impact of short-term incubation (STI) protocol on clinical outcomes of bloodstream infection (BSI) patients.

METHODS

A total of 1363 positive blood culture records from January 2019 to December 2021 were included. The main clinical outcomes included pathogen identification turnaround time (TAT), antimicrobial susceptibility testing (AST) TAT, and length of total hospital stay.

RESULTS

The TAT of pathogen identification and AST significantly decreased after implementing the STI protocol (2.2 vs 1.4 days and 3.4 vs 2.5 days, respectively, with P < .001 for both). Moreover, for patients with Gram-negative bacteria (GNB)-infected BSIs, the length of total hospital stay decreased from 31.9 days to 27.1 days, indicating that these patients could be discharged 5 days earlier after implementing the STI protocol (P < .01).

CONCLUSION

The protocol led to a significant reduction in TAT and improved clinical outcomes, particularly for GNB organisms. The findings suggest that the STI protocol can improve patient outcomes and hospital resource utilization in the management of BSIs.

A Machine Learning Predictive Model of Bloodstream Infection in Hospitalized Patients

The aim of the study was to build a machine learning-based predictive model to discriminate between hospitalized patients at low risk and high risk of bloodstream infection (BSI). A Data Mart including all patients hospitalized between January 2016 and December 2019 with suspected BSI was built. Multivariate logistic regression was applied to develop a clinically interpretable machine learning predictive model. The model was trained on 2016-2018 data and tested on 2019 data. A feature selection based on a univariate logistic regression first selected candidate predictors of BSI. A multivariate logistic regression with stepwise feature selection in five-fold cross-validation was applied to express the risk of BSI. A total of 5660 hospitalizations (4026 and 1634 in the training and the validation subsets, respectively) were included. Eleven predictors of BSI were identified. The performance of the model in terms of AUROC was 0.74. Based on the interquartile predicted risk score, 508 (31.1%) patients were defined as being at low risk, 776 (47.5%) at medium risk, and 350 (21.4%) at high risk of BSI. Of them, 14.2% (72/508), 30.8% (239/776), and 64% (224/350) had a BSI, respectively. The performance of the predictive model of BSI is promising. Computational infrastructure and machine learning models can help clinicians identify people at low risk for BSI, ultimately supporting an antibiotic stewardship approach.

Increase in antioxidant capacity associated with the successful subclone of hypervirulent carbapenem-resistant Klebsiella pneumoniae ST11-KL64

The acquisition of exogenous mobile genetic material imposes an adaptive burden on bacteria, whereas the adaptational evolution of virulence plasmids upon entry into carbapenem-resistant Klebsiella pneumoniae (CRKP) and its impact remains unclear. To better understand the virulence in CRKP, we characterize virulence plasmids utilizing a large genomic data containing 1219 K. pneumoniae from our long-term surveillance and publicly accessible databases. Phylogenetic evaluation unveils associations between distinct virulence plasmids and serotypes. The sub-lineage ST11-KL64 CRKP acquires a pK2044-like virulence plasmid from ST23-KL1 hypervirulent K. pneumoniae, with a 2698 bp region deletion in all ST11-KL64. The deletion is observed to regulate methionine metabolism, enhance antioxidant capacity, and further improve survival of hypervirulent CRKP in macrophages. The pK2044-like virulence plasmid discards certain sequences to enhance survival of ST11-KL64, thereby conferring an evolutionary advantage. This work contributes to multifaceted understanding of virulence and provides insight into potential causes behind low fitness costs observed in bacteria.

Tracheal epithelial cell-exosome-derived MiR-21-5p inhibits alveolar macrophage pyroptosis to resist pulmonary bacterial infection through PIK3CD-autophagy pathway

AIMS

Structural cells play an important role in regulating immune cells during infection. Our aim was to determine whether structural porcine tracheal epithelial cells (PTECs) can regulate alveolar macrophages (AMs) to prevent bacterial pneumonia, explore the underlying mechanism(s) and therapeutic target.

MATERIALS AND METHODS

Actinobacillus pleuropneumoniae (APP) was used as the model strain for infection studies. Small RNA sequencing was used to identify differentially abundant exosome-derived miRNAs. The role of PTECs exosome-derived miR-21-5p in regulating AMs autophagy, pyroptosis, reactive oxygen species (ROS) was determined using RT-qPCR, western-blotting, flow cytometry, immunohistochemistry. Luciferase reporter assays were conducted to identify potential binding targets of miR-21-5p. The universality of miR-21-5p action on resistance to bacterial pulmonary infection was demonstrated using Klebsiella pneumoniae or Staphylococcus aureus in vitro and in vivo infection models.

KEY FINDINGS

MiR-21-5p was enriched in PETCs-derived exosomes, which protected AMs against pulmonary bacterial infection. Mechanistically, miR-21-5p targeted PIK3CD, to promote autophagy of AMs, which reduced the pyroptosis induced by APP infection via inhibiting the over-production of ROS, which in turn suppressed the over-expression of pro-inflammatory cytokines, and increased bacterial clearance. Importantly, the protective effect and mechanism of miR-21-5p were universal as they also occurred upon challenge with Klebsiella pneumoniae and Staphylococcus aureus.

SIGNIFICANCE

Our data reveals miR-21-5p can promote pulmonary resistance to bacterial infection by inhibiting pyroptosis of alveolar macrophages through the PIK3CD-autophagy-ROS pathway, suggesting PIK3CD may be a potential therapeutic target for bacterial pneumonia.

Rising Drug Resistance Among Gram-Negative Pathogens in Bloodstream Infections: A Multicenter Study in Ulanhot, Inner Mongolia (2017-2021)

BACKGROUND Bloodstream infections, which arise when pathogenic microorganisms infiltrate the bloodstream, present a grave health risk. Their potentially lethal nature combined with the ability to severely impair physiological functions underscore the importance of understanding and mitigating such infections. This study aimed to elucidate drug sensitivity profiles and distribution of these pathogens in hospitals in Ulanhot, Inner Mongolia. MATERIAL AND METHODS From 2017 to 2021, we gathered blood culture-positive samples from several hospitals across Ulanhot. Using combined diagnostic techniques, including the instrument method, paper diffusion, and Epsilometer test (E-test), we determined the identity of pathogens and assessed their drug sensitivity. Subsequent data processing with WHONET 5.6 software provided insights into the patterns of microbial distribution and extent of drug resistance. RESULTS Of 2498 pathogenic strains identified, 35.83% were gram-positive, 62.45% were gram-negative, and a smaller fraction of 1.72% were fungi. Escherichia coli and Klebsiella pneumoniae were the primary bacteria, contributing to 35.15% and 15.73% of infections, respectively. Alarmingly, methicillin-resistant strains exhibited pronounced resistance to drugs, notably penicillin G (resistance rates of 80.87% to 100.00%) and erythromycin (resistance rates of 91.16% to 97.28%). Acinetobacter baumannii had a particularly high resistance profile, surpassing Pseudomonas aeruginosa, which exhibited a resistance rate below 30.00%. CONCLUSIONS Ulanhot's primary bloodstream infection agents were gram-negative bacteria, specifically E. coli and K. pneumoniae. The growing drug resistance observed, particularly among strains like A. baumannii, highlights the pressing need for rigorous drug resistance surveillance and the strategic use of antibiotics, ensuring their efficacy is preserved for future medical needs.

Roquin-1 resolves sepsis-associated acute liver injury by regulating inflammatory profiles via miRNA cargo in extracellular vesicles

Sepsis-associated acute liver injury (SALI) is an independent risk for sepsis-induced death orchestrated by innate and adaptive immune responses. Here, we found that Roquin-1 was decreased during SALI and expressed mainly in monocyte-derived macrophages. Meanwhile, Roquin-1 was correlated with the inflammatory profiles in humans and mice. Mechanically, Roquin-1 in macrophages promoted Ago2-K258-ubiquitination and inhibited Ago2-S387/S828-phosphorylation. Ago2-S387-phosphorylation inhibited Ago2-miRNA's complex location in multivesicular bodies and sorting in macrophages-derived extracellular vesicles (MDEVs), while Ago2-S828-phosphorylation modulated the binding between Ago2 and miRNAs by special miRNAs-motifs. Then, the anti-inflammatory miRNAs in MDEVs decreased TSC22D2 expression directly, upregulated Tregs-differentiation via TSC22D2-STAT3 signaling, and inhibited M1-macrophage-polarization by TSC22D2-AMPKα-mTOR pathway. Furthermore, WT MDEVs in mice alleviated SALI by increasing Tregs ratio and decreasing M1-macrophage frequency synchronously. Our study showed that Roquin-1 in macrophages increased Tregs-differentiation and decreased M1-macrophage-polarization simultaneously via miRNA in MDEVs, suggesting Roquin-1 can be used as a potential tool for SALI treatment and MDEVs engineering.

Current and Future Landscape of the Antimicrobial Resistance of Nosocomial Infections in China

The rapid increase in antimicrobial resistance driven by the widespread use, abuse, and misuse of antibiotics constitutes one of China's most challenging healthcare problems. In particular, nosocomial infections caused by multidrug-resistant organisms such as methicillin-resistant Staphylococcus aureus (MRSA), carbapenem-resistant Acinetobacter baumannii (CRAB), and carbapenem-resistant Enterobacterales (CRE), which exhibit resistance to most available antibiotics, lead to high mortality and enormous economic and human costs. Here, we summarize the current patterns of the antimicrobial resistance of nosocomial infections in China and address possible interventions to combat antimicrobial resistance.

Incidence, Clinical Features, and Association with Prognosis of Bloodstream Infection in Pediatric Patients After Percutaneous or Surgical Treatment for Ventricular Septal Defect or Atrial Septal Defect: A Retrospective Cohort Study

INTRODUCTION

Bloodstream infection (BSI) may occur after cardiac procedures, but this has rarely been investigated specifically in pediatric patients after percutaneous or surgical treatment for ventricular septal defect (VSD) or atrial septal defect (ASD) with recent data. The current study aimed to investigate the incidence, clinical features, and association with prognosis of BSI in this patient population.

METHODS

Pediatric patients who received percutaneous or surgical procedure for VSD or ASD between 2010 and 2018 in a large children's hospital in China were retrospectively enrolled via the Pediatric Intensive Care database, but only those who had blood culture records within 24 h after the procedure and who had no prior positive blood culture records were included. BSI after the procedure was identified by reviewing blood culture records, and baseline characteristics associated with BSI were explored by univariable logistic regression. In-hospital mortality and length of hospitalization were studied as prognostic outcomes and compared between patients with and without BSI.

RESULTS

A total of 1340 pediatric patients were included. Among them, 46 (3.43%) patients had BSI within 24 h after the procedure, of which the majority (78.26%, 36/46) were caused by Gram-positive bacteria and 65.22% (30/46) had antibiotic-resistant organisms. Age [odds ratio (OR) 0.98 per 1-month increase, 95% confidence interval (CI) 0.97-1.00, P = 0.021] and antibiotic use within 72 h before the procedure (OR 1.81, 95% CI 1.00-3.26, P = 0.049) were statistically significantly associated with developing BSI. Compared with patients without BSI, there was no statistically significant difference in in-hospital mortality (0.00% versus 0.54%, P = 1.000), but patients with BSI had statistically significantly longer length of hospitalization (median 14.51 versus 12.94 days, P = 0.006), while the association was not statistically significant after adjustment for baseline characteristics by multivariable linear regression (β = 1.73, 95% CI -0.59 to 4.04, P = 0.144).

CONCLUSION

BSI is relatively uncommon in pediatric patients after procedures for VSD or ASD, but a younger age seems a risk factor. Developing BSI appears to be associated with increased length of hospitalization but not in-hospital mortality.

Changes in Antimicrobial Resistance and Etiology of Blood Culture Isolates: Results of a Decade (2010-2019) of Surveillance in a Northern Region of Colombia

Background

Bloodstream infections (BSI) are important causes of morbidity and mortality worldwide. Antimicrobial surveillance is essential for identifying emerging resistance and generating empirical treatment guides, the purpose of this study is to analyze trends in antimicrobial susceptibility of BSI from 2010 to 2019 in healthcare institutions from Medellin and nearby towns in Colombia.

Methods

A Whonet database was analyzed from the GERMEN antimicrobial surveillance network; frequency and antibiotic susceptibility trends were calculated on more frequent microorganisms using Mann Kendall and Sen’s Slope Estimator Test.

Results

61,299 isolates were included; the three microorganisms more frequent showed a significant increasing trend through time E. coli (Sen’s Slope estimator = 0.7 p = <0.01) S. aureus (Sen’s Slope estimator = 0.60 p = <0.01) and K. pneumonia (Sen’s Slope estimator = 0.30 p = <0.01). E. coli showed a significant increase trend in cefepime and ceftazidime resistance, while K. pneumoniae showed a significant increase in resistance to cefepime, ciprofloxacin, and gentamicin. P. aeruginosa increases its susceptibility to all analyzed antibiotics and S. aureus to oxacillin. No increasing trend was observed for carbapenem resistance.

Conclusion

An upward trends was observed in more frequent microorganisms and resistance to third and fourth-generation cephalosporins for E. coli and K pneumoniae; in contrast, not increasing trends in antibiotic resistance was observed for P. aeruginosa and S. aureus. The essential role of AMR-surveillance programs is to point out and identify these trends, which should improve antibiotic resistance control.

Three-Year Evaluation of Pseudomonas aeruginosa Bacteremia in Patients Admitted to a University-Affiliated Hospital, Mashhad, Iran

Background: Pseudomonas aeruginosa is an opportunistic gram-negative pathogen that can cause infection in almost any body part. Objectives: We aimed to evaluate the characteristics of patients with P. aeruginosa bloodstream infection (BSI). Methods: In this cross-sectional study, we retrospectively evaluated the records of 35 patients with P. aeruginosa BSI admitted to the Imam Reza Hospital, Mashhad, Iran, during 2012 - 2015. Age, sex, clinical symptoms, risk factors, underlying diseases, and the antibiogram test results were recorded and compared between nosocomial and community-acquired infection (CAI) dead and alive patients using the chi-square test. Data were analyzed using SPSS software, version 21. Results: The patients had a mean age of 54.57 ± 20.75 years, with 19 of them being men (54.3%). Intubation was only required in the deceased group (N = 19; P = 0.014). Tachypnea was more frequent (63.2% vs. 13.2%, P = 0.003), and appropriate treatment was less frequent (27.8% vs. 66.7%; P = 0.02) in the deceased group compared to the control group. Most patients with nosocomial infection (N = 24) passed away (66.7%; P = 0.03). All nine patients with a history of burning had a nosocomial infection (P = 0.01). Shivering and decreased consciousness were more frequent in patients with CAI (both P = 0.03) than in other patients. The antibiogram test results showed high resistance to multiple antibiotics. Conclusions: Considering the high mortality rate of P. aeruginosa BSI and resistance to multiple antibiotics, it is necessary to pay greater attention to the prevention of nosocomial infection with this pathogen, especially in patients admitted to burn centers and those with specific clinical signs, like tachypnea and leukocytosis.

Clinical factors predictive of Gram-negative bloodstream infection at the Emergency Department

Introduction

Bloodstream infection is a common condition at the Emergency Department (ED). Appropriate antibiotic therapy is also crucial for patients with bloodstream infection particularly at the ED. This study therefore aimed to find clinical factors predictive of types of bacterial pathogens in bloodstream infection patients presenting at the ED focused on Gram-negative bacterial infections.

Methods

This was a retrospective study. The inclusion criteria were adult patients who were suspected for bloodstream infection defined by blood culture collection presenting at the ED and intravenous antibiotics were initiated during the ED visits. The study period was between January 1^st, 2016 and December 31^st, 2018. Clinical data of the eligible patients were retrieved from the ED database. Factors associated with Gram-negative infection were calculated by logistic regression analysis.

Results

There were 727 patients at the ED who had positive blood culture for bacteria. Of those, 504 patients (69.33%) had positive blood culture for Gram-negative bacteria. There were three independent factors for Gram-negative infection including sex, solid organ malignancy, and body temperature. The highest adjusted odds ratio (95% confidence interval) was 2.004 (1.330, 3.020) for solid organ malignancy.

Conclusions

Gram-negative bacterial infection was more prominent than Gram-positive bacterial infection in patients presenting at the ED (69.33%). Solid organ malignancy, being female, and a high body temperature were independent factors of Gram-negative bacterial infection.

In Vitro Activity of KBP-7072 against 536 Acinetobacter baumannii Complex Isolates Collected in China

Acinetobacter baumannii has emerged globally as a difficult-to-treat nosocomial pathogen and become resistant to carbapenems, resulting in limited treatment options. KBP-7072 is a novel semisynthetic aminomethylcycline, expanded spectrum tetracycline antibacterial agent with completed phase 1 clinical development studies. This study aimed to evaluate the in vitro activity of KBP-7072 and several comparators against clinical A. baumannii isolates collected from China. A collection of 536 A. baumannii clinical isolates were isolated from 20 hospitals across 13 provinces and cities in China between 2018 and 2019. Antimicrobial susceptibility testing of 12 antimicrobial agents was performed utilizing the broth microdilution method recommended by CLSI. KBP-7072 has shown active antibacterial activity against 536 A. baumannii isolates. It inhibited the growth of all isolates at 4 mg/liter, including 372 carbapenem-resistant isolates, 37 tigecycline MIC ≥ 4 mg/liter isolates, and 138 omadacycline MIC ≥ 4 mg/liter isolates. Compared with other expanded spectrum tetracyclines, KBP-7072 (MIC₉₀, 1 mg/liter) outperformed 2-fold and 4-fold more active against 536 A. baumannii isolates than tigecycline (MIC₉₀, 2 mg/liter) and omadacycline (MIC₉₀, 4 mg/liter). KBP-7072 was as equally active as colistin (MIC₉₀, 1 mg/liter, 99.4% susceptible). Doxycycline (33.4% susceptible), gentamicin (31.3% susceptible), meropenem (30.6%, susceptible), imipenem (30.2% susceptible), ceftazidime (27.8% susceptible), piperacillin-tazobactam (27.2% susceptible), and levofloxacin (27.2% susceptible) showed marginally poor antibacterial activity against tested isolates according to CLSI breakpoints, except for minocycline (73.7% susceptible). KBP-7072 is a potential alternative agent for the treatment of infection caused by A. baumannii, including carbapenem-resistant species.

IMPORTANCE It is reported that A. baumannii has emerged as an intractable nosocomial pathogen in hospitals especially when it develops resistance to carbapenems and other antibiotics, which limits treatment options and leads to high mortality. In February 2017, the WHO published a list of ESKAPE pathogens designated “priority status” for which new antibiotics are urgently needed. Therefore, the epidemiological surveillance and new therapeutic development of A. baumannii must be strengthened to confront an emerging global epidemic. KBP-7072 is a novel, expanded spectrum tetracycline antibacterial and has demonstrated good in vitro activity against recent geographically diverse A. baumannii isolates collected from North America, Europe, Latin America, and Asia-Pacific. This study has shown excellent in vitro activity of KBP-7072 against clinical A. baumannii isolates collected from different regions of China, regarded as supplementary to KBP-7072 pharmacodynamics data, which is of great significance, as it is promising an alternative treatment in CRAB isolates infections in China.

Polymyxin B Combined with Minocycline: A Potentially Effective Combination against blaOXA-23-harboring CRAB in In Vitro PK/PD Model

Polymyxin-based combination therapy is commonly used to treat carbapenem-resistant Acinetobacter baumannii (CRAB) infections. In the present study, the bactericidal effect of polymyxin B and minocycline combination was tested in three CRAB strains containing bla_OXA-23 by the checkerboard assay and in vitro dynamic pharmacokinetics/pharmacodynamics (PK/PD) model. The combination showed synergistic or partial synergistic effect (fractional inhibitory concentration index ≤0.56) on the tested strains in checkboard assays. The antibacterial activity was enhanced in the combination group compared with either monotherapy in in vitro PK/PD model. The combination regimen (simultaneous infusion of 0.75 mg/kg polymyxin B and 100 mg minocycline via 2 h infusion) reduced bacterial colony counts by 0.9–3.5 log₁₀ colony forming units per milliliter (CFU/mL) compared with either drug alone at 24 h. In conclusion, 0.75 mg/kg polymyxin B combined with 100 mg minocycline via 2 h infusion could be a promising treatment option for CRAB bloodstream infections.

Rapid visualization and detection of Staphylococcus aureus based on loop-mediated isothermal amplification

Staphylococcus aureus is a common clinical bacterial pathogen that can cause a diverse range of infections. The establishment of a rapid and reliable assay for the early diagnosis and detection of S. aureus is of great significance. In this study, we developed a closed-tube loop-mediated isothermal amplification (LAMP) assay for the visual detection of S. aureus using the colorimetric indicator hydroxy naphthol blue (HNB). The LAMP reaction was optimized by adjusting the amplification temperature, the concentrations of Mg²⁺, dNTP, and HNB, and the incubation time. In the optimized reaction system, the specificity of LAMP for S. aureus was 100%. The results established that this method accurately identified S. aureus, with no cross-reactivity with 14 non-S. aureus strains. The limit of detection (LOD) of LAMP was 8 copies/reaction of purified plasmid DNA or 400 colony-forming units/reaction of S. aureus. Compared with conventional PCR, LAMP lowered the LOD by tenfold. Finally, 220 clinically isolated strains of S. aureus and 149 non-S. aureus strains were used to evaluate the diagnostic efficacy of LAMP (test accuracy, 99.46%). The findings indicated that LAMP is a reliable test for S. aureus and could be a promising tool for the rapid diagnosis of S. aureus infections.

Evolution of Acinetobacter baumannii in Clinical Bacteremia Patients

Introduction

Colonization of the respiratory tract by Acinetobacter baumannii has been established as an independent risk factor for bacteremia. However, within-host evolution of A. baumannii in bacteremia has not been extensively investigated.

Methods

We performed whole-genome sequencing to discover the evolutionary characteristics that accompany the transition from respiratory tract carriage to bloodstream infection in three patients with A. baumannii bacteremia.

Results

Within-host genetic diversity was identified. A total of 21 single nucleotide variants (SNVs) were detected. Genic and intergenic evolution occurred particularly in secretion system, DNA recombination, and cell motility genes. Intergenic SNVs occurred more frequently compared to synonymous and non-synonymous SNVs, which indicated potential transcription or translation regulation. Non-synonymous mutations mostly occurred during the transition from respiratory tract carriage to bloodstream infection. Isolates of clonal complex 208 (CC208) had lower substitution rate with approximately 10⁻⁶ nucleotide substitutions per site year⁻¹, compared with non-CC208 isolates (approximately 10⁻⁵). We found evidence for the occurrence of recombination in one patient. A total of 259 genes were found to be gained or lost during the within-host evolution, and 231 genes were only detected in one patient. Gene function annotation results suggested that most genes (71/259) were related to replication, recombination, and repair. Universal bloodstream specific genes were not found in all three patients, and only one putative membrane protein related gene was lost in two patients.

Conclusion

Our results indicated that within-host evolution of A. baumannii bacteremia was driven by mutations, gene content changes, and limited effect of recombination. Gene content diversity between different patients was identified, which suggested interplay of both host and pathogen factors in within-host genetic diversity. Secretion system-related genes showed higher frequency of genomic variations during the within-host evolution. Our findings enhanced our understanding of within-host evolution of A. baumannii bacteremia and provided a framework for discovering novel genomic changes and pathogenicity genes important for bacteremia, which will be validated in future studies.