Clinical analysis of Enterobacter bacteremia in pediatric patients: a 10-year study

Risk factors for microbiologic failure in children with Enterobacter species bacteremia

Background

Enterobacter species are an important cause of healthcare-associated bloodstream infections (BSI) in children. Up to 19% of adult patients with Enterobacter BSI have recurrence of infection resistant to third-generation cephalosporins (3GCs) while on therapy with a 3GC. Data are lacking regarding the incidence of and risk factors for recurrence of infection in children with Enterobacter BSI.

Methods

We conducted a retrospective case-control study of patients aged ≤21 years old admitted to Texas Children’s Hospital from January 2012 through December 2018 with Enterobacter BSI. The primary outcome was microbiologic failure from 72 hours to 30 days after the initial BSI (cases). The secondary outcome was isolation of a 3GC non-susceptible Enterobacter sp. from a patient with an initial 3GC-susceptible isolate.

Results

Twelve patients (6.7%) had microbiologic failure compared to 167 controls without microbiologic failure. Of the 138 patients (77.1%) with an Enterobacter sp. isolate that was initially susceptible to 3GCs, 3 (2.2%) developed a subsequent infection with a non-susceptible isolate. Predictors of microbiologic failure were having an alternative primary site of infection besides bacteremia without a focus or an urinary tract infection (OR, 9.64; 95% CI, 1.77–52.31; P < 0.01) and inadequate source control (OR, 22.16; 95% CI, 5.26–93.36; P < 0.001).

Conclusions

Source of infection and adequacy of source control are important considerations in preventing microbiologic failure. In-vitro susceptibilities can be used to select an antibiotic regimen for the treatment of Enterobacter BSI in children.

Metagenomic analysis of viruses, bacteria and protozoa in irrigation water

Viruses (e.g., noroviruses and hepatitis A and E virus), bacteria (e.g., Salmonella spp. and pathogenic Escherichia coli) and protozoa (e.g., Cryptosporidium parvum and Giardia intestinalis) are well-known contributors to food-borne illnesses linked to contaminated fresh produce. As agricultural irrigation increases the total amount of water used annually, reclaimed water is a good alternative to reduce dependency on conventional irrigation water sources. European guidelines have established acceptable concentrations of certain pathogens and/or indicators in irrigation water, depending on the irrigation system used and the irrigated crop. However, the incidences of food-borne infections are known to be underestimated and all the different pathogens contributing to these infections are not known. Next-generation sequencing (NGS) enables the determination of the viral, bacterial and protozoan populations present in a water sample, providing an opportunity to detect emerging pathogens and develop improved tools for monitoring the quality of irrigation water. This is a descriptive study of the virome, bacteriome and parasitome present in different irrigation water sources. We applied the same concentration method for all the studied samples and specific metagenomic approaches to characterize both DNA and RNA viruses, bacteria and protozoa. In general, most of the known viral species corresponded to plant viruses and bacteriophages. Viral diversity in river water varied over the year, with higher bacteriophage prevalences during the autumn and winter. Reservoir water contained Enterobacter cloacae, an opportunistic human pathogen and an indicator of fecal contamination, as well as Naegleria australiensis and Naegleria clarki. Hepatitis E virus and Naegleria fowleri, emerging human pathogens, were detected in groundwater. Reclaimed water produced in a constructed wetland system presented a virome and bacteriome that resembled those of freshwater samples (river and reservoir water). Viral, bacterial and protozoan pathogens were occasionally detected in the different irrigation water sources included in this study, justifying the use of improved NGS techniques to get a comprehensive evaluation of microbial species and potential environmental health hazards associated to irrigation water.

Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes

Currency is possibly one of the main media transmitting pathogens and drug resistance due to its wide circulation in daily life. In this study, we made a comprehensive characterization of the bacterial community present on banknotes collected from different geographical regions of Hong Kong (HK) by performing in vitro characterization of the bacterial presence and resistome profile, as well as metagenomic analysis including microbial diversity, the prevalence of potential pathogens, the dissemination potential of antibiotic-resistance genes (ARGs), among others. When comparing the bacterial community of HK banknotes with other HK environmental samples, including water and marine sediment, we revealed that HK banknotes cover nearly 50% of total genera found in all the environmental samples, implying that banknotes harbor diverse bacteria originated from a variety of environments. Furthermore, the banknotes have higher abundance of potential pathogenic species (~5 times more) and ARGs (~5 times more) with higher dissemination potential (~48 times more) compared with other environmental samples. These findings unveiled the capabilities of this common medium of exchange to accommodate various bacteria, and transmit pathogens and antibiotic resistance. Furthermore, the observed independence of microbiome profile from the city's topological indices led us to formulate a hypothesis that due to their high circulation banknotes may harbor a homogenized microbiome.

Nosocomial outbreak of extended-spectrum β-lactamase-producing Enterobacter ludwigii co-harbouring CTX-M-8, SHV-12 and TEM-15 in a neonatal intensive care unit in Venezuela

Enterobacter spp. have emerged as an important group of pathogens linked to outbreaks in neonatal intensive care units (NICUs), usually involving strains expressing extended-spectrum β-lactamases (ESBLs). The aim of this study was to describe the first nosocomial bloodstream infection outbreak caused by Enterobacter ludwigii co-harbouring CTX-M-8, SHV-12 and TEM-15 in a NICU in a Venezuelan hospital. Initial bacterial identification was achieved by VITEK^®2 system and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (VITEK^® MS) and was subsequently confirmed by nucleotide sequencing of the 16S rDNA gene and hsp60 genotyping. Antimicrobial susceptibility testing was determined by AST-GN-299 VITEK^®2 system cards and Etest strips. Isolates were typed by repetitive element sequence-based PCR (rep-PCR). Detection of bla_ESBL genes was carried out by molecular methods. Plasmid analysis included Southern blot and restriction pattern analysis, with transferability of resistance genes being assessed by conjugation. ESBL-producing E. ludwigii isolates were recovered from three neonates with bloodstream infection from the NICU in a 21-day period. rep-PCR fingerprints were indistinguishable among all of the isolates, strongly suggesting spread of a clonal strain. All isolates carried an ca. 56kb conjugative plasmid harbouring the bla_CTX-M-8, bla_SHV-12 and bla_TEM-15 genes. Considering that isolation of ESBL-producing E. ludwigii remains an unusual phenomenon, not previously reported in Venezuela, the results of this study reveal the potential role of E. ludwigii as an emerging pathogen and highlight the importance of microbiological surveillance and judicious antibiotic use as measures to curb the emergence and spread of ESBL-producing bacteria.

Clinical characteristics and outcomes of spontaneous bacterial peritonitis caused by Enterobacter species versus Escherichia coli: a matched case-control study

Background

Enterobacter species are important nosocomial pathogens, and there is growing concern about their ability to develop resistance during antimicrobial therapy. However, few data are available on the clinical characteristics and outcomes of Enterobacter spontaneous bacterial peritonitis (SBP).

Methods

We retrospectively identified all patients with SBP caused by Enterobacter species admitted to a tertiary care hospital between January 1997 and December 2013. Each case was age- and sex-matched with four patients with Escherichia coli SBP.

Results

A total of 32 cases with Enterobacter SBP and 128 controls with E. coli SBP were included. Twenty-one (65.6 %) cases and 111 (86.7 %) controls had Child-Pugh class C (P = 0.006). Cases were significantly more likely to have hepatocellular carcinoma (65.6 % vs. 37.5 %, P = 0.004) and upper gastrointestinal bleeding (28.1 % vs. 9.4 %, P = 0.005). The initial response to empirical therapy (81.3 % vs. 81.2 %, P = 0.995) and the 30-day mortality (37.5 % vs. 28.9 %, P = 0.35) were not significantly different between the groups. Drug resistance emerged in one case and in no controls (4.3 % [1/23] vs. 0 % [0/98], P = 0.19).

Conclusions

Compared with E. coli SBP, patients with Enterobacter SBP more frequently had hepatocellular carcinoma and upper gastrointestinal bleeding, yet clinical outcomes were comparable. Development of resistance during third-generation cephalosporin therapy was infrequent in patients with Enterobacter SBP.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-016-1595-y) contains supplementary material, which is available to authorized users.

Enterobacter bugandensis sp. nov., isolated from neonatal blood

A total of 17 Enterobacter-like isolates were obtained from blood during a septicaemia outbreak in a neonatal unit, Tanzania, that could not be assigned based on phenotypic test to any existing Enterobacter species. Eight representative outbreak isolates were investigated in detail. Fermentation characteristics, biochemical assays and fatty acid profiles for taxonomic analysis were determined and supplemented with information derived from whole genome sequences. Phenotypic and morphological tests revealed that these isolates were Gram-stain-negative, rod-shaped, highly motile and facultatively anaerobic. The fatty acid profile was similar to those of the type strains for all recognized Enterobacter species, with quantitative differences in C_17 : 0, C_18 : 1ω7c and C_17 : 0 cyclo fatty acids. Whole genome sequencing was used to identify taxonomically relevant characteristics, i.e. for 16S rRNA gene sequence analysis, multi-locus sequence analysis (MLSA), in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI). Draft genomes were approximately 4.9 Mb in size with a G+C content of 56.0 mol%. The 16S rRNA gene sequence of these eight isolates showed >97 % similarity to all Enterobacter species, while MLSA clustered them closely with the type strains of Enterobacter xiangfangensis and Enterobacter hormaechei. These eight strains showed less than 70 % isDDH identity with the type strains of Enterobacter species. In addition, less than 95 % ANI to the type strains of Enterobacter species was observed. From these results, it is concluded that these isolates possess sufficient characteristics to differentiate them from all recognized Enterobacter species, and should therefore be considered as representing a novel species. The name Enterobacter bugandensis sp. nov. is proposed with EB-247^T ( = DSM 29888^T = NCCB 100573^T) as the type strain.

Pyrosequencing analysis of microbial community and food-borne bacteria on restaurant cutting boards collected in Seri Kembangan, Malaysia, and their correlation with grades of food premises

This study adopts the pyrosequencing technique to identify bacteria present on 26 kitchen cutting boards collected from different grades of food premises around Seri Kembangan, a city in Malaysia. Pyrosequencing generated 452,401 of total reads of OTUs with an average of 1.4×10(7) bacterial cells/cm(2). Proteobacteria, Firmicutes and Bacteroides were identified as the most abundant phyla in the samples. Taxonomic richness was generally high with >1000 operational taxonomic units (OTUs) observed across all samples. The highest appearance frequencies (100%) were OTUs closely related to Enterobacter sp., Enterobacter aerogenes, Pseudomonas sp. and Pseudomonas putida. Several OTUs were identified most closely related to known food-borne pathogens, including Bacillus cereus, Cronobacter sakazaki, Cronobacter turisensis, Escherichia coli, E. coli O157:H7, Hafnia alvei, Kurthia gibsonii, Salmonella bongori, Salmonella enterica, Salmonella paratyphi, Salmonella tyhpi, Salmonella typhimurium and Yersinia enterocolitica ranging from 0.005% to 0.68% relative abundance. The condition and grade of the food premises on a three point cleanliness scale did not correlate with the bacterial abundance and type. Regardless of the status and grades, all food premises have the same likelihood to introduce food-borne bacteria from cutting boards to their foods and must always prioritize the correct food handling procedure in order to avoid unwanted outbreak of food-borne illnesses.