Controlled performance evaluation of the DiversiLab repetitive-sequence-based genotyping system for typing multidrug-resistant health care-associated bacterial pathogens

Clonal spread of trimethoprim-sulfamethoxazole-resistant Stenotrophomonas maltophilia isolates in a tertiary hospital

Aim

The aims of this study were to: (i) determine antibiotic susceptibility of clinical Stenotrophomonas maltophilia isolates, (ii) investigate the presence of different classes of integrons and sul genes responsible for sulphonamide resistance, (iii) assess the molecular epidemiology of the isolates by determining their clonal relatedness, and (iv) investigate the potential sources of infection by collecting environmental samples when necessary.

Methods

99 S. maltophilia isolates from clinical specimens of hospitalized patients were screened by PCR for sul1, sul2, sul3 genes, and integron-associated integrase genes: intI1, intI2, and intI3. PFGE was used to determine the clonal relatedness of the isolates.

Results

Susceptibility rates for trimethoprim-sulfamethoxazole, levofloxacin, and ceftazidime were 90.9%, 91.9%, and 53.5% respectively. All trimethoprim-sulfamethoxazole-resistant isolates were positive for intI1 and sul1. PFGE analysis revealed that 24 of the isolates were clonally related, clustering in seven different clones. Five of the nine trimethoprim-sulfamethoxazole-resistant isolates were clonally related. The first isolate in this clone was from a wound sample of a patient in the infectious diseases clinic, and the other four were isolated from the bronchoalveolar lavage samples of patients in the thoracic surgery unit. The patient with the first isolate neither underwent bronchoscopy nor stayed in the thoracic surgery unit. Although clustering was observed in bronchoalveolar lavage samples, no S. maltophilia growth was detected in environmental samples.

Conclusion

The findings demonstrated that the sul1 gene carried by class 1 integrons plays an important role in trimethoprim-sulfamethoxazole resistance in S. maltophilia isolates. PFGE analysis revealed a high degree of genetic diversity. However, detection of clonally related isolates suggests the acquisition from a common source and/or cross-transmission of this microorganism between the patients.

Genetic relatedness of serial rectal isolates of Acinetobacter baumannii in an adult intensive care unit of a tertiary hospital in Kuwait

Acinetobacter baumannii is an opportunistic pathogen of intensive care unit (ICU) patients. A. baumannii colonizes many parts of the body including the gastrointestinal tract. Endemic and epidemic strains are polyclonal. There is no clarity on the origin of polyclonality of A. baumannii. The objective of the study was to define the genetic relatedness of serial isolates and the origin of polyclonality. Serial rectal isolates from ICU patients whose rectum was colonized on ≥5 sampling occasions were selected. From a total of 32 eligible colonized patients, isolates from a subgroup of 13 patients (a total of 108 isolates) showing different patterns of colonization as revealed by pulsed-field gel electrophoresis (PFGE) were studied. The isolates were analyzed by PFGE pulsotypes, sequence types (STs) by multi-locus sequence typing (MLST) and clonal complex (CC) by eBURST analysis. Serial isolates constituted a mixture of identical, related and unrelated pulsotypes. Analysis by STs and CCs were less discriminatory. The data suggest a combination of an initial colonizing isolate undergoing mutation as well as colonization by independent isolates. Further clarity on the origin of diversity should be better obtained by whole-genome sequencing.

How to: molecular investigation of a hospital outbreak

BACKGROUND

Studying hospital outbreaks by using molecular tools, i.e. synthesizing the molecular epidemiology data to its appropriate clinical-epidemiologic context, is crucial in order to identify infection source, infer transmission dynamics, appropriately allocate prevention resources and implement control measures. Whole-genome sequencing (WGS) of pathogens has become the reference standard, as it is becoming more accessible and affordable. Consequently, sequencing of the full pathogen genome via WGS and major progress in fit-for-purpose genomic data analysis tools and interpretation is revolutionizing the field of outbreak investigations in hospitals. Metagenomics is an additional evolving field that might become commonly used in the future for outbreak investigations. Nevertheless, practitioners are frequently limited in terms of WGS or metagenomics, especially for local outbreak analyses, as a result of costs or logistical considerations, reduced or lack of locally available resources and/or expertise. As a result, traditional approaches, including pulsed-field gel electrophoresis, repetitive-element palindromic PCR and multilocus sequence typing, along with other typing methods, are still widely used.

AIMS

To provide practitioners with evidenced-based action plans for usage of the various typing techniques in order to investigate the molecular epidemiology of nosocomial outbreaks, of clinically significant pathogens in acute-care hospitals.

SOURCES

PubMed search with relevant keywords along with personal collection of relevant publications.

CONTENT

Representative case scenarios and critical review of the relevant scientific literature.

IMPLICATIONS

The review provides practical action plans to manage molecular epidemiologic investigations of outbreaks caused by clinically significant nosocomial pathogens, while prioritizing the use and timely integration of the various methodologies.

Recent Advances in Molecular Diagnosis of Pseudomonasaeruginosa Infection by State-of-the-Art Genotyping Techniques

Pseudomonas aeruginosa is a rod-shaped Gram-negative bacterium which is notably known as a pathogen in humans, animals, and plants. Infections caused by P. aeruginosa especially in hospitalized patients are often life-threatening and rapidly increasing worldwide throughout the years. Recently, multidrug-resistant P. aeruginosa has taken a toll on humans' health due to the inefficiency of antimicrobial agents. Therefore, the rapid and advanced diagnostic techniques to accurately detect this bacterium particularly in clinical samples are indeed necessary to ensure timely and effective treatments and to prevent outbreaks. This review aims to discuss most recent of state-of-the-art molecular diagnostic techniques enabling fast and accurate detection and identification of P. aeruginosa based on well-developed genotyping techniques, e.g., polymerase chain reaction, pulse-field gel electrophoresis, and next generation sequencing. The advantages and limitations of each of the methods are also reviewed.

Increasing proportion of carbapenemase-producing Enterobacteriaceae and emergence of a MCR-1 producer through a multicentric study among hospital-based and private laboratories in Belgium from September to November 2015

Carbapenemase-producing Enterobacteriaceae (CPE) strains have been increasingly reported in Belgium. We aimed to determine the proportion of CPE among Enterobacteriaceae isolated from hospitalised patients and community outpatients in Belgium in 2015. For the hospitalised patients, the results were compared to a previous similar survey performed in the same hospitals in 2012. Twenty-four hospital-based and 10 private laboratories collected prospectively 200 non-duplicated Enterobacteriaceae isolates from clinical specimens. All isolates were screened locally by carbapenem disk diffusion using European Committee on Antimicrobial Susceptibility Testing methodology. Putative CPE strains with inhibition zone diameters below the screening breakpoints were referred centrally for confirmation of carbapenemase production. From September to November 2015, we found a proportion of clinical CPE of 0.55% (26/4,705) and of 0.60% (12/1,991) among hospitalised patients and among ambulatory outpatients respectively. Klebsiella pneumoniae (26/38) and OXA-48-like carbapenemase (28/38) were the predominant species and enzyme among CPE. One OXA-48-producing Escherichia coli isolated from a hospital was found carrying plasmid-mediated MCR-1 colistin resistance. Compared with the 2012 survey, we found a significant increased proportion of clinical CPE (0.55% in 2015 vs 0.25% in 2012; p = 0.02) and an increased proportion of hospitals (13/24 in 2015 vs 8/24 in 2012) with at least one CPE detected. The study results confirmed the concerning spread of CPE including a colistin-resistant MCR-1 producer in hospitals and the establishment of CPE in the community in Belgium.

Control of carbapenem-resistant Acinetobacter baumannii outbreak in an intensive care unit of a teaching hospital in Southern Italy

Background

Acinetobacter baumannii is an opportunistic pathogen that has become a major cause of concern, since it is a frequent cause of healthcare-associated infections (HAIs). The aim of the study was to describe the occurrence, the management and the control of an outbreak that occurred in an intensive care unit (ICU) of a teaching hospital in Southern Italy caused by multiple strains of extensively drug-resistant A. baumannii (XDRAB).

Methods

Case-patient was defined as a patient with an healthcare-associated infection caused by an XDRAB isolate identified in a clinically significant culture. Environmental samples were collected from different surfaces. The isolates were identified by typical Gram stain morphology, using the Vitek 2 system (bioMérieux, France) and by MALDI-TOF MS mass spectrometry (bioMèrieux, France). Genotyping was performed through rep-PCR analysis.

Results

A patient presented an XDRAB ventilator-associated pneumonia at admission and was managed with strict isolation precautions until discharge. Five patients had a ventilator-associated pneumonia and two had a central line-associated bloodstream infection. Of the environmental samples, 1 sample obtained from the side of the bed of an infected patient yielded growth of XDRAB. Infection control measures were adopted. Rep-PCR analysis identified four patterns.

Conclusions

The integration of epidemiological and microbiological data and the application of infection control measures were crucial to bring such an outbreak to a rapid halt. The distinctive characteristic of this study was the complex molecular pattern of the outbreak, which subsided in a short period of time due to adherence to infection-control measures, confirming the fundamental role of molecular typing in the comprehension of outbreaks dynamics and of integrated control interventions for the interruption of epidemic events.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-016-2036-7) contains supplementary material, which is available to authorized users.

Prolonged outbreak of clonal MDR Pseudomonas aeruginosa on an intensive care unit: contaminated sinks and contamination of ultra-filtrate bags as possible route of transmission?

BACKGROUND

We report on an outbreak in a surgical, interdisciplinary intensive care unit (ICU) of a tertiary care hospital. We detected a cluster of ICU patients colonized or infected with multidrug-resistant Pseudomonas aeruginosa. We established an outbreak investigation team, performed an exploratory epidemiological analysis and initiated an epidemiology-based intervention.

METHODS

As part of the outbreak investigation, we performed microbiological examinations of the sinks in the patient rooms and a retrospective case-control study. All patients admitted to the outbreak ICU between January 2012 and February 2014 were included. Cases were patients colonized with the outbreak strain. Controls were patients with a different Pseudomonas aeruginosa strain. Risk factors were evaluated using multivariable conditional logistic regression analysis. Strain typing was performed using the repetitive element-based polymerase chain reaction (rep-PCR) DiversiLab system.

RESULTS

The outbreak strain was found in the sinks of five (of 16) patient rooms. Altogether 21 cases and 21 (randomly selected) controls were included. In the univariate analysis, there was no significant difference in baseline data of the patients. In the multivariate analysis, stay in a room with a colonized sink (Odds Ratio[OR] 11.2, p = 0.007) and hemofiltration (OR 21.9, p = 0.020) were independently associated with an elevated risk for colonization or infection by the outbreak strain. In a subsequent evaluation of the work procedures associated with hemofiltration, we found that the ultra-filtrate bags had been on average five times per day emptied in the sinks of the patient rooms and were used multiple for the same patient. We exchanged the traps of the contaminated sinks and eliminated work procedures involving sinks in patient rooms by implementation of single use bags, which are emptied outside patient rooms to reduce splash water at the sinks. In the 20 month follow-up period, the outbreak strain was detected only once, which indicated that the outbreak had been ceased (incidence 0.75% vs. 0.04%, p < 0.001) Furthermore, the incidence of Pseudonomas aeruginosa overall was significantly decreased (2.5% vs. 1.5%, p < 0.001).

CONCLUSION

In ICUs, limiting work processes involving sinks results in reduced multidrug-resistant Pseudomonas aeruginosa rates. ICUs with high rates of Pseudomonas aeruginosa should consider eliminating work processes that involve sinks and potentially splash water in close proximity to patients.

TRIAL REGISTRATION

All data were surveillance based data which were obtained within the German Law on Protection against Infection ("Infektionsschutzgesetz"). Therefore a trial registration was not required.

Is airborne transmission of Acinetobacter baumannii possible: A prospective molecular epidemiologic study in a tertiary care hospital

BACKGROUND

Understanding the dynamics of aerial spread of Acinetobacter may provide useful information for production of effective control measurements. We investigated genetic relationships between air and clinical isolates of Acinetobacter baumannii in an intensive care unit (ICU) setting.

METHODS

We conducted a prospective surveillance study in a tertiary care hospital for 8 months. A total of 186 air samples were taken from 2 ICUs. Clonal characteristics of air isolates were compared with the prospective clinical strains and the previously isolated strains of ICU patients over a 23-month period.

RESULTS

Twenty-six (11.4%) air samples yielded A baumannii, of which 24 (92.3%) isolates were carbapenem-resistant. The Acinetobacter concentration was the highest in bedside sampling areas of infected patients (0.39 CFU/m³). Air isolates were clustered in 13 genotypes, and 7 genotypes (including 18 air strains) were clonally related to the clinical strains of 9 ICU patients. One clone continued to be cultured over 27 days in ICU air, and air isolates could be clonally related to 7-week retrospective and approximately 15-week prospective clinical strains.

CONCLUSIONS

The results of this study suggest that infected patients could spread significant amounts of Acinetobacter to ICU air. These strains could survive in air for some weeks and could likely still infect new patients after some months. Special control measurements may be required against the airborne spread of Acinetobacter in ICUs.

High-level resistance to meropenem in clinical isolates of Pseudomonas aeruginosa in the absence of carbapenemases: role of active efflux and porin alterations

High-level carbapenem resistance is worryingly increasing in clinical isolates and is often attributed to carbapenemase expression. This study aimed to determine the mechanisms leading to high-level meropenem resistance in six carbapenemase-negative Pseudomonas aeruginosa isolated from cystic fibrosis (CF) patients and seven carbapenemase-positive isolates from patients suffering from hospital-acquired pneumonia (HAP). MICs were determined in the absence or presence of l-arginine or glycine-glutamate as competitive substrates for OprD (OccD1) or OpdP (OccD3), respectively, or the efflux pump inhibitor Phe-Arg β-naphthylamide (PAβN). β-Lactamases were screened by phenotypic tests and/or PCR. The oprD gene and its promoter were sequenced; protein expression was evidenced by SDS-PAGE. mexA, mexX, mexC and mexE transcripts were evaluated by real-time and semiquantitative PCR. Meropenem/imipenem MICs were 64-128/16-32 mg/L and 128/128-256 mg/L in CF and HAP isolates, respectively; PAβN reduced meropenem MICs to 4-16 mg/L only and specifically in CF isolates; porin competitors had no effect on MICs. All isolates showed an increase in transcription levels of mexA, mexX and/or mexC and mutations in oprD leading to production of truncated proteins. AmpC-type cephalosporinases were overexpressed in CF isolates and VIM-2 was expressed in HAP isolates. Antibiotic exclusion from bacteria by concomitant efflux and reduced uptake is sufficient to confer high-level resistance to meropenem in isolates overexpressing AmpC-type cephalosporinases. As efflux is preponderant in these isolates, it confers a paradoxical phenotype where meropenem is less active than imipenem. Concomitant susceptibility testing of both carbapenems and rapid elucidation of the most probable resistance mechanisms is thus warranted.

Molecular Epidemiology of Carbapenem-Resistant Acinetobacter Baumannii Complex Isolates from Patients that were Injured During the Eastern Ukrainian Conflict

This study addressed carbapenem-resistant Acinetobacter baumannii complex (ABC) isolates from patients that were injured during the military conflict in the Eastern Ukraine and treated at German Armed Forces Hospitals in 2014 and 2015. Clonal diversity of the strains and potential ways of transmission were analyzed.

Patients with one or several isolation events of carbapenem-resistant ABC were included. Isolates were characterized by VITEK II-based identification and resistance testing, molecular screening for frequent carbapenemase genes, and DiversiLab rep-PCR-based typing. Available clinical information of the patients was assessed.

From 21 young male Ukrainian patients with battle injuries, 32 carbapenem- and fluoroquinolone-resistant ABC strains were isolated. Four major clonal clusters were detected. From four patients (19%), ABC isolates from more than one clonal cluster were isolated. The composition of the clusters suggested transmission events prior to the admission to the German hospitals.

The infection and colonization pressure in the conflict regions of the Eastern Ukraine with ABC of low clonal diversity is considerable. Respective infection risks have to be considered in case of battle-related injuries in these regions. The low number of local clones makes any molecular exclusion of transmission events difficult.

Could the DiversiLab® semi-automated repetitive-sequence-based PCR be an acceptable technique for typing isolates ofPseudomonas aeruginosa? An answer from our experience and a review of the literature

Recently the DiversiLab® (DL) system (bioMérieux) was developed as an automated platform that uses repetitive element polymerase chain reaction (rep-PCR) technology for standardized, reproducible DNA fingerprinting of bacteria. The purpose of this study was to evaluate the usefulness of DL rep-PCR for typing Pseudomonas aeruginosa isolates. The performance of DL rep-PCR was compared with that of pulsed-field gel electrophoresis (PFGE) in a prospective multicenter study of patients with ventilator-associated pneumonia due to P. aeruginosa, conducted in 3 intensive care units over a 31-month period. In total, 203 P. aeruginosa isolates from 66 patients, from whom at least 2 consecutive respiratory samples each were collected more than 48 h apart, were typed using DL rep-PCR. Forty isolates (corresponding to 20 patients) were also typed using PFGE of SpeI-digested DNA. The typeability was 100% with DL rep-PCR and 95% with PFGE. The discriminatory power was close for DL rep-PCR and for PFGE (Simpson’s diversity indices of 0.901 and 0.947, respectively). Insufficient agreement between DL rep-PCR and PFGE typing results was observed for the 40 selected isolates (adjusted Rand coefficient of 0.419), mostly due to isolates of the same DL rep-PCR type but of different PFGE types (adjusted Wallace coefficients of 0.306 for DL rep-PCR with PFGE, and of 0.667 for PFGE with DL rep-PCR). Considered together with published data, DL rep-PCR results should be interpreted with caution for the investigation of outbreaks caused by P. aeruginosa and evaluated in conjunction with epidemiological data.

Analysis of Transmission of MRSA and ESBL-E among Pigs and Farm Personnel

Livestock-associated bacteria with resistance to two or more antibiotic drug classes have heightened our awareness for the consequences of antibiotic consumption and spread of resistant bacterial strains in the veterinary field. In this study we assessed the prevalence of concomitant colonization with livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) and enterobacteriaceae expressing extended-spectrum betalactamases (ESBL-E) in farms at the German-Dutch border region. Nasal colonization of pigs with MRSA (113/547 (20.7%)) was less frequent than rectal colonization with ESBL-E (163/540 (30.2%)). On the individual farm level MRSA correlated with ESBL-E recovery. The data further provide information on prevalence at different stages of pig production, including abattoirs, as well as in air samples and humans living and working on the farms. Notably, MRSA was detected in stable air samples of 34 out of 35 pig farms, highlighting air as an important MRSA transmission reservoir. The majority of MRSA isolates, including those from humans, displayed tetracycline resistance and spa types t011 and t034 characteristic for LA-MRSA, demonstrating transmission from pigs to humans. ESBL-E positive air samples were detected on 6 out of 35 farms but no pig-to-human transmission was found. Detection of ESBL-E, e.g. mostly Escherichia coli with CTX-M-type ESBL, was limited to these six farms. Molecular typing revealed transmission of ESBL-E within the pig compartments; however, related strains were also found on unrelated farms. Although our data suggest that acquisition of MRSA and ESBL-E might occur among pigs in the abattoirs, MRSA and ESBL-E were not detected on the carcasses. Altogether, our data define stable air (MRSA), pig compartments (ESBL-E) and abattoir waiting areas (MRSA and ESBL-E) as major hot spots for transmission of MRSA and/or ESBL-E along the pig production chain.

The increasing threat of Pseudomonas aeruginosa high-risk clones

The increasing prevalence of chronic and hospital-acquired infections produced by multidrug-resistant (MDR) or extensively drug-resistant (XDR) Pseudomonas aeruginosa strains is associated with significant morbidity and mortality. This growing threat results from the extraordinary capacity of this pathogen for developing resistance through chromosomal mutations and from the increasing prevalence of transferable resistance determinants, particularly those encoding carbapenemases or extended-spectrum β-lactamases (ESBLs). P. aeruginosa has a nonclonal epidemic population structure, composed of a limited number of widespread clones which are selected from a background of a large quantity of rare and unrelated genotypes that are recombining at high frequency. Indeed, recent concerning reports have provided evidence of the existence of MDR/XDR global clones, denominated high-risk clones, disseminated in hospitals worldwide; ST235, ST111, and ST175 are likely those more widespread. Noteworthy, the vast majority of infections by MDR, and specially XDR, strains are produced by these and few other clones worldwide. Moreover, the association of high-risk clones, particularly ST235, with transferable resistance is overwhelming; nearly 100 different horizontally-acquired resistance elements and up to 39 different acquired β-lactamases have been reported so far among ST235 isolates. Likewise, MDR internationally-disseminated epidemic strains, such as the Liverpool Epidemic Strain (LES, ST146), have been noted as well among cystic fibrosis patients. Here we review the population structure, epidemiology, antimicrobial resistance mechanisms and virulence of the P. aeruginosa high-risk clones. The phenotypic and genetic factors potentially driving the success of high-risk clones, the aspects related to their detection in the clinical microbiology laboratory and the implications for infection control and public health are also discussed.

Molecular Typing of Enterobacteriaceae from Pig Holdings in North-Western Germany Reveals Extended- Spectrum and AmpC β-Lactamases Producing but no Carbapenem Resistant Ones

The increase of extended- spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) in humans and in food-producing animals is of public health concern. The latter could contribute to spreading of these bacteria or their resistance genes to humans. Several studies have reported the isolation of third generation cephalosporin resistant bacteria in livestock animals. However, the number of samples and the methodology used differ considerably between studies limiting comparability and prevalence assessment. In the present study, a total of 564 manure and dust samples were collected from 47 pig farms in Northern Germany and analysed to determine the prevalence of ESBL-E. Molecular typing and characterization of resistance genes was performed for all ESBL-E isolates. ESBL-E isolates were found in 55.3% of the farms. ESBL-Escherichia coli was found in 18.8% of the samples, ESBL-Klebsiella pneumoniae in 0.35%. The most prevalent ESBL genes among E. coli were CTX-M-1 like (68.9%), CTX-M-15 like (16%) and CTX-M-9 group (14.2%). In 20% of the latter two, also the OXA-1 like gene was found resulting in a combination of genes typical for isolates from humans. Genetic relation was found between isolates not only from the same, but also from different farms, with multilocus sequence type (ST) 10 being predominant among the E. coli isolates. In conclusion, we showed possible spread of ESBL-E between farms and the presence of resistance genes and STs previously shown to be associated with human isolates. Follow-up studies are required to monitor the extent and pathways of ESBL-E transmission between farms, animals and humans.

Sequence type 131 fimH30 and fimH41 subclones amongst Escherichia coli isolates in Australia and New Zealand

The clonal composition of Escherichia coli causing extra-intestinal infections includes ST131 and other common uropathogenic clones. Drivers for the spread of these clones and risks for their acquisition have been difficult to define. In this study, molecular epidemiology was combined with clinical data from 182 patients enrolled in a case-control study of community-onset expanded-spectrum cephalosporin-resistant E. coli (ESC-R-EC) in Australia and New Zealand. Genetic analysis included antimicrobial resistance mechanisms, clonality by DiversiLab (rep-PCR) and multilocus sequence typing (MLST), and subtyping of ST131 by identification of polymorphisms in the fimH gene. The clonal composition of expanded-spectrum cephalosporin-susceptible E. coli and ESC-R-EC isolates differed, with six MLST clusters amongst susceptible isolates (median 7 isolates/cluster) and three clusters amongst resistant isolates, including 40 (45%) ST131 isolates. Population estimates indicate that ST131 comprises 8% of all E. coli within our population; the fluoroquinolone-susceptible H41 subclone comprised 4.5% and the H30 subclone comprised 3.5%. The H30 subclone comprised 39% of all ESC-R-EC and 41% of all fluoroquinolone-resistant E. coli within our population. Patients with ST131 were also more likely than those with non-ST131 isolates to present with an upper than lower urinary tract infection (RR=1.8, 95% CI 1.01-3.1). ST131 and the H30 subclone were predominant amongst ESC-R-EC but were infrequent amongst susceptible isolates where the H41 subclone was more prevalent. Within our population, the proportional contribution of ST131 to fluoroquinolone resistance is comparable with that of other regions. In contrast, the overall burden of ST131 is low by global standards.

Outbreak of Mycobacterium mucogenicum Bloodstream Infections among Patients with Sickle Cell Disease in an Outpatient Setting

Objective.

To study an outbreak of Mycobacterium mucogenicum bloodstream infections in an outpatient setting.

Design.

Outbreak investigation and retrospective chart review.

Setting.

University outpatient clinic.

Patients.

Patients whose blood cultures tested positive for M. mucogenicum in May or June 2008.

Methods.

An outbreak investigation and a review of infection control practices were conducted. During the process, environmental culture samples were obtained. Isolates from patients and the environment were genotyped with the DiversiLab typing system to identify the source. Chart reviews were conducted to study the management and outcomes of the patients.

Results.

Four patients with sickle cell disease and implanted ports followed in the same hematology outpatient clinic developed blood cultures positive for M. mucogenicum. A nurse in the clinic had prepared intravenous port flushes on the sink counter, using a saline bag that was hanging over the sink throughout the shift. None of the environmental cultures grew M. mucogenicum except for the tap water from 2 rooms, 1 of which had a faucet aerator. The 4 patient isolates and the tap water isolate from the room with the aerator were found to have greater than 98.5% similarity. The subcutaneous ports were removed, and patients cleared their infections after a course of antibiotic therapy.

Conclusion.

The source of the M. mucogenicum bacteremia outbreak was identified by genotyping analysis as the clinic tap water supply. The preparation of intravenous medications near the sink was likely an important factor in transmission, along with the presence of a faucet aerator.

Phenotypic and molecular characteristics of carbapenem-resistant Enterobacteriaceae in a health care system in Los Angeles, California, from 2011 to 2013

Carbapenem-resistant Enterobacteriaceae (CRE) are a concern for health care in the United States but remain relatively uncommon in California. We describe the phenotype, clonality, and carbapenemase-encoding genes present in CRE isolated from patients at a Californian tertiary health care system. CRE for this study were identified by evaluating the antibiograms of Enterobacteriaceae isolated in the UCLA Health System from 2011 to 2013 for isolates that were not susceptible to meropenem and/or imipenem. The identification of these isolates was subsequently confirmed by matrix-associated laser desorption ionization-time of flight, and broth microdilution tests were repeated to confirm the CRE phenotype. Real-time PCR for bla(KPC), bla(SME), bla(IMP), bla(NDM-1), bla(VIM), and bla(OXA-48) was performed. Clonality was assessed by repetitive sequence-based PCR (repPCR) and multilocus sequence typing (MLST). Of 15,839 nonduplicate clinical Enterobacteriaceae isolates, 115 (0.73%) met the study definition for CRE. This number increased from 0.5% (44/8165) in the first half of the study to 0.9% (71/7674) in the second (P = 0.004). The most common CRE species were Klebsiella pneumoniae, Enterobacter aerogenes, and Escherichia coli. A carbapenemase-encoding gene was found in 81.7% (94/115) of CRE and included bla(KPC) (78.3%), bla(NDM-1) (0.9%), and bla(SME) (2.6%). The majority of bla(KPC) genes were in K. pneumoniae isolates, which fell into 14 clonal groups on typing. bla(KPC) was identified in more than one species of CRE cultured from the same patient in four cases. Three bla(SME)-carrying Serratia marcescens isolates and one bla(NDM-1) carrying Providencia rettgeri isolate were detected. CRE are increasing in California, and carbapenemases, particularly KPC, are a common mechanism for carbapenem resistance in this region.

A multicentre cohort study on colonization and infection with ESBL-producing Enterobacteriaceae in high-risk patients with haematological malignancies

BACKGROUND

Bloodstream infections (BSIs) caused by enterobacteria remain a leading cause of mortality in patients with chemotherapy-induced neutropenia. The rate and type of colonization and infection with ESBL-producing Enterobacteriaceae (ESBL-E) and their mode of transmission in German cancer centres is largely unknown.

METHODS

We performed a prospective, observational study at five German university-based haematology departments. Participating sites screened for intestinal ESBL-E colonization within 72 h of admission, every 10 ± 2 days thereafter and before discharge. Three of the five centres performed contact isolation for patients colonized or infected with ESBL-E. Molecular characterization of resistance mechanisms and epidemiological typing of isolates by repetitive extragenic palindromic PCR (rep-PCR) and PFGE was performed to assess strain transmission between patients.

RESULTS

Between October 2011 and December 2012, 719 hospitalizations of 497 haematological high-risk patients comprising 20,143 patient-days were analysed. Mean duration of in-hospital stay was 36.6 days (range: 2-159 days). ESBL-E were identified from screening samples (82.8% Escherichia coli and 14.6% Klebsiella pneumoniae) in 55/497 patients (11.1%; range by centre: 5.8%-23.1%). PFGE and rep-PCR revealed only a single case of potential cross-transmission among two patients colonized with K. pneumoniae. Six episodes of BSI with ESBL-E were observed. Multivariate analysis revealed previous colonization with ESBL-E as the most important risk factor for BSI with ESBL-E (OR 52.00; 95% CI 5.71-473.89).

CONCLUSIONS

Even though BSI with ESBL-E is still rare in this high-risk population, colonization rates are substantial and vary considerably between centres. In-hospital transmission of ESBL-E as assessed by molecular typing was the exception.

Investigation of mechanism and molecular epidemiology of linezolid-resistant Enterococcus faecalis in China

Enterococcus is a major cause of important nosocomial infections. Linezolid, the first member of an entirely new class of antibiotics (oxazolidinones), is effective against serious infections caused by Enterococcus. However, resistance to linezolid has been discovered throughout the world rapidly. From 2011 to 2013, nine linezolid-resistant E. faecalis isolates were collected and the possible mechanisms of linezolid resistance, including mutations in domain V of 23S rRNA genes and in ribosomal proteins L3 and L4, and the multiresistance gene cfr, were investigated. Furthermore, an epidemiological survey of the nine linezolid-resistant E. faecalis isolates was performed by pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and DiversiLab. The three methods were compared to evaluate their merits and demerits, respectively. We failed to find the resistance mechanisms that have been revealed in recent years by PCR and sequencing analysis in the linezolid-resistant E. faecalis. Epidemiological investigation suggested that a small-scale outbreak of linezolid-resistant E. faecalis emerged in neurosurgery ICU from March to May of 2013. DiversiLab was a reliable typing tool and a suitable alternative to PFGE because it was as discriminatory as PFGE and better than MLST.

Clinical Application of the DiversiLab Microbial Typing System Using Repetitive Sequence-Based PCR for Characterization of Helicobacter pylori in Japan

We evaluated the DiversiLab (DL) system with universal primers, a semiautomated repetitive extragenic palindromic sequence-based polymerase chain reaction (PCR) (rep-PCR) system, for the characterization of Helicobacter pylori in Japan. All 135 isolates from Japanese patients with gastric cancer (GC, n = 55) or non-GC (n = 80) were used and subjected to the drug susceptibility examinations (amoxicillin, AMPC; metronidazole, MNZ; and clarithromycin, CAM) by E-test. There were 28 MNZ-resistant (20.7%), 35 CAM-resistant (25.9%), and 16 MNZ/CAM-resistant (11.9%) isolates. DL rep-PCR fingerprinting analysis at the level of 95% similarity revealed five major groups (A-E) and the other including 45 isolates. The occupation rates of GC-derived isolates in groups B (54.2%) and E (58.8%) were higher than in the other groups: A (26.7%), C (28.6%), D (30.0%), and the other (40.0%). Relative higher occupation rates of drug resistants, such as MNZ-, CAM- and double MNZ/CAM-resistant isolates, were observed in groups B (45.8%), C (42.6%), and D (40%). Five of eight GC-derived isolates with MNZ/CAM resistance were significantly assigned to group B (P = 0.0312, χ(2) -test). These results suggest that the isolates classified in group B have a potential to contribute to the development of severe gastric disorders. The DL system, rapid and high sensitive technology, would be widely available in clinical laboratory for pathological and epidemiological analyses even in H. pylori.

The deletion of TonB-dependent receptor genes is part of the genome reduction process that occurs during adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung

Chronic Pseudomonas aeruginosa infections are the main cause of morbidity among patients with cystic fibrosis (CF) due to persistent lung inflammation caused by interaction between this bacterium and the immune system. Longitudinal studies of clonally related isolates of a dominant CF clone have indicated that genome reduction frequently occurs during adaptation of P. aeruginosa in the CF lung. In this study, we have evaluated the P. aeruginosa population structure of patients attending the Universitair Ziekenhuis Brussel (UZ Brussel) CF reference center using a combination of genotyping methods. Although the UZ Brussel P. aeruginosa CF population is characterized by the absence of a dominant CF clone, some potential interpatient transmissions could be detected. Interestingly, one of these clones showed deletion of the alternative type I ferripyoverdine receptor gene fpvB. Furthermore, we found that several other TonB-dependent receptors are deleted as well. The genome of one potentially transmissible CF clone was sequenced, revealing large deleted regions including all type III secretion system genes and several virulence genes. Remarkably, a large number of deleted genes are shared between the P. aeruginosa CF clone described in this study and isolates belonging to the dominant Copenhagen CF DK2 clone, suggesting parallel evolution.

Emergence of extended-spectrum β-lactamase-producing Escherichia coli in catheter-associated urinary tract infection in neurogenic bladder patients

BACKGROUND

Catheter-associated urinary tract infection (CAUTI) is a common clinic problem. The purpose of this study was to investigate recent trends in CAUTI in neurogenic bladder patients focusing on extended-spectrum β-lactamase (ESBL)-producing Escherichia coli.

METHODS

Isolates from the urine of neurogenic bladder patients with UTI were investigated. Nine strains of ESBL-producing E coli were assayed by molecular strain typing using the Diversilab system for repetitive-sequence-based polymerase chain reaction (rep-PCR).

RESULTS

E coli accounted for most of the bacteria (74.1% to 81.0%) that produced ESBLs. Rep-PCR data showed that 7 out of 9 ESBL-producing E coli belonged to the same typing group with high similarity (more than 97% similarity) and that this distribution corresponded with antibiotic resistance patterns.

CONCLUSION

ESBL producing E coli strains isolated from CAUTI patients could be discriminated by rep-PCR typing using the Diversilab system in consistent with antibiotic resistance patterns.

Four genotyping schemes for phylogenetic analysis of Pseudomonas aeruginosa: comparison of their congruence with multi-locus sequence typing

Several molecular typing schemes have been proposed to differentiate among isolates and clonal groups, and hence establish epidemiological or phylogenetic links. It has been widely accepted that multi-locus sequence typing (MLST) is the gold standard for phylogenetic typing/long-term epidemiological surveillance, but other recently described methods may be easier to carry out, especially in settings with limited access to DNA sequencing. Comparing the performance of such techniques to MLST is therefore of relevance. A study was therefore carried out with a collection of P. aeruginosa strains (n = 133) typed by four typing schemes: MLST, multiple-locus variable number tandem repeat analysis (MLVA), pulsed-field gel electrophoresis (PFGE) and the commercial DiversiLab microbial typing system (DL). The aim of this study was to compare the results of each typing method with MLST. The Simpson's indices of diversity were 0.989, 0.980, 0.961 and 0.906 respectively for PFGE, MLVA, DL and MLST. The congruence between techniques was measured by the adjusted Wallace index (W): this coefficient indicates the probability that a pair of isolates which is assigned to the same type by one typing method is also typed as identical by the other. In this context, the congruence between techniques was recorded as follow: MLVA-type to predict MLST-type (93%), PFGE to MLST (92%), DL to MLST (64.2%), PFGE to MLVA (63.5%) and PFGE to DL (61.7%). Conversely, for all above combinations, prediction was very poor. The congruence was increased at the clonal complex (CC) level. MLST is regarded the gold standard for phylogenetic classification of bacteria, but is rather laborious to carry out in many settings. Our data suggest that MLVA can predict the MLST-type with high accuracy, and even higher when studying the clonal complex level. Of the studied three techniques MLVA was therefore the best surrogate method to predict MLST.

Detection of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli on flies at poultry farms

In the Netherlands, extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli bacteria are highly prevalent in poultry, and chicken meat has been implicated as a source of ESBL-producing E. coli present in the human population. The current study describes the isolation of ESBL-producing E. coli from house flies and blow flies caught at two poultry farms, offering a potential alternative route of transmission of ESBL-producing E. coli from poultry to humans. Overall, 87 flies were analyzed in 19 pools. ESBL-producing E. coli bacteria were detected in two fly pools (10.5%): a pool of three blow flies from a broiler farm and a pool of eight house flies from a laying-hen farm. From each positive fly pool, six isolates were characterized and compared with isolates obtained from manure (n = 53) sampled at both farms and rinse water (n = 10) from the broiler farm. Among six fly isolates from the broiler farm, four different types were detected with respect to phylogenetic group, sequence type (ST), and ESBL genotype: A0/ST3519/SHV-12, A1/ST10/SHV-12, A1/ST58/SHV-12, and B1/ST448/CTX-M-1. These types, as well as six additional types, were also present in manure and/or rinse water at the same farm. At the laying-hen farm, all fly and manure isolates were identical, carrying blaTEM-52 in an A1/ST48 genetic background. The data imply that flies acquire ESBL-producing E. coli at poultry farms, warranting further evaluation of the contribution of flies to dissemination of ESBL-producing E. coli in the community.

High rate of faecal carriage of extended-spectrum β-lactamase and OXA-48 carbapenemase-producing Enterobacteriaceae at a university hospital in Morocco

Carbapenemase-producing Enterobacteriaceae isolates are being increasingly reported, particularly from countries surrounding the Mediterranean area. We aimed to quantify the prevalence of carbapenemase- and extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in rectal swabs from hospitalized patients in a University hospital in Morocco, and to compare the performance of three screening media: ChromID ESBL (bioMérieux), Brilliance CRE (OXOID, Thermofisher) and SUPERCARBA (home made). Genetic detection and plasmid analysis were performed by PCR and sequencing. Strain comparison was performed by multi-locus sequence typing and the Diversilab technique (bioMérieux). The prevalence of multidrug-resistant Enterobacteriaceae was high, with 33 ESBL producers (42.85%, mainly CTX-M-15) and 10 OXA-48 producers (13%), corresponding to two major clones of K. pneumoniae (70%) and a clone of Enterobacter cloacae (30%). The three screening media showed the same sensitivity for detection of carbapenemase-producing Enterobacteriaceae, whereas the SUPERCARBA medium was more specific than the two other media. The average faecal carriage of ESBL or carbapenemase-producing Enterobacteriaceae varied from 1 × 10(2) to >1 × 10(8) CFU/g of stools. This study shows a high prevalence of multidrug-resistant Enterobacteriaceae, and particularly of OXA-48 producers. The new carbapenem-containing medium, SUPERCARBA, was as sensitive as Brilliance CRE and ChromID ESBL, and more specific for the detection of Enterobacteriaceae expressing those carbapenemases.

Clinical isolates of Pseudomonas aeruginosa from superficial skin infections have different physiological patterns

Pseudomonas aeruginosa are known to have a wide physiological potential allowing them to constantly populate diverse environments leading to severe infections of humans such as septicemia, leg ulcers, and burn wounds. We set out to probe physiological characteristics of P. aeruginosa isolates from diabetic leg ulcers collected from Helsinki metropolitan area. A total of 61 clinical isolates were obtained. Detailed phenotypic (physiological) characteristics [outer membrane (OM) permeability, membrane voltage, and activity of multidrug resistance pumps] were determined in several growth phases leading to the division of the analyzed set of P. aeruginosa strains into five distinct clusters including cells with similar physiological properties. In addition, their antibiotic resistance patterns and genetic heterogeneity were determined. Multiple isolates from the same patient were genetically very closely related and belonged to the same phenotypic cluster. However, genetically close isolates from different patients expressed very different phenotypic properties. The characteristics of infected patients seem to determine the growth environments for microorganisms that adapt by changing their physiological and/or genetic properties.

Epidemiological investigation of a nosocomial outbreak of multidrug-resistant Corynebacterium striatum at one Belgian university hospital

During an 8-month period, 24 Corynebacterium striatum isolates recovered from lower respiratory tract specimens of 10 hospitalized patients were characterized. The organisms were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and by 16S rRNA gene sequencing. The cluster of C. striatum exclusively affected patients who had been admitted to an intensive care unit and/or subsequently transferred to one medium-size respiratory care unit. Prolonged duration of hospitalization, advanced stage of chronic obstructive pulmonary disease, recent administration of antibiotics and exposure to an invasive diagnostic procedure were the most commonly found risk factors in these patients. Seven patients were colonized and three infected. All strains displayed a similar broad spectrum resistance to antimicrobial agents, remaining susceptible to vancomycin only. Typing analysis by MALDI-TOF MS and by semi-automated repetitive sequence-based PCR (DiversiLab typing) showed that all outbreak-associated C. striatum isolates clustered together in one single type while they differed markedly from epidemiologically unrelated C. striatum isolates. Pulsed-field gel electrophoresis (PFGE) profiles revealed three distinct PFGE types among the C. striatum isolates associated with the outbreak while all external strains except one belonged to a distinct type. We conclude that C. striatum is an opportunistic nosocomial pathogen in long-term hospitalized patients and can be at the origin of major outbreaks. The routine use of MALDI-TOF MS greatly facilitated the recognition/identification of this organism in clinical samples and this technique could also offer the potential to be used as an easy and rapid epidemiological typing tool for outbreak investigation.

International dissemination of Escherichia coli strains with discrepant behaviour in phenotypic antimicrobial susceptibility tests

Preventing the dissemination of antimicrobial resistance depends on appropriate antibiotic stewardship and accurate antimicrobial susceptibility testing (AST). We report the international dissemination of Escherichia coli strains, showing discrepancies between reference methods when phenotypically tested for susceptibility to piperacillin/tazobactam (TZP). We demonstrate that these related strains are predisposed to problematic TZP AST interpretations.

Epidemiology and resistance of Achromobacter xylosoxidans from cystic fibrosis patients in Dijon, Burgundy: first French data

BACKGROUND

Achromobacter xylosoxidans is an emerging pathogen in cystic fibrosis (CF) patients recognised as causal agent of inflammation. The prevalence of infection or colonisation is variable among CF centres. We report here the first epidemiological data about A. xylosoxidans in a French CF centre: Dijon, Burgundy.

METHODS

All isolates recovered from the patients affiliated with our centre in 2010 since their first visit were included. Antimicrobial susceptibility was determined by disk diffusion method and E-test. Molecular epidemiology was performed by Pulsed Field Gel Electrophoresis (PFGE) and compared with repetitive sequence-based PCR (rep-PCR, DiversiLab®). We also sequenced the constitutive bla-oxa-114 gene.

RESULTS

Out of 120 patients, 21 (17.5%) had at least one positive culture with A. xylosoxidans since they started to receive routine care in our CF centre (447 isolates). Median age at first positive culture was 16 years (range 3-34 years). Most patients were colonised by their own strain, cross-contamination was very rare. We observed two cases of intra-family spread. DiversiLab® is a useful tool as efficient as PFGE to compare isolates recovered simultaneously from different patients when an outbreak is suspected. However, PFGE remains the reference method for long-term survey of chronically colonised patients. We detected new OXA-114 variants and the new oxacillinase OXA-243 (88% amino acid identity with OXA-114). Acquired resistance to ciprofloxacin, ceftazidime and carbapenems was frequent. In 2010, 7 patients harboured strains resistant to ceftazidime, 6 patients strains with decreased susceptibility to carbapenems (especially meropenem) and 12 patients strains resistant to ciprofloxacin.

CONCLUSIONS

In our centre, the high prevalence of colonisation is not due to cross-contamination. Our main concern is the high rate of antimicrobial resistance.

Microsatellite genotyping clarified conspicuous accumulation of Candida parapsilosis at a cardiothoracic surgery intensive care unit

Candida parapsilosis has become a significant cause of invasive fungal infections in seriously ill patients. Nosocomial outbreaks through direct and indirect contact have been described. The aim of this study was the molecular characterization of what appeared to be an ongoing C. parapsilosis outbreak at the cardiothoracic intensive care unit of the University Hospital of Vienna between January 2007 and December 2008. Using two different molecular typing methods-automated repetitive sequence-based PCR (DiversiLab; bioMérieux) and microsatellite genotyping-we investigated the genetic relationship of 99 C. parapsilosis isolates. Eighty-three isolates originated from the cardiothoracic intensive care unit, while 16 isolates were random control isolates from other intensive care units and a different Austrian hospital. The 99 C. parapsilosis isolates analyzed by repetitive-element PCR all showed identical genotypes, suggesting an ongoing outbreak. In contrast, microsatellite genotyping showed a total of 56 different genotypes. Two major genotypes were observed in 10 and 15 isolates, respectively, whereas another 13 genotypes were observed in 2 to 4 isolates each. Forty-one genotypes were observed only once. Closely related genotypes that differed in only a single microsatellite marker were grouped into clonal complexes. When it comes to C. parapsilosis, microsatellite genotyping is a more discriminative method than repetitive-element PCR genotyping to investigate outbreaks.

Insights into the global molecular epidemiology of carbapenem non-susceptible clones of Acinetobacter baumannii

The global emergence of multidrug resistance (MDR) among Gram-negative bacteria has dramatically limited the therapeutic options. During the last two decades, Acinetobacter baumannii has become a pathogen of increased clinical importance due to its remarkable ability to cause outbreaks of infections and to acquire resistance to almost all currently used antibiotics, including the carbapenems. This review considers the literature on A. baumannii and data from multilocus sequence typing studies to explore the global population structure of A. baumannii and detect the occurrence of clonality, with the focus on the presence of specific resistance mechanisms such as the OXA-carbapenemases. The worldwide dissemination of MDR and carbapenem non-susceptible A. baumannii is associated with diverse genetic backgrounds, but predominated by a number of extensively distributed clones, such as CC92(B)/CC2(P) and CC109(B)/CC1(P), which have frequently been supplemented by acquired OXA-type carbapenemase genes.

Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology

Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.

Rapid emergence and spread of OXA-48-producing carbapenem-resistant Enterobacteriaceae isolates in Belgian hospitals

During a polymerase chain reaction (PCR)-based surveillance study of β-lactam resistance, 19 OXA-48-positive enterobacterial isolates were detected at nine Belgian hospitals from January 2010 to April 2011. Most cases were presumed to have been locally acquired and were detected in patients who had not travelled abroad. Clonally related outbreaks occurred in two different cities. The majority of isolates co-produced several β-lactamases as well as non-β-lactam resistance genes. This report highlights the rapid emergence and spread of OXA-48-producing Enterobacteriaceae in Belgium.