Sub-typing of extended-spectrum-β-lactamase-producing isolates from a nosocomial outbreak: application of a 10-loci generic Escherichia coli multi-locus variable number tandem repeat analysis

Knockout of Targeted Plasmid-Borne β-Lactamase Genes in an Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strain: Impact on Resistance and Proteomic Profile

Resistance to β-lactams is known to be multifactorial, although the underlying mechanisms are not well established. The aim of our study was to develop a system for assessing the phenotypic and proteomic responses of bacteria to antibiotic stress as a result of the loss of selected antimicrobial resistance genes. We applied homologous recombination to knock out plasmid-borne β-lactamase genes (blaOXA-1, blaTEM-1, and blaCTX-M15) in Escherichia coli CCUG 73778, generating knockout clone variants lacking the respective deleted β-lactamases. Quantitative proteomic analyses were performed on the knockout variants and the wild-type strain, using bottom-up liquid chromatography tandem mass spectrometry (LC-MS/MS), after exposure to different concentrations of cefadroxil. Loss of the blaCTX-M-15 gene had the greatest impact on the resulting protein expression dynamics, while losses of blaOXA-1 and blaTEM-1 affected fewer proteins' expression levels. Proteins involved in antibiotic resistance, cell membrane integrity, stress, and gene expression and unknown function proteins exhibited differential expression. The present study provides a framework for studying protein expression in response to antibiotic exposure and identifying the genomic, proteomic, and phenotypic impacts of resistance gene loss. IMPORTANCE The critical situation regarding antibiotic resistance requires a more in-depth effort for understanding underlying mechanisms involved in antibiotic resistance, beyond just detecting resistance genes. The methodology presented in this work provides a framework for knocking out selected resistance factors, to study the adjustments of the bacterium in response to a particular antibiotic stress, elucidating the genetic response and proteins that are mobilized. The protocol uses MS-based determination of the proteins that are expressed in response to an antibiotic, enabling the selection of strong candidates representing putative resistance factors or mechanisms and providing a basis for future studies to understand their implications in antibiotic resistance. This allows us to better understand how the cell responds to the presence of the antibiotic when a specific gene is lost and, consequently, identify alternative targets for possible future treatment development.

The impact of the ST131 clone on recurrent ESBL-producing E. coli urinary tract infection: a prospective comparative study

The global emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli), mainly causing urinary tract infections (UTI), is of great concern. Almost one third of patients with UTI, develop recurrent UTI (RUTI). We followed 297 patients for one year after their first episode of UTI due to ESBL-E. coli. Our aim was to evaluate the impact of the globally dominant sequence type (ST)131 clone and its clades, on the risk of subsequent recurrences with ESBL-E. coli. Isolates from patients developing RUTI (68/297) were compared with those from patients with sporadic UTI (SUTI, 229/297). No association was found between RUTI and the two most prevalent phylogroups B2 and D, bla_CTX-M genes, or resistance profile. Half of the patients with RUTI were infected with ST131 isolates. Clade C2 were in dominance (50/119) among ST131 isolates. They were more common in patients with RUTI than SUTI (28% vs 13%) and multivariate analysis showed an increased odds-ratio (OR = 2.21, p = 0.033) for recurrences in patients infected with these isolates as compared to non-ST131 isolates. Detecting specific biomarkers, as ST131 clade C2, in ESBL-E. coli UTI isolates may aid in prediction of RUTI and improve diagnostics and care of patients with a risk of ESBL-E. coli recurrences.

Subtyping β-lactamase-producing Escherichia coli strains isolated from patients with UTI by MLVA and PFGE methods

OBJECTIVES

Strain subtyping is an important epidemiological tool to trace contamination, determine clonal relationships between different strains, and the cause of outbreaks. Current subtyping methods, however, yield less than optimal subtype discrimination. Pulsed-field gel electrophoresis is the gold standard method for Escherichia coli and Multiple-Locus Variable-number tandem repeat Analysis is a rapid PCR-based method. The purpose of this study was to evaluate MLVA and PFGE methods for subtyping β -lactamase-producing E. coli strains isolated from urinary tract infections.

MATERIALS AND METHODS

Overall, 230 E. coli isolates from patients with urinary tract infections were examined for antimicrobial susceptibility testing. 10-loci and 7-loci MLVA and PFGE methods were used for molecular typing of β -lactamase-producing E. coli isolates.

RESULTS

Out of 230 isolates, 130 (56.5%) β -lactamase-producing E. coli isolates were found in this study. The diversity indices of the VNTR loci showed an average diversity of 0.48 and 0.54 for 7-loci and 10-loci MLVA, respectively. The discriminatory power of PFGE showed a value of 0.87. The discordance between the methods was high.

CONCLUSION

Our study showed that PFGE is more discriminatory than MVLA. MLVA is a PCR- based method and can generate unmistakable data, in contrast to PFGE. Optimization of polymorphic VNTR is essential to improve the discriminatory power of MLVA based on geographical region.

Genomic and Proteomic Characterization of the Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli Strain CCUG 73778: A Virulent, Nosocomial Outbreak Strain

Escherichia coli strain CCUG 78773 is a virulent extended-spectrum β-lactamase (ESBL)-producing ST131-O25b type strain isolated during an outbreak at a regional university hospital. The complete and closed genome sequence, comprising one chromosome (5,076,638 bp) and six plasmids (1718–161,372 bp), is presented. Characterization of the genomic features detected the presence of 59 potential antibiotic resistance factors, including three prevalent β-lactamases. Several virulence associated elements were determined, mainly related with adherence, invasion, biofilm formation and antiphagocytosis. Twenty-eight putative type II toxin-antitoxin systems were found. The plasmids were characterized, through in silico analyses, confirming the two β-lactamase-encoding plasmids to be conjugative, while the remaining plasmids were mobilizable. BLAST analysis of the plasmid sequences showed high similarity with plasmids in E. coli from around the world. Expression of many of the described virulence and AMR factors was confirmed by proteomic analyses, using bottom-up, liquid chromatography-tandem mass spectrometry (LC-MS/MS). The detailed characterization of E. coli strain CCUG 78773 provides a reference for the relevance of genetic elements, as well as the characterization of antibiotic resistance and the spread of bacteria harboring ESBL genes in the hospital environment.

Recurrence of urinary tract infections with extended-spectrum β-lactamase-producing Escherichia coli caused by homologous strains among which clone ST131-O25b is dominant

OBJECTIVES

Bacterial features associated with recurrent urinary tract infections (RUTIs) due to extended-spectrum β-lactamase-producingEscherichia coli (ESBL-E. coli) are not well understood. In this study, phylogenetic groups and ST131 subclones were investigated to assess strain homology of ESBL-E. coli isolates in patients with RUTIs in inpatient and outpatient settings in western Sweden.

METHODS

Almost all isolates (319/356) from 123 patients with 2-7 episodes (median 2 episodes) of ESBL-E. coli UTI within 1 year were examined for seven E. coli phylogroups, the ST131-O25b clone and its subclone fimH30-Rx. Antimicrobial resistance and ESBL genes were determined for the index isolates. A subset of isolates was typed using pulsed-field gel electrophoresis (PFGE).

RESULTS

The same phylogroup and ST131 subclones were seen for all recurrences in 119/123 patients, and PFGE confirmed strain homology in recurrences for 43/44 patients tested. Phylogroup B2 dominated (56%), followed by D (19%) and F (10%). ST131-O25b andfimH30-Rx isolates were detected in 44% and 30%, respectively. CTX-M group 1 (71%) predominated. Elderly patients were in the majority. There were no associations between patient demographics or time to recurrence and bacterial characteristics. The fimH30-Rx subclone was associated with a higher number of recurrences (P = 0.015) compared with the remaining B2 isolates.

CONCLUSION

In ESBL-E. coli RUTI, most recurrences were caused by the initial infecting strain. The high frequency of the multidrug-resistant fimH30-Rx subclone and its association with multiple recurrences warrants further attention and early detection of this subclone in patients at risk of developing RUTI with ESBL-E. coli.

Reduced antibiotic use in extremely preterm infants with an antimicrobial stewardship intervention

INTRODUCTION

Excessive administration of antibiotics to preterm infants is associated with increased rates of complications. The purpose of the study was to evaluate the effect of an antimicrobial stewardship intervention on antibiotic use in extremely preterm infants.

DESIGN SETTING PATIENTS AND INTERVENTION

A before and after study of infants born at ≤28 weeks' gestational age was performed in the neonatal intensive care unit of Queen Silvia's Children's Hospital, Gothenburg, Sweden. Retrospective analysis of the baseline period (January-December 2014) guided the development of a limited antimicrobial stewardship intervention. The intervention consisted of updated local guidelines with a focus on shortened and standardised treatment duration plus increased access to infectious disease consultant advice. It was fully implemented during the intervention period (October 2017-September 2018).

OBJECTIVE

Primary aim was to compare antibiotic use, defined as antibiotic treatment days per 1000 patient-days, between the two periods, and the secondary aim was to evaluate the number of days with meropenem-based regimens before and after the intervention.

RESULTS

We included 145 infants with a median birth weight of 870 g and median gestational age of 26 weeks. The baseline period comprised 82 infants and 3478 patient-days, the intervention period comprised 63 infants and 2753 patient-days. Overall antibiotic use (treatment and prophylaxis) was 534 versus 466 days per 1000 patient-days during the baseline and intervention periods, respectively. Antibiotic treatment days decreased from 287 to 197 days per 1000 patient-days. The proportion of meropenem-based regimens was 69% versus 44%, respectively. No increases in mortality or reinitiation of antibiotics were seen.

CONCLUSIONS

Implementation of a limited antimicrobial stewardship intervention anchored in analysis of previous prescription patterns can contribute to safe decreases in antibiotic use in extremely preterm infants.

Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages

Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a majority of human extraintestinal infections globally, resulting in enormous direct medical and social costs. ExPEC strains are comprised of many lineages, but only a subset is responsible for the vast majority of infections. Few systematic surveillance systems exist for ExPEC. To address this gap, we systematically reviewed and meta-analyzed 217 studies (1995 to 2018) that performed multilocus sequence typing or whole-genome sequencing to genotype E. coli recovered from extraintestinal infections or the gut. Twenty major ExPEC sequence types (STs) accounted for 85% of E. coli isolates from the included studies. ST131 was the most common ST from 2000 onwards, covering all geographic regions. Antimicrobial resistance-based isolate study inclusion criteria likely led to an overestimation and underestimation of some lineages. European and North American studies showed similar distributions of ExPEC STs, but Asian and African studies diverged. Epidemiology and population dynamics of ExPEC are complex; summary proportion for some STs varied over time (e.g., ST95), while other STs were constant (e.g., ST10). Persistence, adaptation, and predominance in the intestinal reservoir may drive ExPEC success. Systematic, unbiased tracking of predominant ExPEC lineages will direct research toward better treatment and prevention strategies for extraintestinal infections.

Subsequent infection with extended-spectrum β-lactamase-producing Enterobacteriaceae in patients with prior infection or fecal colonization

In clinical practice, there is a growing need to assess the impact of prior colonization or infection with extended-spectrum β-lactamase-producing Enterobacteriaceae (EPE) on new EPE infections. We have investigated the frequency of, and duration to, a subsequent EPE infection in patients with prior fecal carriage or infection with EPE. Culture data for 3272 EPE-positive patients in Western Sweden during 2004-2014 were evaluated. The median follow-up time was 3.7 years. The first recorded EPE-positive fecal screen, or clinical (urine, blood) culture, and subsequent EPE-positive clinical samples were analyzed, focusing on the first and last recurrence of EPE infection. ESBL Escherichia coli dominated (95%). Almost all (94%) patients initially positive in fecal screen (n = 1436) and 72 and 71% of those initially positive in urine (n = 1717) and blood (n = 119) had no further EPE clinical isolates. Subsequent EPE bacteremia was only detected in 0.7, 1.6, and 4.2% of the respective patient group. Recurrent EPE-positive urine cultures occurred in 27% (460/1717), most (75%) within 6 months, and rarely (13%) after 1 year. Repeated EPE-positive clinical samples were significantly (p < 0.01) more common in patients > 65 years and in men with ESBL Klebsiella pneumoniae. In our low-endemic setting, subsequent EPE infections in previously colonized patients were rare. On the other hand, in patients previously EPE-positive in urine or blood, subsequent EPE urinary tract infections were common, especially within 6 months and in patients > 65 years old.

Genotypic characterization of gentamicin and cephalosporin resistant Escherichia coli isolates from blood cultures in a Norwegian university hospital 2011-2015

Background

Cephalosporin resistance in clinical E. coli isolates is increasing internationally. The increase has been caused by virulent and often multidrug-resistant clones, especially the extended spectrum β-lactamase (ESBL) producing E. coli clone O25b-ST131.

Methods

In Norway, recommended empirical treatment of sepsis consists of gentamicin and penicillin combined, or a broad-spectrum cephalosporin. To investigate if increased gentamicin and cephalosporins resistance rates in our hospital could be caused by specific clones, we conducted a retrospective study on E. coli blood culture isolates from 2011 through 2015. All E. coli isolates non-susceptible to gentamicin and/or third-generation cephalosporins were genotyped using multiple-locus variable-number of tandem repeat analysis (MLVA) and compared with antibiotic susceptible isolates. The frequency of the most common genes causing ESBL production (bla_CTX-M, bla_ampC) was examined by Real-Time PCR.

Results

A total of 158 cephalosporin and/or gentamicin resistant and 97 control isolates were differentiated into 126 unique MLVA types. Of these, 31% of the isolates belonged to a major MLVA cluster consisting of 41% of the gentamicin resistant and 35% of the cephalosporin resistant isolates. The majority (65/80 isolates) of this MLVA cluster contained MLVA types associated with the E. coli O25b-ST131 clone. Genes encoding CTX-M enzyme phylogroups 1 and 9 occurred in 65% and 19% of cephalosporin resistant isolates, respectively, whereas bla_ampC-CIT was identified in 3%.

Conclusion

No local E. coli bacteraemia clone was identified. Antibiotic resistance was dispersed over a variety of genotypes. However, association with the international E. coli O25b-ST131 clone was frequent and may be an important driver behind increased resistance rates. Monitoring and preventing dissemination of these resistant clones are important for continued optimal treatment.

A comparison of extended spectrum β-lactamase producing Escherichia coli from clinical, recreational water and wastewater samples associated in time and location

Extended spectrum β-lactamase producing Escherichia coli (ESBL-EC) are excreted via effluents and sewage into the environment where they can re-contaminate humans and animals. The aim of this observational study was to detect and quantify ESBL-EC in recreational water and wastewater, and perform a genetic and phenotypic comparative analysis of the environmental strains with geographically associated human urinary ESBL-EC. Recreational fresh- and saltwater samples from four different beaches and wastewater samples from a nearby sewage plant were filtered and cultured on differential and ESBL-selective media. After antimicrobial susceptibility testing and multi-locus variable number of tandem repeats assay (MLVA), selected ESBL-EC strains from recreational water were characterized by whole genome sequencing (WGS) and compared to wastewater and human urine isolates from people living in the same area. We detected ESBL-EC in recreational water samples on 8/20 occasions (40%), representing all sites. The ratio of ESBL-EC to total number of E. coli colony forming units varied from 0 to 3.8%. ESBL-EC were present in all wastewater samples in ratios of 0.56-0.75%. ST131 was most prevalent in urine and wastewater samples, while ST10 dominated in water samples. Eight STs and identical ESBL-EC MLVA-types were detected in all compartments. Clinical ESBL-EC isolates were more likely to be multidrug-resistant (p<0.001). This study confirms that ESBL-EC, including those that are capable of causing human infection, are present in recreational waters where there is a potential for human exposure and subsequent gut colonisation and infection in bathers. Multidrug-resistant E. coli strains are present in urban aquatic environments even in countries where antibiotic consumption in both humans and animals is highly restricted.

Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics

Methods for rapid and reliable microbial identification are essential in modern healthcare. The ability to detect and correctly identify pathogenic species and their resistance phenotype is necessary for accurate diagnosis and efficient treatment of infectious diseases. Bottom-up tandem mass spectrometry (MS) proteomics enables rapid characterization of large parts of the expressed genes of microorganisms. However, the generated data are highly fragmented, making downstream analyses complex. Here we present TCUP, a new computational method for typing and characterizing bacteria using proteomics data from bottom-up tandem MS. TCUP compares the generated protein sequence data to reference databases and automatically finds peptides suitable for characterization of taxonomic composition and identification of expressed antimicrobial resistance genes. TCUP was evaluated using several clinically relevant bacterial species (Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae), using both simulated data generated by in silico peptide digestion and experimental proteomics data generated by liquid chromatography-tandem mass spectrometry (MS/MS). The results showed that TCUP performs correct peptide classifications at rates between 90.3 and 98.5% at the species level. The method was also able to estimate the relative abundances of individual species in mixed cultures. Furthermore, TCUP could identify expressed β-lactamases in an extended spectrum β-lactamase-producing (ESBL) E. coli strain, even when the strain was cultivated in the absence of antibiotics. Finally, TCUP is computationally efficient, easy to integrate in existing bioinformatics workflows, and freely available under an open source license for both Windows and Linux environments.

Fecal carriage of extended spectrum β-lactamase producing Escherichia coli and Klebsiella pneumoniae after urinary tract infection - A three year prospective cohort study

We have performed a prospective cohort study to investigate the duration of and risk factors for prolonged fecal carriage of ESBL-producing Escherichia coli or Klebsiella pneumoniae in patients with community acquired urinary tract infection caused by these bacteria. From 2009 to 2011, 101 Norwegian patients were recruited. Stool swabs and questionnaires were collected every three months for one year and at the end of the study in 2012. Information on antibiotic prescriptions was collected from the Norwegian Prescription Database. Stool samples were cultured directly on ChromID ESBL agar as well as in an enrichment broth, and culture positive isolates were examined by blaCTX-M multiplex PCR. Isolates without blaCTX-M were investigated for alternative ESBL-determinants with a commercial microarray system. Time to fecal clearance of ESBL producing Enterobacteriaceae was also analysed using Kaplan-Meier estimates. Uni- and multivariate logistic regression was used to compare groups according to previously described risk factors. The ESBL point prevalence of fecal carriage were 61% at 4 months, 56% at 7 months, 48% at 10 months, 39% at 13 months, 19% after two years, and 15% after three years or more. We found no correlation between duration of carriage, comorbidity, antibiotic use or travel to ESBL high-prevalence countries. Prolonged carriage was associated with E. coli isolates of phylogroup B2 or D. Importantly, comparative MLST and MLVA analyses of individual paired urine and fecal E. coli isolates revealed that ESBL production commonly occurred in diverse strains within the same host. When investigating cross-transmission of ESBL producing bacteria in health care institutions, this notion should be taken into account.

Evaluation of MLVA for epidemiological typing and outbreak detection of ESBL-producing Escherichia coli in Sweden

BACKGROUND

To identify the spread of nosocomial infections and halt outbreak development caused by Escherichia coli that carry multiple antibiotic resistance factors, such as extended-spectrum beta-lactamases (ESBLs) and carbapenemases, is becoming demanding challenges due to the rapid global increase and constant and increasing influx of these bacteria from the community to the hospital setting. Our aim was to assess a reliable and rapid typing protocol for ESBL-E. coli, with the primary focus to screen for possible clonal relatedness between isolates. All clinical ESBL-E. coli isolates, collected from hospitals (n = 63) and the community (n = 41), within a single geographical region over a 6 months period, were included, as well as clinical isolates from a polyclonal outbreak (ST131, n = 9, and ST1444, n = 3). The sporadic cases represented 36 STs, of which eight STs dominated i.e. ST131 (n = 33 isolates), ST648 (n = 10), ST38 (n = 9), ST12 and 69 (each n = 4), ST 167, 405 and 372 (each n = 3). The efficacy of multiple-locus variable number tandem repeat analysis (MLVA) was evaluated using three, seven or ten loci, in comparison with that of pulsed-field gel electrophoresis (PFGE) and multi locus sequence typing (MLST).

RESULTS

MLVA detected 39, 55 and 60 distinct types, respectively, using three (GECM-3), seven (GECM-7) or ten (GECM-10) loci. For GECM-7 and -10, 26 STs included one type and eleven STs each included several types, the corresponding numbers for GECM-3 were 29 and 8. The highest numbers were seen for ST131 (7,7 and 8 types, respectively), ST38 (5,5,8) and ST648 (4,5,5). Good concordance was observed with PFGE and GECM-7 and -10, despite fewer types being identified with MLVA; 78 as compared to 55 and 60 types. The lower discriminatory power of MLVA was primarily seen within the O25b-ST131 lineage (n = 34) and its H30-Rx subclone (n = 21). Epidemiologically unrelated O25b-ST131 isolates were clustered with O25b-ST131 outbreak isolates by MLVA, whereas the ST1444 outbreak isolates were accurately distinguished from unrelated isolates.

CONCLUSION

MLVA, even when using only three loci, represents an easy initial typing tool for epidemiological screening of ESBL-E. coli. For the ST131-O25b linage, complementary methods may be needed to obtain sufficient resolution.

Draft Genome Sequence of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strain CCUG 62462, Isolated from a Urine Sample

The draft genome sequence has been determined for an extended-spectrum-β-lactamase (ESBL)-producing (bla_CTX-M-15) Escherichia coli strain (CCUG 62462), composed of 119 contigs and a total size of 5.27 Mb. This E. coli is serotype O25b and sequence type 131, a pandemic clonal group, causing worldwide antimicrobial-resistant infections.

Low Enteric Colonization with Multidrug-Resistant Pathogens in Soldiers Returning from Deployments- Experience from the Years 2007-2015

This assessment describes the enteric colonization of German soldiers 8–12 weeks after returning from mostly but not exclusively subtropical or tropical deployment sites with third-generation cephalosporin-resistant Enterobacteriaceae, vancomycin-resistant enterococci (VRE), and methicillin-resistant Staphylococcus aureus (MRSA). Between 2007 and 2015, 828 stool samples from returning soldiers were enriched in nonselective broth and incubated on selective agars for Enterobacteriaceae expressing extended-spectrum beta-lactamases (ESBL), VRE and MRSA. Identification and resistance testing of suspicious colonies was performed using MALDI-TOF-MS, VITEK-II and agar diffusion gradient testing (bioMérieux, Marcy-l’Étoile, France). Isolates with suspicion of ESBL were characterized by ESBL/ampC disc-(ABCD)-testing and molecular approaches (PCR, Sanger sequencing). Among the returnees, E. coli with resistance against third-generation cephalosporins (37 ESBL, 1 ESBL + ampC, 1 uncertain mechanism) were found in 39 instances (4.7%). Associated quinolone resistance was found in 46.2% of these isolates. Beta-lactamases of the bla_CTX-M group 1 predominated among the ESBL mechanisms, followed by the bla_CTX-M group 9, and bla_SHV. VRE of vanA-type was isolated from one returnee (0.12%). MRSA was not isolated at all. There was no clear trend regarding the distribution of resistant isolates during the assessment period. Compared with colonization with resistant bacteria described in civilians returning from the tropics, the colonization in returned soldiers is surprisingly low and stable. This finding, together with high colonization rates found in previous screenings on deployment, suggests a loss of colonization during the 8- to 12-week period between returning from the deployments and assessment.

Rapid Tracing of Resistance Plasmids in a Nosocomial Outbreak Using Optical DNA Mapping

Resistance to life-saving antibiotics increases rapidly worldwide, and multiresistant bacteria have become a global threat to human health. Presently, the most serious threat is the increasing spread of Enterobacteriaceae carrying genes coding for extended spectrum β-lactamases (ESBL) and carbapenemases on highly mobile plasmids. We here demonstrate how optical DNA maps of single plasmids can be used as fingerprints to trace plasmids, for example, during resistance outbreaks. We use the assay to demonstrate a potential transmission route of an ESBL-carrying plasmid between bacterial strains/species and between patients, during a polyclonal outbreak at a neonatal ward at Sahlgrenska University Hospital (Gothenburg, Sweden). Our results demonstrate that optical DNA mapping is an easy and rapid method for detecting the spread of plasmids mediating resistance. With the increasing prevalence of multiresistant bacteria, diagnostic tools that can aid in solving ongoing routes of transmission, in particular in hospital settings, will be of paramount importance.

Fecal Carriage of Enterobacteriaceae Producing Extended-Spectrum Beta-Lactamases in Hospitalized Patients and Healthy Community Volunteers in Burkina Faso

Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) have been described worldwide, but few reports focused on Burkina Faso. To assess the prevalence of digestive carriage of such bacteria in the community and in the hospital, 214 fecal samples, 101 from healthy volunteers and 113 from hospitalized patients without digestive pathology, were collected in Bobo Dioulasso, Burkina Faso economic capital, during July and August 2014. Stool samples were screened using ESBL agar plates. Strains were identified by mass spectrometry using the Biotyper MALDI-TOF. ESBL production was confirmed with the double-disc synergy test. Susceptibility was tested using the disk diffusion method on Müller-Hinton agar. The main ESBL genes were detected using multiplex PCR and bidirectional gene sequencing. Escherichia coli phylogenetic groups were identified using a PCR-based method. During the study period, prevalence of subjects with fecal ESBL-PE was 32% (69/214), 22% among healthy volunteers and 42% among inpatients. All but two ESBL, CTX-M-15 and ESBL-PE, were mostly E. coli (78%). Among the 60 ESBL-producing E. coli strains, 26% belonged to phylogenetic group D, 23.3% to group A, 20% to group B1, 6.6% to group B2, and 3.3% to the ST131 clone. Univariate analysis showed that history of hospitalization and previous antibiotic use were risk factors associated with ESBL-PE fecal carriage. In Burkina Faso, the prevalence of both healthy subjects from the community and hospitalized patients with fecal ESBL-PE is alarmingly high. This feature should be taken into consideration by both general practitioners and hospital doctors with regard to empirical treatments of infections, notably urinary tract infections.

Outbreaks of extended spectrum beta-lactamase-producing Enterobacteriaceae in neonatal intensive care units: a systematic review

OBJECTIVE

To establish the number of outbreaks of extended spectrum beta-lactamase (ESBL) producing organisms in neonatal intensive care units (NICUs), to determine causes, mortality rates, proportions of infants colonised and infected and the interventions that terminated outbreaks.

METHODS

A systematic review of the literature in English, Spanish and French was undertaken with searches in four databases. The review conformed to the PRISMA guidelines, and the data extraction was modelled on the ORION criteria for studies of nosocomial infection.

RESULTS

75 studies fulfilled the inclusion criteria. There were 1185 cases of colonisation, 860 infections and 139 deaths. The median outbreak duration was 6.2 months (IQR 2.0-7.5 months). Klebsiella pneumoniae was the most frequently implicated pathogen. Understaffing was the most frequent risk factor for outbreaks. The most commonly identified source was admission of an ESBL-colonised infant with subsequent horizontal dissemination. The main interventions described were improved infection-control procedures and screening of staff and the environment. 26 studies were included in the quantitative analysis. Random effects meta-analysis indicated high mortality rates in infants who developed infection (31%, 95% CI 20% to 43%).

CONCLUSION

ESBL outbreaks in NICUs are associated with significant mortality and prolonged disruption. Understaffing is a major risk factor, but is infrequently addressed by interventions. Poor infection-control procedures are frequently implicated as contributing to ESBL spread. Better reporting of outbreaks may help clarify the role for routine ESBL screening in NICUs.

About the usefulness of contact precautions for carriers of extended-spectrum beta-lactamase-producing Escherichia coli

BACKGROUND

Extended-spectrum β-lactamases producing Escherichia coli (ESBL-E) are increasingly identified in health care facilities. As previously done for the control of methicillin-resistant Staphylococcus aureus, many hospitals have established screening strategies for early identification of patients being carriers of ESBL producers in general and ESBL-E in particular, and have implemented contact precautions (CP) for infected and colonized patients.

METHODS

The incidence of ESBL-E has been compared retrospectively between two French university hospitals (A and B) with different infection control policies over a 5-year long period of time (2006-2010).

RESULTS

While hospital A only implemented standard precautions after identification of patients colonized with ESBL-E, hospital B recommended additional CP. During the period of the study, the ESBL-E incidence rate significantly increased in both hospitals, but no significant difference was observed between the two hospitals.

CONCLUSIONS

This observational study did not reveal that additional CP measures had a greater impact on the incidence of ESBL-E in hospital settings.

Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics

High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type 131 (ST131)-a set of rapidly radiating pandemic clones. The highly infectious clades of ST131 originated firstly by a mutation enhancing conjugation and adhesion. Secondly, single-nucleotide polymorphisms occurred enabling fluoroquinolone-resistance, which is near-fixed in all ST131. Thirdly, broader resistance through beta-lactamases has been gained and lost frequently, symptomatic of conflicting environmental selective effects. This flexible approach to gene exchange is worrying and supports the proposition that ST131 will develop an even wider range of plasmid and chromosomal elements promoting antimicrobial resistance. To stop ST131, deep genome sequencing is required to understand the origin, evolution and spread of antimicrobial resistance genes. Phylogenetic methods that decipher past events can predict future patterns of virulence and transmission based on genetic signatures of adaptation and gene exchange. Both the effect of partial antimicrobial exposure and cell dormancy caused by variation in gene expression may accelerate the development of resistance. High-throughput sequencing can decode measurable evolution of cell populations within patients associated with systems-wide changes in gene expression during treatments. A multi-faceted approach can enhance assessment of antimicrobial resistance in E. coli ST131 by examining transmission dynamics between hosts to achieve a goal of pre-empting resistance before it emerges by optimising antimicrobial treatment protocols.