Colonization of the gut with Gram-negative bacilli, its association with neonatal sepsis and its clinical relevance in a developing country

Application of Next-Generation Sequencing to Enterobacter Hormaechei Subspecies Analysis during a Neonatal Intensive Care Unit Outbreak

INTRODUCTION

The Enterobacter cloacae complex (ECC) species are potential neonatal pathogens, and ECC strains are among the most commonly encountered Enterobacter spp. associated with nosocomial bloodstream infections. Outbreaks caused by ECC can lead to significant morbidity and mortality in susceptible neonates. At the molecular level, ECC exhibits genomic heterogeneity, with six closely related species and subspecies. Genetic variability poses a challenge in accurately identifying outbreaks by determining the clonality of ECC isolates. This difficulty is further compounded by the limitations of the commonly used molecular typing methods, such as pulsed field gel electrophoresis, which do not provide reliable accuracy in distinguishing between ECC strains and can lead to incorrect conclusions. Next-generation sequencing (NGS) offers superior resolution in determining strain relatedness. Therefore, we investigated the clinical pertinence of incorporating NGS into existing bundle measures to enhance patient management during an outbreak of ECC in a level-3 neonatal intensive care unit (NICU) in Germany.

METHODS

As the standard of care, all neonates on the NICU received weekly microbiological swabs (nasopharyngeal and rectal) and analysis of endotracheal secretion, where feasible. During the 2.5-month outbreak, colonisation with ECC was detected in n = 10 neonates. The phylogenetic relationship and potential antimicrobial resistance genes as well as mobile genetic elements were identified via bacterial whole-genome sequencing (WGS) using Illumina MiSeq followed by in silico data analysis.

RESULTS

Although all ECC isolates exhibited almost identical antimicrobial susceptibility patterns, the WGS data revealed the involvement of four different ECC clones. The isolates could be characterised as Enterobacter hormaechei subspecies steigerwaltii (n = 6, clonal), subsp. hoffmannii (n = 3, two clones) and subsp. oharae (n = 1). Despite the collection of environmental samples, no source of this diffuse outbreak could be identified. A new standardised operating procedure was implemented to enhance the management of neonates colonised with MRGN. This collaborative approach involved both parents and medical professionals and successfully prevented further transmission of ECC.

CONCLUSIONS

Initially, it was believed that the NICU outbreak was caused by a single ECC clone due to the similarity in antibiotic resistance. However, our findings show that antibiotic susceptibility patterns can be misleading in investigating outbreaks of multi-drug-resistant ECC. In contrast, bacterial WGS accurately identified ECC at the clonal level, which significantly helped to delineate the nature of the observed outbreak.

Surveillance of Multidrug-Resistant Pathogens in Neonatal Intensive Care Units of Palermo, Italy, during SARS-CoV-2 Pandemic

BACKGROUND

Antimicrobial resistance (AMR) is a topic of concern, especially in high-level care departments like neonatal intensive care units (NICUs). The systematic use of an "active" epidemiological surveillance system allows us to observe and analyze any changes in microbial distribution, limiting the risk of healthcare-associated infection (HAI) development.

METHODS

We have conducted a longitudinal observational study in the five NICUs of Palermo, comparing the "pre-pandemic period" (March 2014-February 2020) with the "pandemic" one (March 2020-February 2022). The primary aim of the study was to evaluate the cumulative prevalence of carriage from multi-drug resistant (MDR) bacteria in the cumulative NICUs (NICU C).

RESULTS

During the "pre-pandemic period", 9407 swabs were collected (4707 rectal, 4700 nasal); on the contrary, during the "pandemic period", a total of 2687 swabs were collected (1345 rectal, 1342 nasal). A statistically significant decrease in MDR-Gram-negative bacteria (GNB) carriage prevalence was detected during the pandemic. At the same time, there was a general worsening of the carriage of carbapenemase-forming MDR-GNB (CARBA-R+) and methicillin-resistant Staphylococcus aureus (MRSA) during the pandemic period. A significant reduction in methicillin-susceptible Staphylococcus aureus (MSSA) carriage was detected too.

CONCLUSIONS

The surveillance of MDRO carriage in NICUs is fundamental for limiting the social and economic burden of HAIs.

Should Perirectal Swab Culture Be Performed in Cases Admitted to the Neonatal Intensive Care Unit? Lessons Learned from the Neonatal Intensive Care Unit

Serial perirectal swabs are used to identify colonization of multidrug-resistant bacteria and prevent spread. The purpose of this study was to determine colonization with carbapenem-resistant Enterobacterales (CRE) and vancomycin-resistant Enterococci (VRE). An additional purpose was to establish whether sepsis and epidemic associated with these factors were present in the neonatal intensive care unit (NICU), to which infants with hospital stays exceeding 48 h in an external healthcare center NICU were admitted. Perirectal swab samples were collected in the first 24 h by a trained infection nurse using sterile cotton swabs moistened with 0.9% NaCl from patients admitted to our unit after hospitalization exceeding 48 h in an external center. The primary outcome was positivity in perirectal swab cultures, and the secondary outcomes were whether this caused invasive infection and significant NICU outbreaks. A total of 125 newborns meeting the study criteria referred from external healthcare centers between January 2018 and January 2022 were enrolled. Analysis revealed that CRE constituted 27.2% of perirectal swab positivity and VRE 4.8%, and that one in every 4.4 infants included in the study exhibited perirectal swab positivity. The detection of colonization by these microorganisms, and including them within the scope of surveillance, is an important factor in the prevention of NICU epidemics.

Minocycline and the SPR741 Adjuvant Are an Efficacious Antibacterial Combination for Acinetobacter baumannii Infections

Antibiotic resistance, when it comes to bacterial infections, is not a problem that is going to disappear anytime soon. With the lack of larger investment in novel antibiotic research and the ever-growing increase of resistant isolates amongst the ESKAPEE pathogens (Enterobacter cloacae, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterococcus sp., and Escherichia coli), it is inevitable that more and more infections caused by extensively drug-resistant (XDR) and pandrug-resistant (PDR) strains will arise. One strategy to counteract the growing threat is to use antibiotic adjuvants, a drug class that on its own lacks significant antibiotic activity, but when mixed with another antibiotic, can potentiate increased killing of bacteria. Antibiotic adjuvants have various mechanisms of action, but polymyxins and polymyxin-like molecules can disrupt the Gram-negative outer membrane and allow other drugs better penetration into the bacterial periplasm and cytoplasm. Previously, we showed that SPR741 had this adjuvant effect with regard to rifampin; however, rifampin is often not used clinically because of easily acquired resistance. To find additional, appropriate clinical partners for SPR741 with respect to pulmonary and wound infections, we investigated tetracyclines and found a previously undocumented synergy with minocycline in vitro and in vivo in murine models of infection.

Genomic epidemiology, antimicrobial resistance and virulence factors of Enterobacter cloacae complex causing potential community-onset bloodstream infections in a tertiary care hospital of Nepal

Objectives

Community-onset bloodstream infections (BSIs) caused by carbapenemase-producing Enterobacter cloacae complex (ECC) species are increasing internationally. This observation suggests that ECC are emerging pathogens, requiring for detailed understanding on their genomic epidemiology including transmission dynamics and antimicrobial resistance profiles.

Patients and methods

We performed WGS on 79 Enterobacter spp. isolated from the patients with clinically significant BSIs and admitted to emergency department of a major tertiary hospital in Nepal between April 2016 and October 2017.

Results

We identified 5 species and 13 STs of ECC. Enterobacter xiangfangensis ST171, one of the globally emerging carbapenem resistant ECC clones with epidemic potential, was the most prevalent (42%). Phylogenetic analysis showed a large (>19 400 SNPs) core genome SNP distance across major STs, which was minimal (<30 SNPs) among the isolates of each prevalent ST, suggesting the relatively recent importation of major STs followed by local clonal expansions. Genomic evidence for resistance to all major antimicrobial classes except for colistin and macrolides was detected. A limited number of isolates also carried bla NDM-1 (n = 2) and bla OXA-48 (n = 1) carbapenemase genes. Virulence factors encoding siderophores (24%), T6SSD (25%) and fimbriae (54%) were detected.

Conclusions

Our study highlighted that MDR ECC clones are important pathogens of BSIs in community. Though of low prevalence, carbapenem resistance observed in our ECC isolates raised concern about further community dissemination, underscoring the need for community surveillance to identify MDR ECC clones with epidemic potential.

Intestinal Colonization Due to Carbapenem-Resistant Enterobacteriaceae Among Hematological Malignancy Patients in India: Prevalence and Molecular Charecterisation

Faecal carriage of Carbapenem-resistant Enterobacteriaceae (CRE) is being observed as an important risk factor for bacteremia among patients with hematological malignancies. A prospective surveillance study was conducted among these patients to determine the gut colonization of CRE. Rectal/perianal swabs were collected to isolate CRE. Carbapenem resistance was detected by disk diffusion, modified-Hodge, Carba-NP test, and PCR for ^bla NDM-1, ^bla KPC, ^bla OXA-48, ^bla VIM, ^bla IMP genes. A total of 209 CRE isolates were identified from 151 patients. E. coli was the most common (83.2%) CRE identified, followed by Klebsiella spp. (9.6%). The majority of CRE were observed resistant to ertapenem (86%). ^bla NDM-1 was the most common gene (57.3%), followed by ^bla OXA-48 (37.8%). 26.8% isolates found to carry both ^bla NDM-1 and ^bla OXA-48 genes. CRE is increasingly observed to cause bacteremia among hematological malignancy patients due to increased colonization. Screening for gut CRE colonization is necessary to guide empirical therapy and apply infection control measures among these patients.

Colonization with Multidrug-Resistant Bacteria in the First Week of Life among Hospitalized Preterm Neonates in Serbia: Risk Factors and Outcomes

The aim of this prospective cohort study was to determine the prevalence of gut colonization with multidrug-resistant (MDR) bacteria, risk factors for colonization, infection risk, and outcomes among preterm neonates hospitalized at a tertiary-care center in Serbia. During the period from December 2017 to April 2018, 103 neonates were screened for rectal carriage at admission and on the seventh day of life. Characterization of MDR strains was done by conventional microbiology and molecular methods. Out of 61 (59.2%) colonized neonates, 12 (11.6%) were found colonized at admission, while 49 (47.6%) became colonized at the study site. Among a total of 72 MDR isolates, extended-spectrum beta-lactamase (ESBL)-producing enterobacteria prevailed (56/72, 77%), followed by Acinetobacter baumannii (14/72, 19%). The majority of ESBL-producing strains carried multiple genes (blaTEM/blaCTX-M-15 or blaTEM/blaSHV). Longer previous hospitalization and delivery by cesarean section were associated with MDR colonization, while mechanical ventilation was a risk factor for colonization at the study site. Infections due to MDR bacteria were more frequent among colonized than non-colonized neonates, but not significantly, and mortality was low (1%) in the studied neonates. These results indicate that hospitalized preterm neonates in Serbia are rapidly colonized with a diversity of MDR species and resistance phenotypes/genotypes.

Neonatal Sepsis: The Impact of Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae

The convergence of a vulnerable population and a notorious pathogen is devastating, as seen in the case of sepsis occurring during the first 28 days of life (neonatal period). Sepsis leads to mortality, particularly in low-income countries (LICs) and lower-middle-income countries (LMICs). Klebsiella pneumoniae, an opportunistic pathogen is a leading cause of neonatal sepsis. The success of K. pneumoniae as a pathogen can be attributed to its multidrug-resistance and hypervirulent-pathotype. Though the WHO still recommends ampicillin and gentamicin for the treatment of neonatal sepsis, K. pneumoniae is rapidly becoming untreatable in this susceptible population. With escalating rates of cephalosporin use in health-care settings, the increasing dependency on carbapenems, a "last resort antibiotic," has led to the emergence of carbapenem-resistant K. pneumoniae (CRKP). CRKP is reported from around the world causing outbreaks of neonatal infections. Carbapenem resistance in CRKP is largely mediated by highly transmissible plasmid-encoded carbapenemase enzymes, including KPC, NDM, and OXA-48-like enzymes. Further, the emergence of a more invasive and highly pathogenic hypervirulent K. pneumoniae (hvKP) pathotype in the clinical context poses an additional challenge to the clinicians. The deadly package of resistance and virulence has already limited therapeutic options in neonates with a compromised defense system. Although there are reports of CRKP infections, a review on neonatal sepsis due to CRKP/ hvKP is scarce. Here, we discuss the current understanding of neonatal sepsis with a focus on the global impact of the CRKP, provide a perspective regarding the possible acquisition and transmission of the CRKP and/or hvKP in neonates, and present strategies to effectively identify and combat these organisms.

Rectal screening displays high negative predictive value for bloodstream infection with (ESBL-producing) Gram-negative bacteria in neonates with suspected sepsis in a low-resource setting neonatal care unit

OBJECTIVES

We analysed the concordance of rectal swab isolates and blood culture for Gram-negative bacteria (GNB) isolates in neonates with a suspicion of neonatal sepsis admitted to a neonatal care unit in Haiti.

METHODS

We matched pairs of blood and rectal samples taken on the date of suspected sepsis onset in the same neonate. We calculated the proportion of rectal isolates in concordance with the blood isolates by species and genus. We calculated the negative predictive value (NPV) for GNB and extended-spectrum β-lactamase (ESBL)-producing GNB for all rectal and blood isolate pairs in neonates with suspected sepsis.

RESULTS

We identified 238 blood and rectal samples pairs, with 238 blood isolate results and 309 rectal isolate results. The overall concordance in genus and species between blood and rectal isolates was 22.3% [95% confidence interval (CI) 17.4-28.0%] and 20.6% (95% CI 16.0-26.2%), respectively. The highest concordance between blood and rectal isolates was observed for samples with no bacterial growth (65%), followed byKlebsiella pneumoniae (18%) and Klebsiella oxytoca (12%). The NPV of detecting GNB bacterial isolates in rectal samples compared with those in blood samples was 81.6% and the NPV for ESBL-positive GNB was 92.6%.

CONCLUSIONS

The NPV of rectal swab GNB isolates was high in all patient groups and was even higher for ESBL-positive GNB. Clinicians can use the results from rectal swabs when taken simultaneously with blood samples during outbreaks to inform the (de-)escalation of antibiotic therapy in those neonates that have an ongoing sepsis profile.

Colonization of the Preterm Neonatal Gut with Carbapenem-resistant Enterobacteriaceae and Its Association with Neonatal Sepsis and Maternal Gut Flora

Background

Multidrug-resistant Gram-negative neonatal sepsis is associated with high mortality and morbidity. Mucosal colonization with these organisms in hospitals may predispose neonates to septicemia.

Aims

The aim of the study was to determine the prevalence and pattern of colonization of neonatal preterm gut with carbapenem-resistant Enterobacteriaceae and identify risk factors associated with colonization.

Settings and Design

The study was a prospective observational study done in a Level 3 neonatal unit of a tertiary care hospital.

Methods

Stool samples from preterm babies were collected soon after birth and at 1 and 3 weeks of age after consent. Maternal stool sample was collected within 48 h after the delivery. Predetermined antenatal, neonatal, and environmental risk factors were recorded. Isolation and identification of organisms was done in a standardized manner; antibiotic susceptibility was done by the Kirby-Bauer method and results interpreted according to the Clinical and Laboratory Standards Institute guidelines.

Results

Seventy-one percent of the babies were colonized by Gram-negative bacteria (GNB) at birth, and 100% were colonized by the end of the 1^st week. The organisms commonly isolated were Escherichia coli, Klebsiella, NFGNB (Nonfermenting Gram-Negative Bacilli), Pseudomonas, and Enterobacter. Sixty-eight percent of the babies were colonized with extended-spectrum beta-lactamase-producing organisms, and 5% of the babies were colonized with carbapenem-resistant organisms (CROs). In the babies who developed culture-positive sepsis, 21% had concordance of strains in the gut and blood. There was no association between maternal and neonatal colonization.

Conclusions

The results show that neonatal gut is colonized by GNB from birth onward. However, the rate of colonization with CRO is low. An association was also observed between colonization and late-onset sepsis.

Similar Strains of Coagulase-Negative Staphylococci Found in the Gastrointestinal Tract and Bloodstream of Bacteremic Neonates

Objectives

Premature neonates are susceptible to opportunistic and nosocomial infections. Efforts have been made to determine whether the neonatal gut microbiome possesses potential for causing bloodstream infections in newborns via microbial translocation from the gastrointestinal tract. We aimed to examine similarities in coagulase-negative staphylococci (CoNS) strains found in the gastrointestinal tract and bloodstream in bacteremic neonates.

Methods

CoNS strains isolated from blood cultures and perianal and pharyngeal swab samples of neonates from two neonatal intensive care units were investigated using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and pulsed-field gel electrophoresis. Molecular mass and genetic similarities of CoNS strains were compared.

Results

Marked similarity was found in the molecular mass and genetic profile of examined CoNS isolates from blood cultures and perianal/pharyngeal samples. The percentage of neonates developing bacteremia following perianal and pharyngeal colonization by CoNS was significantly higher when compared to those colonized by Enterobacteriales species (p < 0.0002).

Conclusions

CoNS colonizing the gut may be a source of bacteremia in neonates. Enterobacteriales species do not contribute as significantly to bacteremia when compared to CoNS, and may be protective against gut mucosa-originated systemic infection.

Longitudinal Assessment of Antibiotic Resistance in Fecal Escherichia coli in Tanzanian Children

Antibiotic-resistant bacterial infections are a major public health problem, and children in low-resource settings represent a particularly high-risk group. Few data are available on the dynamics of and risk factors for gastrointestinal carriage of antibiotic-resistant bacteria in these vulnerable populations. In this study, we described the antibiotic susceptibility profiles of Escherichia coli isolated from stool specimens collected from children aged 6 to 60 months enrolled in a birth cohort study in Haydom, Tanzania. We estimated the association between sociodemographic risk factors, child illnesses, and antibiotic exposure and E. coli drug resistance. Carriage of antibiotic-resistant E. coli was common starting early in life and did not clearly increase with age. The majority of isolates were resistant to ampicillin (749/837; 89.5%), cefazolin (742/837; 88.6%), and cotrimoxazole (721/837; 86.1%). Resistance to amoxicillin/clavulanate (361/836; 43.2%), ampicillin/sulbactam (178/819; 21.7%), nalidixic acid (131/831; 15.8%), and azithromycin (115/837; 13.7%) was also seen. Only 1.8% (15/837) of the pooled E. coli isolates met the criteria for extended-spectrum beta-lactamase production. High antibiotic use (0.26 additional resistant antibiotic classes; 95% CI: 0.05, 0.47) and high income (0.28 additional resistant antibiotic classes; 95% CI: 0.06, 0.50) were associated with the carriage of antibiotic-resistant E. coli, whereas hospital birth, crowding in the home, improved drinking water and sanitation, and common childhood illnesses were not. In this setting, the carriage of antibiotic-resistant E. coli was common. Other than recent antibiotic exposure and high income, individual risk factors for the acquisition and carriage of resistance could not be identified, suggesting that population-level interventions are needed.

Fecal carriage and molecular epidemiology of carbapenem-resistant Enterobacteriaceae from outpatient children in Shanghai

Background

Fecal colonization with carbapenem-resistant Enterobacteriaceae (CRE) is a risk factor for bacterial translocation resulting in subsequent endogenous infections. The purpose of this study is to investigate the prevalence of CRE strains colonization in stool samples of outpatient in a tertiary pediatric hospital of Shanghai, China.

Methods

In a retrospective study, fecal samples were consecutively obtained from patients in 2016 and screening test for CRE was conducted by using home-made MacConkey agar. Antimicrobial susceptibility was determined by the broth microdilution method and β-lactamases were characterized by polymerase chain reaction (PCR) assays and DNA sequencing. Multilocus sequence typing (MLST) was performed for the genetic relationships of the isolates.

Results

A total of 880 fecal samples were included for this screening test and 32 CRE strains were identified in 32 non-duplicate fecal samples from 32 children (1.3 ± 1.5 years), with a carriage rate of 3.6%. These strains mainly distributed in Klebsiella pnuemoniae (37.5%) and Escherichia coli (37.5%). All CRE strains showed high resistance to most of the routinely used antibiotics (> 90%) except for polymyxin B and tigecycline. The bla_NDM gene was the major carbapenemase gene harbored by gastrointestinal CRE strains, followed by bla_KPC-2, bla_IMP-26, and bla_IMP-4. Other β-Lactamase genes including bla_CTX-M, bla_SHV, bla_TEM-1, and bla_DHA-1 were also detected. MLST analysis revealed that various sequence types (STs) were detected in these strains, with ST11 and ST37 being more prevalent in K.pneumoniae and ST101 in E.coli.

Conclusions

This study revealed the prevalence of CRE fecal carriage in children from outpatient and urgent implementation of infection control measure should be conducted to limit the spread of CRE strains.

Central Line-Associated Blood Stream Infections and Non-Central Line-Associated Blood Stream Infections Surveillance in Canadian Tertiary Care Neonatal Intensive Care Units

OBJECTIVE

To determine if the reported reduction in hospital-acquired infections is due to reduced central line-associated blood stream infections (CLABSI) or non-CLABSIs.

STUDY DESIGN

A retrospective cohort study design was used to describe the change in organism pattern and incidence of hospital-acquired infections (CLABSIs and non-CLABSIs) in neonates <33 weeks of gestation admitted to tertiary neonatal intensive care units in the Canadian Neonatal Network between January 1, 2010, and December 31, 2016. Hospital-acquired infection was diagnosed when a pathogenic organism was isolated from blood or cerebrospinal fluid in a neonate with suspected sepsis. CLABSI was diagnosed when a central venous catheter was present at the time or removed in the 2 days before a hospital-acquired infection diagnosis. Cochran-Armitage and Mann-Kendall trend tests and linear regression models were used for statistical analyses.

RESULTS

Of 28 144 eligible neonates from 30 Canadian Neonatal Network neonatal intensive care units, 3306 (11.7%) developed hospital-acquired infections. There was a significant decrease in the rate of hospital-acquired infections (14.2% in 2010 and 9.2% in 2016; P < .01), and the rate of both CLABSIs and non-CLABSIs (P < .01) over the study period concomitant with a significant decrease in the duration of central line use (P = .01). The rates of meningitis also decreased during the study period (1.2% in 2010 and 0.9% in 2016; P < .01). Infections owing to gram-positive cocci significantly decreased, but infections owing to gram-negative organisms remained unchanged.

CONCLUSION

Although there was a significant decrease in CLABSIs and non-CLABSIs, hospital-acquired infections in preterm neonates remained high. Infections owing to gram-negative organisms remained unchanged and are a target for future preventative efforts.

Neonatal sepsis due to glycopeptide resistant Enterococcus faecium from colonized maternal gut- rare case evidence

Background

Vancomycin-resistant enterococcal infections in the neonatal ICU are growing global problems. We report a case of neonatal septicemia by multidrug-resistant vancomycin-resistant Enterococcus faecium (VRE), the source of infection being the mother's gut.

Case presentation

A newborn male child admitted to the neonatal intensive care unit (NICU) was diagnosed to have mild meconium aspiration syndrome, early onset neonatal septicemia, and bacteremia by multidrug and vancomycin-resistant Enterococcus faecium. Screening of gut flora of the baby and the mother were carried out to trace the source of infection. Stool cultures of the mother and the baby yielded Vancomycin-Resistant Enterococcus faecium. All three isolates of Enterococcus faecium had similar antibiogram, harbored the vanA gene and similar pulsed-field gel electrophoresis pattern. Baby responded to the 1 week therapy with oral linezolid suspension 20 mg/kg/day, 1 ml/t.d.s. No VRE was isolated from baby on a repeat stool culture 1 week after the linezolid therapy. He was discharged with the advice for the continuance of linezolid for seven more days.

Conclusion

Isolation of MDR-VRE from the blood culture of the baby and stool specimens of the mother and the baby with the same antibiogram profile and clonal similarities reveals that maternal gut colonization was responsible for neonatal sepsis. Optimal infection control measures and the development of guidelines for monitoring VRE colonization in pregnant women might be useful in reducing the occurrence of neonatal sepsis.

Outgrowing the Immaturity Myth: The Cost of Defending From Neonatal Infectious Disease

Newborns suffer high rates of mortality due to infectious disease-this has been generally regarded to be the result of an "immature" immune system with a diminished disease-fighting capacity. However, the immaturity dogma fails to explain (i) greater pro-inflammatory responses than adults in vivo and (ii) the ability of neonates to survive a significantly higher blood pathogen burden than of adults. To reconcile the apparent contradiction of clinical susceptibility to disease and the host immune response findings when contrasting newborn to adult, it will be essential to capture the entirety of available host-defense strategies at the newborn's disposal. Adults focus heavily on the disease resistance approach: pathogen reduction and elimination. Newborn hyperactive innate immunity, sensitivity to immunopathology, and the energetic requirements of growth and development (immune and energy costs), however, preclude them from having an adult-like resistance response. Instead, newborns also may avail themselves of disease tolerance (minimizing immunopathology without reducing pathogen load), as a disease tolerance approach provides a counterbalance to the dangers of a heightened innate immunity and has lower-associated immune costs. Further, disease tolerance allows for the establishment of a commensal bacterial community without mounting an unnecessarily dangerous immune resistance response. Since disease tolerance has its own associated costs (immune suppression leading to unchecked pathogen proliferation), it is the maintenance of homeostasis between disease tolerance and disease resistance that is critical to safe and effective defense against infections in early life. This paradigm is consistent with nearly all of the existing evidence.

NDM-1- and OXA-23-producing Acinetobacter baumannii isolated from intensive care unit patients in Tunisia

Gastrointestinal colonisation by carbapenem-resistant Acinetobacter baumannii (CRAB) is a critical step before nosocomial infection. This study evaluated CRAB intestinal carriage in patients admitted to a Tunisian ICU and determined the antimicrobial resistance mechanisms involved. From December 2014 to February 2015, all 63 patients admitted to the ICU were screened for rectal CRAB colonisation upon admission and once weekly thereafter. ICU patients who acquired a CRAB nosocomial infection were also included. β-Lactamases and associated resistance genes were screened by PCR sequencing, and molecular typing was performed by PFGE and MLST. The CRAB faecal carriage rate at admission was 4.8% (3/63). The CRAB acquisition rate during ICU stay was analysed in 39 of the remaining 60 patients and the rate of acquired CRAB faecal carriage was 15.4% (6/39); 4 patients also showed an ICU-acquired CRAB infection (one patient was a faecal carrier and suffered infection). Overall, 13 CRAB isolates were collected from 12 patients, of which 11 isolates showed resistance to all antibiotics tested except colistin. bla_OXA-23 and bla_NDM-1 were detected in 11 and 2 isolates, respectively. All OXA-23-producing strains carried armA, tetB, sul1 and catB, and some of them carried aph(3')-VIa, bla_TEM-1, aph(3')-Ia and ant(2'')-Ia. The bla_NDM-1-positive isolates harboured aph(3')-VIa and catB. Three PFGE patterns and two STs were identified [ST195 (n = 11), ST1089 (n = 2, NDM-1-positive)]. Whether imported or acquired during ICU stay, CRAB colonisation is a major risk factor for the occurrence of serious nosocomial infection. Systematic screening of faecal carriage is mandatory to prevent their spread.

Acquisition of extended spectrum beta-lactamase-producing enterobacteriaceae in neonates: A community based cohort in Madagascar

In low and middle income countries (LMICs), where the burden of neonatal sepsis is the highest, the spread of extended spectrum beta-lactamase-producing enterobacteriaceae (ESBL-PE) in the community, potentially contributing to the neonatal mortality, is a public health concern. Data regarding the acquisition of ESBL-PE during the neonatal period are scarce. The routes of transmission are not well defined and particularly the possible key role played by pregnant women. This study aimed to understand the neonatal acquisition of ESBL-PE in the community in Madagascar. The study was conducted in urban and semi-rural areas. Newborns were included at birth and followed-up during their first month of life. Maternal stool samples at delivery and six stool samples in each infant were collected to screen for ESBL-PE. A Cox proportional hazards model was performed to identify factors associated with the first ESBL-PE acquisition. The incidence rate of ESBL-PE acquisition was 10.4 cases/1000 newborn-days [95% CI: 8.0–13.4 cases per 1000 newborn-days]. Of the 83 ESBL-PE isolates identified, Escherichia coli was the most frequent species (n = 28, 34.1%), followed by Klebsiella pneumoniae (n = 20, 24.4%). Cox multivariate analysis showed that independent risk factors for ESBL-PE acquisition were low birth weight (adjusted Hazard-ratio (aHR) = 2.7, 95% CI [1.2; 5.9]), cesarean-section, (aHR = 3.4, 95% CI [1.7; 7.1]) and maternal use of antibiotics at delivery (aHR = 2.2, 95% CI [1.1; 4.5]). Our results confirm that mothers play a significant role in the neonatal acquisition of ESBL-PE. In LMICs, public health interventions during pregnancy should be reinforced to avoid unnecessary caesarean section, unnecessary antibiotic use at delivery and low birth weight newborns.

The relationship between Gram-negative colonization and bloodstream infections in neonates: a systematic review and meta-analysis

OBJECTIVES

Neonates admitted to neonatal intensive care units (NICU) are at significant risk of developing bloodstream infections (BSIs). Gram-negative bacteria (GNB) both colonize and infect, but the association between these entities is unclear. By conducting a systematic literature review, we aimed to explore the impact of factors on the association between GN colonization and GN-BSI at both baby-level and unit-level.

METHODS

We searched Medline, Embase, and Cochrane Library. Observational cohort studies published after 2000 up to June 2016 reporting data on the total number of neonates (0-28 days) colonized with GNB assessed by rectal/skin swab culture and the total number of neonates with GN-BSI (same bacteria) were included. Studies were excluded if data on skin/rectal colonization, neonates, and GNB could not be identified separately. Meta-analyses along with multivariate meta-regression with a random-effect model were performed to investigate factors associated with the GN colonization and GN-BSI at baby-level and unit-level.

RESULTS

Twenty-seven studies fulfilled our inclusion criteria, 15 for the baby-level and 12 for the unit-level analysis. Study heterogeneity was high, with suboptimal overall quality of reporting assessed by the STROBE-NI statement (44.8% of items adequately reported). In 1984 colonized neonates, 157 (7.9%) developed GN-BSI compared with 85 of 3583 (2.4%) non-colonized neonates. Considerable heterogeneity was observed across studies. Four factors were included in the meta-regression model: gross domestic product (GDP), pathogen, outbreak, and frequency of screening. There was no statistically significant impact of these factors on GN colonization and GN-BSI in baby-level. We were unable to perform the multivariate meta-regression because of insufficient reported data for unit-level.

CONCLUSIONS

Study limitations include the small number and the high heterogeneity of the included studies. While this report shows a correlation between colonization and BSI risk, these data currently do not support routine screening for GNB. Analysis of large cohorts of colonized neonates with clinical outcomes is still needed to define the major determinants leading from colonization to infection.

High Prevalence of Antimicrobial-resistant Gram-negative Colonization in Hospitalized Cambodian Infants

BACKGROUND

Antimicrobial-resistant Gram-negative infections are a significant cause of mortality in young infants. We aimed to determine characteristics of, and risk factors for, colonization and invasive infection caused by 3rd generation cephalosporin (3GC) or carbapenem-resistant organisms in outborn infants admitted to a neonatal unit (NU) in Cambodia.

METHODS

During the first year of operation, patients admitted to the Angkor Hospital for Children NU, Siem Reap, Cambodia, underwent rectal swabbing on admission and twice weekly until discharge. Swabs were taken also from 7 environmental sites. Swabs were cultured to identify 3GC or carbapenem-resistant Acinetobacter sp., Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa.

RESULTS

The study included 333 infants with a median age at NU admission of 10 days (range, 0-43). Colonization by ≥1 3GC-resistant organism was detected in 85.9% (286/333). Admission swabs were collected in 289 infants: 61.9% were colonized by a 3GC-resistant organism at the time of admission, and a further 23.2% were colonized during hospitalization, at a median of 4 days [95% confidence interval: 3-5]. Probiotic treatment (hazard ratio: 0.58; 95% confidence interval: 0.35-0.98) was associated with delayed colonization. Colonization by a carbapenem-resistant organism occurred in 25 (7.5%) infants. Six infants had NU-associated K. pneumoniae bacteremia; phenotypically identical colonizing strains were found in 3 infants. Environmental colonization occurred early.

CONCLUSIONS

Colonization by antimicrobial-resistant Gram-negative organisms occurred early in hospitalized Cambodian infants and was associated with subsequent invasive infection. Trials of potential interventions such as probiotics are needed.

Gastric fluid versus amniotic fluid analysis for the identification of intra-amniotic infection due to Ureaplasma species

OBJECTIVE

Early neonatal sepsis is often due to intra-amniotic infection. The stomach of the neonate contains fluid swallowed before and during delivery. The presence of bacteria as well as neutrophils detected by culture or Gram stain of the gastric fluid during the first day of life is suggestive of exposure to bacteria or inflammation. We undertook this study to determine the relationship between gastric fluid analysis and amniotic fluid obtained by transabdominal amniocentesis in the detection of Ureaplasma species, the most frequent microorganisms responsible for intra-amniotic infection.

MATERIALS AND METHODS

The study population consisted of 100 singleton pregnant women who delivered preterm neonates (<35 weeks) within 7 days of amniocentesis. Gastric fluid of newborns was obtained by nasogastric intubation on the day of birth. Amniotic fluid and gastric fluid were cultured for genital Mycoplasmas, and polymerase chain reaction (PCR) for Ureaplasma species was performed. Intra-amniotic inflammation was defined as an elevated amniotic fluid matrix metalloproteinase-8 concentration (>23 ng/mL).

RESULTS

(1) Ureaplasma species were detected by culture or PCR in 18% (18/100) of amniotic fluid samples and in 5% (5/100) of gastric fluid samples; (2) among the amniotic fluid cases positive for Ureaplasma species, these microorganisms were identified in 27.8% (5/18) of gastric fluid samples; (3) none of the cases negative for Ureaplasma species in the amniotic fluid were found to be positive for these microorganisms in the gastric fluid; (4) patients with amniotic fluid positive for Ureaplasma species but with gastric fluid negative for these microorganisms had a significantly higher rate of intra-amniotic inflammation, acute histologic chorioamnionitis, and neonatal death than those with both amniotic fluid and gastric fluid negative for Ureaplasma species; and (5) no significant differences were observed in the rate of intra-amniotic inflammation, acute histologic chorioamnionitis, and neonatal death between patients with amniotic fluid positive for Ureaplasma species but with gastric fluid negative for these microorganisms and those with both amniotic fluid and gastric fluid positive for Ureaplasma species.

CONCLUSIONS

Gastric fluid analysis has 100% specificity in the identification of intra-amniotic infection with Ureaplasma species. However, the detection of Ureaplasma species by culture or PCR in the gastric fluid of neonates at birth did not identify these microorganisms in two-thirds of cases with microbial invasion of the amniotic cavity. Thus, amniotic fluid analysis is superior to that of gastric fluid in the identification of intra-amniotic infection.

Prevalence of fecal carriage of extended-spectrum- and metallo-β-lactamase-producing gram-negative bacteria among neonates born in a hospital setting in central Saudi Arabia

BACKGROUND AND OBJECTIVES

Commensal neonatal fecal flora constitute a reservoir of antibiotic resistance. The aim of this study was to characterize the prevalence of fecal carriage of extended spectrum beta lactamases (ESBLs) and carbapenemase producing gram-negative bacteria among 150 neonates who were born in two hospitals in central Saudi Arabia.

PATIENTS AND METHODS

From June 2012 to January 2013, 150 healthy neonates.

Arginine depletion increases susceptibility to serious infections in preterm newborns

Preterm newborns are highly susceptible to bacterial infections. This susceptibility is regarded as being due to immaturity of multiple pathways of the immune system. However, it is unclear whether a mechanism that unifies these different, suppressed pathways exists. Here, we argue that the immune vulnerability of the preterm neonate is critically related to arginine depletion. Arginine, a "conditionally essential" amino acid, is depleted in acute catabolic states, including sepsis. Its metabolism is highly compartmentalized and regulated, including by arginase-mediated hydrolysis. Recent data suggest that arginase II-mediated arginine depletion is essential for the innate immune suppression that occurs in newborn models of bacterial challenge, impairing pathways critical for the immune response. Evidence that arginine depletion mediates protection from immune activation during first gut colonization suggests a regulatory role in controlling gut-derived pathogens. Clinical studies show that plasma arginine is depleted during sepsis. In keeping with animal studies, small clinical trials of L-arginine supplementation have shown benefit in reducing necrotizing enterocolitis in premature neonates. We propose a novel, broader hypothesis that arginine depletion during bacterial challenge is a key factor limiting the neonate's ability to mount an adequate immune response, contributing to the increased susceptibility to infections, particularly with respect to gut-derived sepsis.

A five-year experience of carbapenem resistance in Enterobacteriaceae causing neonatal septicaemia: predominance of NDM-1

Treatment of neonatal sepsis has become a challenge with the emergence of carbapenemase-producing bacteria. This study documents the trend of carbapenem susceptibility in Enterobacteriaceae that caused septicaemia in neonates over a five year period (2007-2011) and the molecular characterisation of Enterobacteriaceae resistant to carbapenems and cephalosporins. Hundred and five Enterobacteriaceae including Escherichia coli (n = 27), Klebsiella pneumoniae (n = 68) and Enterobacter spp. (n = 10) were isolated from blood of septicaemic neonates followed by antibiotic susceptibility tests, determination of MIC values, phenotypic and genotypic detection of β-lactamases. Carbapenem was the most active antimicrobial tested after tigecycline. CTX-M type was the most prevalent ESBL throughout the period (82%). New Delhi Metallo-β-lactamase-1 (NDM-1), which is a recent addition to the carbapenemase list, was the only carbapenemase identified in our setting. Fourteen percent of the isolates possessed blaNDM-1. Carbapenem non-susceptibility was first observed in 2007 and it was due to loss of Omp F/Ompk36 in combination with the presence of ESBLs/AmpCs. NDM-1 first emerged in E. coli during 2008; later in 2010, the resistance was detected in K. pneumoniae and E. cloacae isolates. NDM-1-producing isolates were resistant to other broad-spectrum antibiotics and possessed ESBLs, AmpCs, 16S-rRNA methylases, AAC(6')-Ib-cr, bleomycin resistant gene and class 1 integron. Pulsed field gel electrophoresis of the NDM-1-producing isolates indicated that the isolates were clonally diverse. The study also showed that there was a significantly higher incidence of sepsis caused by NDM-1-harbouring isolates in the male sex, in neonates with low birth weight and neonates born at an extramural centre. However, sepsis with NDM-1-harbouring isolates did not result in a higher mortality rate. The study is the first to review the carbapenem resistance patterns in neonatal sepsis over an extended period of time. The study highlights the persistence of ESBLs (CTX-Ms) and the emergence of NDM-1 in Enterobacteriaceae in the unit.

Neonatal sepsis: the gut connection

Colonization of the neonatal gut takes place immediately after birth. Bacteria that get colonized are considered to be "normal" flora derived principally from the mother and the immediate environment. However, for some neonates, the colonization of the gut, particularly with potential pathogens, may lead to subsequent infections or sepsis. The immune system and the gut barrier in neonates is vulnerable, with decreased acid secretion, low levels of protective mucous, and decreased motility, particularly in those who are premature and of low birth weight. This makes the neonatal gut especially prone to colonization with aerobic Gram-negative bacilli (GNB). And these GNB may later, under circumstances favorable to them, cause disease in the neonates. In developing countries, it is the GNB that cause the majority of the infections. In addition, the use of antibiotics in the neonatal intensive care unit also triggers colonization with antibiotic-resistant bacteria. This review discusses various aspects of neonatal gut colonization, neonatal sepsis, and tries to gather support to understand the connection between the gut and subsequent sepsis in neonates.

Treatment option for sepsis in children in the era of antibiotic resistance

Sepsis caused by multidrug-resistant microorganisms is one of the most serious infectious diseases of childhood and poses significant challenges for pediatricians involved in management of critically ill children. This review discusses the use of pharmacokinetic/dynamic principles (i.e., prolonged infusion of β-lactams and vancomycin, once-daily administration of aminoglycosides and rationale of therapeutic drug monitoring) when prescribing antibiotics to critically ill patients. The potential of 'old' agents (i.e., colistin, fosfomycin) and newly approved antibiotics is critically reviewed. The pros and cons of combination antibacterial therapy are discussed and finally suggestions for the treatment of sepsis caused by multidrug-resistant organisms are provided.

The high prevalence of serine protease autotransporters of Enterobacteriaceae (SPATEs) in Escherichia coli causing neonatal septicemia

Serine protease autotransporters of Enterobacteriaceae (SPATEs) are secreted proteins demonstrating diverse virulence functions. The distribution of SPATEs is studied among diarrheagenic and extraintestinal pathogenic Escherichia coli. However, the contribution of SPATEs to the virulence of neonatal septicemic Escherichia coli (NSEC) has not yet been elucidated. This study was undertaken to evaluate the prevalence and phylogenetic distribution of different subtypes of SPATEs among NSEC. The presence of virulence factors and subtypes of SPATEs among different E. coli isolates was determined by polymerase chain reaction (PCR). E. coli phylogrouping was done by triplex PCR. Clonality of the isolates was assessed by pulsed-field gel electrophoresis (PFGE). The presence of SPATEs was significantly higher among the septicemic isolates (89 %) than the fecal (7.5 %) and environmental isolates (2.5 %). Vat (vacuolating autotransporter toxin) and Sat (secreted autotransporter toxin) were found to be the two most predominant SPATEs. The incidence of SPATEs was high in septicemic isolates of phylogroups A and B1 (87 %), lacking other virulence factors. The high prevalence of SPATEs in the non-B2 phylogroups of septicemic isolates in comparison with fecal and environmental isolates indicates an association of SPATEs with NSEC. The NSEC isolates were found to be clonally distinct, suggesting that the high prevalence of SPATEs was not due to clonal relatedness of the isolates. This study is the first to show the association of SPATEs with NSEC. The presence of SPATEs in the septicemic/NSEC isolates may be considered as the most discriminatory trait studied here.

Carriage prevalence of carbapenem-resistant Enterobacteriaceae in stool samples: A surveillance study

BACKGROUND

With more people being exposed to antibiotics, intestinal microflora faces constant pressure of antibiotic selection, which has resulted in the emergence of multidrug resistant strains. This may pose a severe problem as intestinal Enterobacteriaceae members are commonly implicated in human infections.

AIMS

This surveillance study was undertaken to investigate the carriage of carbapenem-resistant Enterobacteriaceae (CRE) in the gastrointestinal tract among patients attending the outpatient clinic in a tertiary care center of East Delhi, India.

METHOD

We performed a prospective surveillance study to screen 242 Enterobacteriaceae isolates for carbapenemase production from the stool samples of 123 outpatients attending a tertiary care hospital in East Delhi over a four-month period.

RESULTS

Twenty-four (9.9 per cent) isolates demonstrated carbapenemase activity among 242 screened Enterobacteriaceae isolates. Four stool samples had two isolates of different species, both eliciting this feature and therefore indicating presence of multiple carbapenem-resistant Enterobacteriaceae (CRE) isolates in a single sample.

CONCLUSION

Screening for carriage of CRE in stools of patients undergoing elective or emergency gastrointestinal surgical procedures, with haematological malignancies taking chemotherapy, or those planned for bone marrow transplantation can guide clinicians about gut colonisation of multidrug-resistant Enterobacteriaceae as these groups of patients are at risk of possible endogenous infection.

Managing and preventing outbreaks of Gram-negative infections in UK neonatal units

De novo guidance on the management of Gram-negative bacteria outbreaks in UK neonatal units was developed in 2012 by a Department of Health, England Antimicrobial Resistance and Healthcare Associated Infection working group. The recommendations included activation of an organisational response and establishing a control team when an outbreak is suspected; screening for the specific organism only during an outbreak; undertaking multidisciplinary reviews of cleaning routines, hand hygiene and Gram-negative bacteria transmission risks; considering deep-cleaning; cohorting colonised and infected babies preferably but not necessarily in isolation cubicles; and considering reducing beds or closing a unit to new admissions as a way of improving spacing and staff:patient ratios until the outbreak is under control. The group advised establishing mechanisms to communicate effectively across the network; informing parents of the outbreak as early as possible, and providing prewritten 'infection outbreak' information sheets. For prevention of outbreaks, the group advised meeting national staffing and cot-spacing requirements; following a Water Action Plan; using infection reduction care bundles and benchmarking; and introducing breast milk early and limiting antibiotic use.

Composition of Escherichia coli population in the neonatal gut: phylogroups and virulence determinants

The composition of Escherichia coli in the neonatal gut has rarely been studied in developing countries. To gain insight into the composition of E. coli in the neonatal gut and to assess factors that could influence colonization by E. coli, analysis of the phylogenetic groups and virulence determinants of E. coli isolated from the guts of neonates in a tertiary care hospital was carried out. The distribution of the phylogroups of 124 E. coli isolates recovered showed that phylogroups A (23 %) and B1 (49 %) accounted for 72 % of the isolates. Isolates of the phylogenetic group B2 were rare (8 %). Virulence factors were also rare with the exception of aerobactin (iucC), which was detected in 45 % of the isolates and was significantly associated with phylogroup B1. Multinomial logistic regression established that colonization with phylogroup B1 was associated with a stay in the neonatal intensive care unit; phylogroup A was associated with a stay on the ward; and phylogroups B2 and D were associated with neonates delivered vaginally. Evaluation of the effect of different E. coli phylogroups, with and without identified virulence determinants, on the gut of neonatal mice showed histopathological changes in the mucosa. The severity of the changes could be correlated with the presence of virulence determinants, irrespective of the phylogroup.

The gut is the epicentre of antibiotic resistance

The gut contains very large numbers of bacteria. Changes in the composition of the gut flora, due in particular to antibiotics, can happen silently, leading to the selection of highly resistant bacteria and Candida species. These resistant organisms may remain for months in the gut of the carrier without causing any symptoms or translocate through the gut epithelium, induce healthcare-associated infections, undergo cross-transmission to other individuals, and cause limited outbreaks. Techniques are available to prevent, detect, and treat the carriage of resistant organisms in the gut. However, evidence on these techniques is scant, the only exception being selective digestive decontamination (SDD), which has been extensively studied in neutropenic and ICU patients. After the destruction of resistant colonizing bacteria, which has been successfully obtained in several studies, the gut could be re-colonized with normal faecal flora or probiotics. Studies are warranted to evaluate this concept.