Rapid, simple multi-locus variable number tandem repeat analysis: a reliable tool for Klebsiella pneumoniae outbreak screening

BACKGROUND

Klebsiella pneumoniae causing nosocomial infections is increasingly multi-drug-resistant. Rapid and efficient typing tools are required for monitoring.

AIM

To assess a simple, rapid (<5 h) multiplex polymerase chain reaction method based on multi-locus variable number tandem repeat analysis (MLVA) as a screening tool to determine whether or not K. pneumoniae strains are related.

METHODS

The global discriminatory power of the method was assessed on 72 unrelated K. pneumoniae isolates, including community carriage isolates, highly virulent strains causing liver abscess, and extended-spectrum beta-lactamase- and carbapenemase-producing strains. Suspected related strains from a suspected outbreak and a relapsed meningitis case were also studied. MLVA results were compared with whole-genome sequencing (WGS) analysis and multi-locus sequence typing (MLST).

FINDINGS

MLVA and MLST had similar discriminatory power, each distinguishing 54 profiles among the 72 unrelated isolates (Hunter-Gaston index 0.989). Each strain belonging to one sequence type (ST) or ST complex had its own MLVA type, with few exceptions. Two strains of ST268 and ST1119 shared the same MLVA profile, and two unrelated strains of ST307, ST86, ST45 and ST37 exhibited two different MLVA types each. Moreover, investigation of seven grouped cases of K. pneumoniae neonatal sepsis pointed to strong suspicion of a common source for five isolates, while two isolates with a different MLVA profile were excluded from this cluster.

CONCLUSION

The MLVA approach is a useful, rapid and reliable tool for epidemiological investigation requiring only basic molecular biology equipment, and permits identification of sporadic isolates that are not part of an outbreak. However, analysis of strains sharing the same MLVA type by a highly discriminatory technique, such as WGS, remains necessary.

Mechanism of lipid bilayer perturbation by bactericidal membrane-active small molecules

Membrane-active small molecules (MASMs) are small organic molecules designed to reproduce the fundamental physicochemical properties of natural antimicrobial peptides: their cationic charge and amphiphilic character. This class of compounds has a promising broad range of antimicrobial activity and, at the same time, solves some major limitations of the peptides, such as their high production costs and low in vivo stability. Most cationic antimicrobial peptides act by accumulating on the surface of bacterial membranes and causing the formation of defects when a threshold is reached. Due to the drastically different structures of the two classes of molecules, it is not obvious that small-molecule antimicrobials act in the same way as natural peptides, and very few data are available on this aspect. Here we combined spectroscopic studies and molecular dynamics simulations to characterize the mechanism of action of two different MASMs. Our results show that, notwithstanding their simple structure, these molecules act just like antimicrobial peptides. They bind to the membrane surface, below the head-groups, and insert their apolar moieties in the core of the bilayer. Like many natural peptides, they cause the formation of defects when they reach a high coverage of the membrane surface. In addition, they cause membrane aggregation, and this property could contribute to their antimicrobial activity.

Epidemiological investigation of Pseudomonas aeruginosa isolates including Multidrug-Resistant serogroup O12 isolates, by use of a rapid and simplified Multiple-Locus Variable-Number of Tandem Repeats Analysis and Whole Genome Sequencing

BACKGROUND

Clustered cases of Pseudomonas aeruginosa infection in immunocompromised patients' wards require rapid characterization of a potential epidemic to guide investigations and identify the potential source of contamination.

AIM

To design and evaluate a rapid and simple typing method for P. aeruginosa in comparison to whole genome sequencing (WGS).

METHODS

We designed and used a simplified PCR based on multiple locus tandem variable number analysis (MLVA) to investigate cases of P. aeruginosa infection and colonization in a paediatric haematology department. The method was compared to WGS by using Illumina method.

FINDINGS

On the 17 isolates recovered from 15 children (8 from blood cultures, 3 from urinary tract infections, 1 from sputum and 5 stool isolates) MLVA distinguished 10 different profiles and 7 isolates from 6 children shared the same profile. Analysis by WGS revealed that these 7 isolates belonged to sequence type ST111 and serotype O12 and permitted to further distinguish at least 3 different genotypes among them. Five environmental strains had 3 MLVA profiles, one shared with a clinical isolate but WGS excluded any relationship.

CONCLUSION

The simplified and inexpensive MLVA method permitted to exclude, in less than five hours, most of unrelated isolates and to focus investigations on a small number of cases while WGS, taking several days of work, drew definitive conclusions concerning the outbreak and the genetic relationships of the ST111 isolates circulating in the department. We conclude that sequential use of both methods is the optimal strategy to investigate grouped cases of P. aeruginosa infections.

MiniBioReactor Array (MBRA) in vitro gut model: a reliable system to study microbiota-dependent response to antibiotic treatment

Background

Antimicrobial drugs are mostly studied for their impact on emergence of bacterial antibiotic resistance, but their impact on the gut microbiota is also of tremendous interest. In vitro gut models are important tools to study such complex drug–microbiota interactions in humans.

Methods

The MiniBioReactor Array (MBRA) in vitro microbiota system; a single-stage continuous flow culture model, hosted in an anaerobic chamber; was used to evaluate the impact of three concentrations of a third-generation cephalosporin (ceftriaxone) on faecal microbiota from two healthy donors (treatment versus control: three replicates per condition). We conducted 16S microbiome profiling and analysed microbial richness, diversity and taxonomic changes. β-Lactamase activities were evaluated and correlated with the effects observed in the MBRA in vitro system.

Results

The MBRA preserved each donor’s specificities, and differences between the donors were maintained through time. Before treatment, all faecal cultures belonging to the same donor were comparable in composition, richness, and diversity. Treatment with ceftriaxone was associated with a decrease in α-diversity, and an increase in β-diversity index, in a concentration-dependent manner. The maximum effect on diversity was observed after 72 h of treatment. Importantly, one donor had a stronger microbiota β-lactamase activity that was associated with a reduced impact of ceftriaxone on microbiota composition.

Conclusions

MBRA can reliably mimic the intestinal microbiota and its modifications under antibiotic selective pressure. The impact of the treatment was donor- and concentration-dependent. We hypothesize these results could be explained, at least in part, by the differences in β-lactamase activity of the microbiota itself. Our results support the relevance and promise of the MBRA system to study drug–microbiota interactions.

Spondylodiscitis in a healthy 12-year-old girl with Extraintestinal pathogenic Escherichia coli (ExPEC) bacteraemia

Background

Escherichia coli (E. coli) is rarely implicated in bone or joint infections in children.

Case presentation

We discuss the case of a healthy 12-year-old girl with an E. coli bacteraemia and a T11-T12 spondylodiscitis revealed by magnetic resonance imaging. The strain harboured serogroup O1:K1 and virulence factors common to highly virulent extra intestinal pathogenic E. coli (ExPEC). Immunological work-up was normal.

Conclusion

The identification of E. coli in a spondylodiscitis should lead to the search for immunosuppression of the host and virulence factors of the strain, particularly those of ExPEC.

[Nosocomial rotavirus gastroenteritis]

Rotavirus is the most common cause of gastroenteritis in children requiring hospitalization. It is a very resistant and contagious virus causing nosocomial gastroenteritis. In France, the vaccine against rotavirus has been available since 2006, but the vaccine is not recommended for infant vaccination. The aim of this retrospective study was to describe nosocomial rotavirus gastroenteritis (NRGE) and to assess its impact on children hospitalized in the General Pediatrics Department of Robert-Debré Hospital (Paris) between 1 January 2009 and 31 December 2013. We analyzed the demographic characteristics of children (age, term birth, underlying diseases) and the severity of the NRGE (oral or intravenous hydration), and assessed whether these children could benefit from vaccination against rotavirus.

RESULTS

One hundred thirty-six children presented nosocomial rotavirus infection, with an incidence of 2.5 NRGE per 1000 days of hospitalization. The incidence of NRGE was stable between 2009 and 2013 despite the introduction of specific hygiene measures. The average age of the children was 7 months (range: 0.5-111 months). Most often NRGE occurred in children hospitalized for respiratory diseases (65% of cases) and requiring prolonged hospitalization (median: 18 days). One-third of children were born premature (25%). Hydration was oral in 80 patients (59%), by intravenous infusion in 18 patients (13%), and intraosseous in one patient. Half of the patients were aged less than 5 months and could benefit from the protection afforded by vaccination.

CONCLUSION

NRGE are common. Rotavirus mass vaccination should have a positive impact on the incidence of NRGE by reducing the number of children hospitalized for gastroenteritis, therefore indirectly reducing the number of hospital cross-infections of hospitalized children who are too young to be vaccinated.

Clinical severity and molecular characteristics of circulating and emerging rotaviruses in young children attending hospital emergency departments in France

Group A rotavirus (RVA) is the leading cause of acute gastroenteritis in young children worldwide. A prospective surveillance network has been set up to investigate the virological and clinical features of RVA infections and to detect the emergence of potentially epidemic strains in France. From 2009 to 2014, RVA-positive stool samples were collected from 4800 children <5 years old attending the paediatric emergency units of 16 large hospitals. Rotaviruses were then genotyped by RT-PCR with regard to their outer capsid proteins VP4 and VP7. Genotyping of 4708 RVA showed that G1P[8] strains (62.2%) were predominant. The incidence of G9P[8] (11.5%), G3P[8] (10.4%) and G2P[4] (6.6%) strains varied considerably, whereas G4P[8] (2.7%) strains were circulating mostly locally. Of note, G12P[8] (1.6%) strains emerged during the seasons 2011-12 and 2012-13 with 4.1% and 3.0% prevalence, respectively. Overall, 40 possible zoonotic reassortants, such as G6 (33.3%) and G8 (15.4%) strains, were detected, and were mostly associated with P[6] (67.5%). Analysis of clinical records of 624 hospitalized children and severity scores from 282 of them showed no difference in clinical manifestations or severity in relation to the genotype. The relative stability of RVA genotypes currently co-circulating and the large predominance of P[8] type strains may ensure vaccine effectiveness in France. The surveillance will continue to monitor the emergence of new reassortants that might not respond to current vaccines, all the more so as all genotypes can cause severe infections in infants.

Fatal necrotizing fasciitis due to necrotic toxin-producing Escherichia coli strain

We report a fatal case of necrotizing soft tissues infection caused by an Escherichia coli strain belonging to phylogenetic group C and harbouring numerous virulence factors reported to be part of a pathogenicity island (PAI) such as PAI II_J96 and conserved virulence plasmidic region.

[Use of group A streptococcal rapid diagnostic test in extra-pharyngeal infections]

The purpose of this study was to assess the performances of the group A streptococcus (GAS) rapid antigen diagnostic tests (RADTs) in extra-pharyngeal infections. Between October 2009 and June 2014, 368 patients (median age: 48 months) were enrolled. The pathologies involved were : 160 perineal infections (44 %), 69 blistering distal dactylitis (19 %), 55 cervical lymphadenitis (15 %), 31 crusty or bleeding rhinitis (8 %), and 53 other diseases (14 %). The sensitivity of GAS-RADT used was 96 % (95 % CI: 92-99 %), the specificity 81 % (95 % CI: 75- 86 %), the negative predictive value 97 % (CI 95 %: 93-99 %), and the positive predictive value 79 % (95 % CI: 73-85 %). Finally, positive and negative likelihood ratio were 5 (95 % CI: 4-7) and 0.05 (95 % CI: 0.02-0.11) respectively. The GAS-RADTs developed for pharyngitis have comparable performances in these settings and therefore can be used.

[Group A streptococcal perineal infection in children]

Perineal diseases in children are usually caused by group A streptococcus (GAS). If the natural course of untreated cases is not known, it is well known that symptoms do not resolve spontaneously and can persist often for many months, until appropriate diagnosis and effective treatment are instituted. Furthermore, failures and recurrences after penicillin treatment are frequent. From 2009 to 2014, 165 perineal infections (median age: 48 months, extremes: 0.4-139) were enrolled by 15 pediatricians: 4 balanitis, 29 vulvo-vaginal diseases and 132 perianal infections. Painful defecation, anal fissures and macroscopic blood in stools were significantly more frequent in GAS perianal infections than negative GAS infections (p<0.01). The performance of GAS-rapid antigen test compared to the GAS culture was : sensitivity 97 % [CI 95 %: 89-100 %], specificity 76 % [CI 95 %: 66-84 %], negative predictive value 97 % [CI 95 %: 91-100 %], positive predictive value 71 % [CI 95 %: 60-80 %].

Genotyping, local prevalence and international dissemination of β-lactamase-producing Kingella kingae strains

β-lactamase production has been sporadically reported in the emerging Kingella kingae pathogen but the phenomenon has not been studied in-depth. We investigated the prevalence of β-lactamase production among K. kingae isolates from different geographical origins and genetically characterized β-lactamase-producing strains. Seven hundred and seventy-eight isolates from Iceland, the USA, France, Israel, Spain and Canada were screened for β-lactamase production and, if positive, were characterized by PFGE and MLST genotyping, as well as rtxA, por, blaTEM and 16S rRNA sequencing. β-lactamase was identified in invasive strains from Iceland (n=4/14, 28.6%), the USA (n=3/15, 20.0%) and Israel (n=2/190, 1.1%) and in carriage strains in the USA (n=5/17, 29.4%) and Israel (n=66/429, 15.4%). No French, Spanish or Canadian isolates were β-lactamase producers. Among β-lactamase producers, a perfect congruency between the different typing methods was observed. Surprisingly, all US and Icelandic β-lactamase-producing isolates were almost indistinguishable, belonged to the major international invasive PFGE clone K/MLST ST-6, but differed from the four genetically unrelated Israeli β-lactamase-producing clones. Representative strains of different genotypes produced the TEM-1 enzyme. K. kingae β-lactamase producers exhibit a clear clonal distribution and have dissimilar invasive potential. The presence of the enzyme in isolates belonging to the major worldwide invasive clone K/ST-6 highlights the possible spread of β-lactam resistance, and emphasizes the importance of routine testing of all K. kingae clinical isolates for β-lactamase production.

Haemolytic-uraemic syndrome with bacteraemia caused by a new hybrid Escherichia coli pathotype

We describe a new atypical Shiga-toxin-producing Escherichia coli (STEC) responsible for a severe episode of haemolytic–uraemic syndrome in an adult with a relapse associated with bacteraemia. This STECs train of serotype O80:H2 harboured stx2c and stx2d gene subtypes, the rare eae ξ variant and a ColV plasmid with a conserved virulence plasmidic region involved in virulence of human and avian extraintestinal pathogenic E. coli. This atypical hybrid pathotype, which represents a new threat, is a further demonstration that STEC may be a recipient for extraintestinal virulence factors and raises again the question of antibiotic therapy during STEC infection.

Association between mortality of Escherichia coli meningitis in young infants and non-virulent clonal groups of strains

To identify factors associated with Escherichia coli meningitis (ECM) mortality in infants aged <3 months, the clinical, biological and bacterial characteristics of isolates from 99 cases of ECM were compared, including the phylogenetic group, multilocus sequence type, O serogroup and sequence O type (a combination of sequence type complex (STc) and O serogroup) and virulence genotype. All 99 isolates were susceptible to the initial antimicrobial treatment. The mortality rate (14%) was not influenced by term or post-natal age. Hypotension or seizures were the sole clinical predictive factors for fatal outcome (p <0.01), and abnormal initial trans-fontanellar ultrasound was associated with death (p 0.03). Seventy-seven isolates belonged to the common sequence O types (STc29(O1), STc29(O18), STc29(O45), STc301(O7), STc304(O16), STc697(O83), STc700(O1)) causing neonatal meningitis. None of the phylogenetic groups and none of the virulence determinants were distributed differently between survivors and non-survivors, except that the aerobactin gene (iucC) was less frequent in lethal isolates (94% vs. 71%, p 0.02). Isolates belonging to rare sequence O types were more likely to be lethal (OR 4.3, p 0.01), although they induced a lower level of bacteraemia than common sequence O types such as STc29(O18) and STc29(O45) in a neonatal rat model. These results suggest that unidentified human genetic risk-factors may be more important than strain virulence in predicting ECM mortality.

Antimicrobial susceptibility of 136 Escherichia coli isolates from cases of neonatal meningitis and relationship with virulence

The susceptibility of 136 Escherichia coli isolates from cases of neonatal meningitis to amoxycillin, ceftriaxone, nalidixic acid, ciprofloxacin and gentamicin was determined in relation to the carriage of virulence factors and phylogenetic group. Only amoxycillin and nalidixic acid resistance was observed (40% and 3%, respectively). Nalidixic acid resistance alone was associated with non-virulent phylogenetic group A (50% vs. 6% of susceptible isolates; p 0.03). No difference in virulence was observed between two representative nalidixic acid-susceptible virulent group B2 isolates and their nalidixic acid-resistant derivatives in a rat model of neonatal meningitis, suggesting that nalidixic acid resistance does not affect the virulence of E. coli strains causing meningitis.

Host and bacterial determinants of initial severity and outcome of Escherichia coli sepsis

A 1-year prospective cohort study of all episodes of Escherichia coli bacteraemia in two French university hospitals was conducted to assess simultaneously the influence of host and bacterial determinants on the initial severity and outcome of E. coli sepsis. Clinical data (community-acquired/nosocomial infection, immune status, underlying disease, primary source of infection, severity sepsis scoring and outcome), phylogenetic groups (A, B1, D and B2), nine virulence factors (VFs) (papC, papGII, papGIII, sfa/foc, hlyC, cnf1, iucC, fyuA and iroN) and the antibiotic susceptibility of isolates were investigated. All VFs except iucC were significantly more prevalent (p <0.05) among the B2 group isolates. The non-B2 isolates were more frequently resistant to antibiotics than were B2 isolates (p <0.05). There were significantly more B2 isolates from immunocompetent than from immunocompromised patients (p <0.05). No bacterial or host determinants influenced the initial severity of sepsis. Multivariate analysis revealed that the presence of papGIII, septic shock at baseline and a non-urinary tract origin of sepsis were associated independently with a fatal outcome (p 0.04, <0.0001 and 0.04, respectively). A factorial analysis of correspondence allowed two populations of isolates to be distinguished: those belonging to the B2 group were associated more frequently with susceptibility to antibiotics, community-acquired infection, a urinary tract origin and immunocompetent hosts; those belonging to the A, B1 or D groups were associated more frequently with resistance to antibiotics, a nosocomial origin, a non-urinary tract source and immunocompromised hosts. Although no influence of host or bacterial determinants on the initial severity of sepsis was detected, bacterial and host determinants both influenced the outcome of E. coli sepsis significantly.

Phylogenetic groups and virulence factors of Escherichia coli strains causing pyelonephritis in children with and without urinary tract abnormalities

Escherichia coli isolates causing acute pyelonephritis in 93 children (25% with urinary tract abnormalities) were tested for nine virulence factors (papC, papGII, papGIII, sfa/foc, hlyC, cnf1, iucC, fyuA and iroN) and their phylogenetic groups were determined. Isolates lacking papGII were more frequent among patients with urinary tract abnormalities (58% vs. 10%, p 0.0003), as were non-virulent phylogenetic group A isolates (25% vs. 5%, p 0.043). Pyelonephritis caused by less virulent E. coli strains was more frequent among patients with significant urinary tract abnormalities. Further studies are required to determine whether screening for E. coli virulence factors may help to identify children warranting anatomical investigations.

Escherichia coli native valve endocarditis

Among 36 cases of Escherichia coli native valve endocarditis (NVE) that met Duke criteria (31 cases in the literature between 1909 and 2002, and five cases seen in Paris, France), the urinary tract was the most common portal of entry. The majority (72.2%) of cases developed in elderly females. Overall, the proportion of patients aged > 70 years rose from 5.3% in 1982 to 22.9% in 2002. Persistent E. coli bacteraemia in the elderly in the absence of cardiac risk-factors may be a sign of NVE and should prompt an investigation by echocardiography.

Outbreak of Burkholderia cepacia bacteremia in a pediatric hospital due to contamination of lipid emulsion stoppers

We describe a 7-month outbreak of nosocomial Burkholderia cepacia bacteremia involving eight children in a pediatric hospital and the results of epidemiological investigations. A B. cepacia strain genotypically identical to the blood isolates was recovered from the upper surface of capped rubber stoppers of bottles of a commercial lipid emulsion used for parenteral nutrition.

Automated ribotyping provides rapid phylogenetic subgroup affiliation of clinical extraintestinal pathogenic Escherichia coli strains

Using the automated Riboprinter system, we have initiated the construction of an electronic Riboprint database composed of 72 ECOR reference strains and 15 archetypal virulent strains in order to provide a new simple molecular characterization method. More than 90% of the ECOR strains clustered in their original phylogenetic group. All but one of the archetypal virulent strains had a profile identical to that of one of the ECOR strains and could be easily affiliated with a phylogenetic group. This method appears to be an accurate and practical tool especially for investigating the genetic relationship between clinical extraintestinal pathogenic strains and B2 subgroup ECOR strains or archetypal pathotype strains.