Pathogen-Specific Clustering of Nosocomial Blood Stream Infections in Very Preterm Infants

Antimicrobial resistance and epidemic clustering of late-onset neonatal infections in a Brazilian intensive care unit

Nosocomial infections in the neonatal intensive care unit (NICU) tend to cluster and multidrug-resistant (MDR) pathogens are rising in developing countries. We did a retrospective cohort study of neonates admitted to a NICU in Brazil with late-onset neonatal sepsis (LOS) confirmed by blood culture from October 2012 to December 2016 and from July 2018 to December 2021. We defined a cluster of infection when at least two cases of LOS occurred within two different time intervals: 15 and 30 days with the same pathogen in different patients. A random amplified polymorphic DNA (RAPD) was performed from samples from one of these clusters. A logistic regression model was applied having death as the outcome and the infection with an MDR pathogen as the exposure of interest. There were 987 blood cultures from 754 neonates, 621 (63%) were gram-positive cocci, 264 (30%) were gram-negative rods and 72 (7%) fungi. A third of Enterobacterales were resistant to cefepime and a third of non-fermenting glucose rods were resistant to carbapenems. There were 100 or 104 clusters of infection in the 15- or 30-day interval, respectively. A RAPD analysis from an outbreak of MDR Acinetobacter baumannii showed that all five samples belonged to a single clone. An infection with an MDR pathogen was associated with death (OR 1.82, 95% CI 1.03-3.21). In conclusion, clusters of infections in a Brazilian NICU are a frequent phenomenon as seen elsewhere. They suggest cross-transmission of pathogens with increasing antimicrobial resistance and should prompt intensified surveillance and infection control measures.

Used Nasogastric Feeding Tubes from Neonates Contain Infant-Specific Bacterial Profiles

Nasogastric feeding tubes (NG-tubes) from neonates contain potentially pathogenic bacteria. Using culture-based techniques, we have previously determined that the usage duration of NG-tubes did not impact the colonization of the nasogastric tubes. In the present study, we performed 16S rRNA gene amplicon sequencing to evaluate the microbial profile of 94 used nasogastric tubes collected from a single neonatal intensive care unit. Using culture-based whole genome sequencing, we as-sessed whether the same strain persisted in NG-tubes collected from the same neonate across different time-points. We found that the most commonly occurring Gram-negative bacteria were Enterobacteriaceae, Klebsiella and Serratia, while the most common Gram-positive bacteria were staphylococci and streptococci. The microbiota of the NG-feeding tube was overall infant-specific, rather than dependent on the duration of use. Furthermore, we determined that reoccurring species from the individual infant represented the same strain and that several strains were common for more than one infant. Our findings indicate that bacterial profiles found in NG-tubes of neonates are host-specific, not dependent on the duration of use and strongly influenced by the environment.

Burnham CA, Warner BB, Tarr PI, Dantas G. Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit

Bacterial bloodstream infections (BSIs) resulting in late-onset sepsis affect up to half of extremely preterm infants and have substantial morbidity and mortality. Bacterial species associated with BSIs in neonatal intensive care units (NICUs) commonly colonize the preterm infant gut microbiome. Accordingly, we hypothesized that the gut microbiome is a reservoir of BSI-causing pathogenic strains that increase in abundance before BSI onset. We analyzed 550 previously published fecal metagenomes from 115 hospitalized neonates and found that recent ampicillin, gentamicin, or vancomycin exposure was associated with increased abundance of Enterobacteriaceae and Enterococcaceae in infant guts. We then performed shotgun metagenomic sequencing on 462 longitudinal fecal samples from 19 preterm infants (cases) with BSI and 37 non-BSI controls, along with whole-genome sequencing of the BSI isolates. Infants with BSI caused by Enterobacteriaceae were more likely than infants with BSI caused by other organisms to have had ampicillin, gentamicin, or vancomycin exposure in the 10 days before BSI. Relative to controls, gut microbiomes of cases had increased relative abundance of the BSI-causing species and clustered by Bray-Curtis dissimilarity according to BSI pathogen. We demonstrated that 11 of 19 (58%) of gut microbiomes before BSI, and 15 of 19 (79%) of gut microbiomes at any time, harbored the BSI isolate with fewer than 20 genomic substitutions. Last, BSI strains from the Enterobacteriaceae and Enterococcaceae families were detected in multiple infants, indicating BSI-strain transmission. Our findings support future studies to evaluate BSI risk prediction strategies based on gut microbiome abundance in hospitalized preterm infants.

Serratia Infection Epidemiology Among Very Preterm Infants in the Neonatal Intensive Care Unit

BACKGROUND

Serratia spp. are opportunistic, multidrug resistant, Gram-negative pathogens, previously described among preterm infants in case reports or outbreaks of infection. We describe Serratia late-onset infection (LOI) in very preterm infants in a large, contemporary, nationally representative cohort.

METHODS

In this secondary analysis of prospectively collected data of preterm infants born 401-1500 grams and/or 22-29 weeks gestational age from 2018 to 2020 at 774 Vermont Oxford Network members, LOI was defined as culture-confirmed blood and/or cerebrospinal fluid infection > 3 days after birth. The primary outcome was incidence of Serratia LOI. Secondary outcomes compared rates of survival and discharge morbidities between infants with Serratia and non-Serratia LOI.

RESULTS

Among 119,565 infants, LOI occurred in 10,687 (8.9%). Serratia was isolated in 279 cases (2.6% of all LOI; 2.3 Serratia infections per 1000 infants). Of 774 hospitals, 161 (21%) reported at least one Serratia LOI; 170 of 271 (63%) cases occurred at hospitals reporting 1 or 2 Serratia infections, and 53 of 271 (20%) occurred at hospitals reporting ≥5 Serratia infections. Serratia LOI was associated with a lower rate of survival to discharge compared with those with non-Serratia LOI (adjusted relative risk 0.88, 95% CI: 0.82-0.95). Among survivors, infants with Serratia LOI had higher rates of tracheostomy, gastrostomy and home oxygen use compared with those with non-Serratia LOI.

CONCLUSIONS

The incidence of Serratia LOI was 2.3 infections per 1000 very preterm infants in this cohort. Lower survival and significant morbidity among Serratia LOI survivors highlight the need for recognition and targeted prevention strategies for this opportunistic nosocomial infection.

Implementation of an automated cluster alert system into the routine work of infection control and hospital epidemiology: experiences from a tertiary care university hospital

Background

Early detection of clusters of pathogens is crucial for infection prevention and control (IPC) in hospitals. Conventional manual cluster detection is usually restricted to certain areas of the hospital and multidrug resistant organisms. Automation can increase the comprehensiveness of cluster surveillance without depleting human resources. We aimed to describe the application of an automated cluster alert system (CLAR) in the routine IPC work in a hospital. Additionally, we aimed to provide information on the clusters detected and their properties.

Methods

CLAR was continuously utilized during the year 2019 at Charité university hospital. CLAR analyzed microbiological and patient-related data to calculate a pathogen-baseline for every ward. Daily, this baseline was compared to data of the previous 14 days. If the baseline was exceeded, a cluster alert was generated and sent to the IPC team. From July 2019 onwards, alerts were systematically categorized as relevant or non-relevant at the discretion of the IPC physician in charge.

Results

In one year, CLAR detected 1,714 clusters. The median number of isolates per cluster was two. The most common cluster pathogens were Enterococcus faecium (n = 326, 19 %), Escherichia coli (n = 274, 16 %) and Enterococcus faecalis (n = 250, 15 %). The majority of clusters (n = 1,360, 79 %) comprised of susceptible organisms. For 906 alerts relevance assessment was performed, with 317 (35 %) alerts being classified as relevant.

Conclusions

CLAR demonstrated the capability of detecting small clusters and clusters of susceptible organisms. Future improvements must aim to reduce the number of non-relevant alerts without impeding detection of relevant clusters. Digital solutions to IPC represent a considerable potential for improved patient care. Systems such as CLAR could be adapted to other hospitals and healthcare settings, and thereby serve as a means to fulfill these potentials.

Sepsis related mortality of extremely low gestational age newborns after the introduction of colonization screening for multi-drug resistant organisms

BACKGROUND

In 2013 German infection surveillance guidelines recommended weekly colonization screening for multidrug-resistant (MDRO) or highly epidemic organisms for neonatal intensive care units (NICUs) and extended hygiene measures based on screening results. It remains a matter of debate whether screening is worth the effort. We therefore aimed to evaluate sepsis related outcomes before and after the guideline update.

METHODS

The German Neonatal Network (GNN) is a prospective cohort study including data from extremely preterm infants between 22 + 0 and 28 + 6 gestational weeks born in 62 German level III NICUs.

RESULTS

Infants treated after guideline update (n = 8.903) had a lower mortality (12.5% vs. 13.8%, p = 0.036), reduced rates for clinical sepsis (31.4 vs. 42.8%, p <  0.001) and culture-proven sepsis (14.4% vs. 16.5%, p = 0.003) as compared to infants treated before update (n = 3.920). In a multivariate logistic regression analysis, nine pathogens of culture-proven sepsis were associated with sepsis-related death, e.g. Pseudomonas aeruginosa [OR 59 (19-180), p <  0.001)]. However, the guideline update had no significant effect on pathogen-specific case fatality, total sepsis-related mortality and culture-proven sepsis rates with MDRO. While the exposure of GNN infants to cefotaxime declined over time (31.1 vs. 40.1%, p <  0.001), the treatment rate with meropenem was increased (31.6 vs. 26.3%, p <  0.001).

CONCLUSIONS

The introduction of weekly screening and extended hygiene measures is associated with reduced sepsis rates, but has no effects on sepsis-related mortality and sepsis with screening-relevant pathogens. The high exposure rate to meropenem should be a target of antibiotic stewardship programs.

Whole-genome sequencing to explore nosocomial transmission and virulence in neonatal methicillin-susceptible Staphylococcus aureus bacteremia

BACKGROUND

Neonatal Staphylococcus aureus (S. aureus) bacteremia is an important cause of morbidity and mortality. In this study, we examined whether methicillin-susceptible S. aureus (MSSA) transmission and genetic makeup contribute to the occurrence of neonatal S. aureus bacteremia.

METHODS

A retrospective, single-centre study was performed. All patients were included who suffered from S. aureus bacteremia in the neonatal intensive care unit (NICU), Erasmus MC-Sophia, Rotterdam, the Netherlands, between January 2011 and November 2017. Whole-genome sequencing (WGS) was used to characterize the S. aureus isolates, as was also done in comparison to reference genomes. Transmission was considered likely in case of genetically indistinguishable S. aureus isolates.

RESULTS

Excluding coagulase-negative staphylococci (CoNS), S. aureus was the most common cause of neonatal bacteremia. Twelve percent (n = 112) of all 926 positive blood cultures from neonates grew S. aureus. Based on core genome multilocus sequence typing (cgMLST), 12 clusters of genetically indistinguishable MSSA isolates were found, containing 33 isolates in total (2-4 isolates per cluster). In seven of these clusters, at least two of the identified MSSA isolates were collected within a time period of one month. Six virulence genes were present in 98-100% of all MSSA isolates. In comparison to S. aureus reference genomes, toxin genes encoding staphylococcal enterotoxin A (sea) and toxic shock syndrome toxin 1 (tsst-1) were present more often in the genomes of bacteremia isolates.

CONCLUSION

Transmission of MSSA is a contributing factor to the occurrence of S. aureus bacteremia in neonates. Sea and tsst-1 might play a role in neonatal S. aureus bacteremia.

Risk Factors and Outcomes of Recurrent Candidemia in Children: Relapse or Re-Infection?

In this paper, our aim was to investigate the incidence, clinical characteristics, risk factors, and outcomes of recurrent candidemia in children. We retrospectively reviewed all children with candidemia from a medical center in Taiwan between 2004 and 2015. Two episodes of candidemia ≥30 days apart with clinical and microbiological resolution in the interim were defined as "late recurrence", and those that had 8⁻29 days apart from previous episodes were defined as "early recurrence". 45 patients (17.2%) had 57 episodes of recurrent candidemia, and 24 had 28 episodes of late recurrent candidemia. The median time between recurrences was 1.8 months (range: <1 month to 13 months). Of those, 29 had relapsed candidemia and 28 were re-infected by different Candida species (n = 24) or by different strains (n = 4). Recurrent candidemia patients were more likely to require echinocandins treatment, had a longer duration of candidemia, and higher rate of treatment failure (p = 0.001, 0.014, and 0.012, respectively). Underlying gastrointestinal diseases (Odds ratio (OR) 3.84; 95% Confidence interval (CI) 1.81⁻8.12) and neurological sequelae (OR 2.32; 95% CI 1.15⁻4.69) were independently associated with the development of recurrent candidemia. 17.2% of pediatric patients with candidemia developed recurrent candidemia, and approximately half were re-infected. Underlying gastrointestinal diseases and neurological sequelae were the independent risk factors for recurrent candidemia.

Factors and outcomes associated with candidemia caused by non-albicans Candida spp versus Candida albicans in children

BACKGROUND

Candidemia in children caused by non-albicans Candida (NAC) spp is increasing in prevalence, but the relevant information is limited.

METHODS

All isolates of pediatric candidemia from a medical center in Taiwan between 2003 and 2015 were enrolled. The characteristics of patients with NAC and Candida albicans candidemia (CAC) were compared.

RESULTS

Among the 319 episodes of candidemia occurring in 262 patients, C albicans accounted for 46.4%. The NAC and CAC groups had no significant differences in demographics, underlying diseases, most risk factors, and clinical characteristics. Patients in the NAC group were significantly more likely to have fluconazole exposure (14.0% vs 6.8%, respectively; P = .045), and NAC species accounted for 70.2% of all recurrent episodes. NAC candidemia had a longer duration of candidemia (median, 3.0 vs 1.0 days after effective antifungal treatment, respectively; P = .001), slower responses to antifungal treatment, and a higher rate of treatment failure than CAC. However, the 2 groups had similar 30-day candidemia-attributable mortality rates. After multivariate logistic regression, longer duration of central venous catheter was the independent risk factor for NAC candidemia in children (odds ratio, 1.21; 95% confidence interval, 1.08-1.35 for every 10-day increment).

CONCLUSIONS

NAC species collectively have emerged as the predominant pathogens of candidemia in children. Prolonged use of a central venous catheter is associated with an increased risk of candidemia caused by NAC species.

Comparison of the incidence, clinical features and outcomes of invasive candidiasis in children and neonates

Background

Invasive candidiasis differs greatly between children and neonates. We aimed to investigate the different therapeutic approaches and their effects on treatment outcomes of these two groups.

Methods

Episodes of neonatal invasive candidiasis were compared with non-neonatal pediatric episodes during a 12-year cohort study. Clinical isolates were documented by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and DNA sequencing, and antifungal susceptibility testing was performed.

Results

A total of 342 episodes of invasive candidiasis (113 neonatal and 229 non-neonatal pediatric episodes) in 281 pediatric patients (96 neonates and 185 children) were identified. Candida albicans was the most common pathogen causing invasive candidiasis in neonates and children (47.8% vs. 44.1%). The antifungal susceptibility profiles were not significantly different between neonates and children. More neonates received amphotericin B as therapy, whereas more children received fluconazole or caspofungin. Compared with children, neonates had a significantly longer duration of fungemia, higher rates of septic shock (34.5% vs. 21.8%; P = 0.013), sepsis-attributable mortality (28.3% vs. 17.5%; P = 0.024) and in-hospital mortality (42.7% vs. 25.4%; P = 0.004) than children. Independent risk factors for treatment failure of invasive candidiasis were septic shock (odds ration [OR] 16.01; 95% confidence interval [CI] 7.64–33.56; P <  0.001), delayed removal of intravenous catheter (OR 6.78; 95% CI 2.80–17.41; P <  0.001), renal failure (OR 5.38; 95% CI 1.99–14.57; P = 0.001), and breakthrough invasive candidiasis (OR 2.99; 95% CI 1.04–8.67; P = 0.043).

Conclusions

Neonatal invasive candidiasis has worse outcomes than non-neonatal pediatric candidiasis. Neonatologists and pediatricians must consider age-specific differences when developing treatment and prevention guidelines, or when interpreting studies of other age groups.

Outbreaks in the neonatal ICU: a review of the literature

PURPOSE OF REVIEW

Neonates in the neonatal ICU (NICU) are uniquely vulnerable to colonization and infection with pathogens such as multidrug resistant Gram-negative bacteria, which in turn are associated with increased infection-related morbidities and higher case-fatality rates. We reviewed the English, French, and German language literature published between 2015 and 2017, for reports of NICU outbreaks.

RECENT FINDINGS

A total of 39 outbreaks in NICUs were reported with Gram-negative bacteria (n = 21; 54%) causing most, and extended spectrum beta-lactamase-producing organisms being the most frequent resistance mechanism reported (n = 5). Five viral outbreaks were reported (respiratory syncytial virus = 3). A significant proportion of outbreaks (33%) did not identify a source. Whole genome sequencing was used more (n = 6 reports). The most common described infection prevention and control interventions included staff and parent education on hand hygiene, patient isolation, additional contact precautions, including discontinuation of 'kangaroo care', and cohorting. Reporting and publication bias are likely common.

SUMMARY

NICUs must be vigilant in identifying outbreaks, conduct comprehensive investigations, and implement targeted infection prevention and control strategies. Molecular epidemiology capacities are an essential element in outbreak investigation. More studies are needed to determine the added value of active colonization screening and their impact on outbreak development.

Clinical and microbiological characteristics, and impact of therapeutic strategies on the outcomes of children with candidemia

We aimed to determine the clinical and microbiological characteristics of Candida bloodstream infections in children and the impact of therapeutic strategies on outcomes. All pediatric patients with candidemia from a medical center in Taiwan over a 13-year period (2003-2015) were included and a total of 262 patients with 319 episodes of candidemia were analyzed. Overall susceptibility to fluconazole was 86.1%. Cumulative mortality at 7 and 30 days after the first episode of candidemia was 13.4% and 25.2%, respectively. The overall in-hospital mortality rate was 35.1%. The treatment outcomes did not change over the study period. Multivariate analysis showed that delayed catheter removal (odds ratio [OR], 5.52; 95% confidence interval [CI]: 2.97-10.25), septic shock (OR, 5.49; 95% CI: 2.85-10.57), and breakthrough candidemia (OR, 3.66; 95% CI: 1.43-9.35) were independently associated with clinical treatment failure. In children with candidemia, underlying renal insufficiency and hematological/oncological malignancy, delayed catheter removal, and septic shock at onset were independently associated final in-hospital mortality. Analyzing the subgroup of non-neonatal children did not change the findings. We concluded overall mortality of pediatric candidemia remains high during the past decade. Prompt early catheter removal and aggressive treatment strategy in patients with septic shock would be critical to improve outcomes.

Breakthrough candidemia in children: clinical and microbiological characteristics, therapeutic strategies and impact on outcomes

AIM

To assess the characteristics, treatments, risk factors and outcomes of breakthrough candidemia in children.

MATERIALS & METHODS

Episodes of breakthrough candidemia in children were compared with the remaining episodes in a 13-year cohort study.

RESULTS

Out of 319 episodes, 45 (14.1%) were breakthrough candidemia. Breakthrough candidemia occurred in patients with more acutely ill conditions, and the majority was caused by non-albicans Candida species (73.3%; 33 episodes). A total of 79.1% of breakthrough candidemia were caused by antifungal-susceptible Candida isolates and emergence of resistance was the mechanism in five cases of patients receiving fluconazole. Episodes of breakthrough candidemia had significantly higher illness severity and higher rates of fungemia-attributable mortality.

CONCLUSION

Breakthrough candidemia independently contributed to unfavorable outcomes, and more aggressive treatment strategies are warranted when breakthrough candidemia is encountered.