Evaluation of the DiversiLab system for detection of hospital outbreaks of infections by different bacterial species

Evaluation of the Efficacy of a Cholera-Toxin-Based Staphylococcus aureus Vaccine against Bovine Intramammary Challenge

Staphylococcus aureus (S. aureus) is a primary agent of bovine mastitis and a source of significant economic loss for the dairy industry. We previously reported antigen-specific immune induction in the milk and serum of dairy cows following vaccination with a cholera toxin A₂ and B subunit (CTA₂/B) based vaccine containing the iron-regulated surface determinant A (IsdA) and clumping factor A (ClfA) antigens of S. aureus (IsdA + ClfA-CTA₂/B). The goal of the current study was to assess the efficacy of this vaccine to protect against S. aureus infection after intramammary challenge. Six mid-lactation heifers were randomized to vaccinated and control groups. On days 1 and 14 animals were inoculated intranasally with vaccine or vehicle control, and on day 20 animals were challenged with S. aureus. Clinical outcome, milk quality, bacterial shedding, and somatic cell count (SCC) were followed for ten days post-challenge. Vaccinated animals did not show signs of clinical S. aureus mastitis and had lower SCCs compared to control animals during the challenge period. Reductions in bacterial shedding were observed but were not significant between groups. Antibody analysis of milk and serum indicated that, upon challenge, vaccinated animals produced enhanced IsdA- and ClfA-CTA₂/B specific immunoglobulin G (IgG) responses, while responses to CTA₂/B alone were not different between groups. Responses after challenge were largely IgG1 against the IsdA antigen and mixed IgG1/IgG2 against the ClfA antigen. In addition, there was a significant increase in interferon gamma (IFN-γ) expression from blood cells in vaccinated animals on day 20. While preliminary, these findings support evidence of the induction of active immunity by IsdA + ClfA-CTA₂/B, and further assessment of this vaccine is warranted.

Novel Sequence Type in Bacillus cereus Strains Associated with Nosocomial Infections and Bacteremia, Japan

This sequence type was dominant in isolates from bacteremia patients in 3 hospitals.

Bacillus cereus is associated with foodborne illnesses characterized by vomiting and diarrhea. Although some B. cereus strains that cause severe extraintestinal infections and nosocomial infections are recognized as serious public health threats in healthcare settings, the genetic backgrounds of B. cereus strains causing such infections remain unknown. By conducting pulsed-field gel electrophoresis and multilocus sequence typing, we found that a novel sequence type (ST), newly registered as ST1420, was the dominant ST isolated from the cases of nosocomial infections that occurred in 3 locations in Japan in 2006, 2013, and 2016. Phylogenetic analysis showed that ST1420 strains belonged to the Cereus III lineage, which is much closer to the Anthracis lineage than to other Cereus lineages. Our results suggest that ST1420 is a prevalent ST in B. cereus strains that have caused recent nosocomial infections in Japan.

Molecular epidemiological analysis and risk factors for acquisition of carbapenemase-producing Enterobacter cloacae complex in a Japanese university hospital

Background

To clarify the molecular epidemiology of carbapenem-resistant Enterobacter cloacae complex (CREC) and the risk factors for acquisition of carbapenemase-producing E. cloacae complex (CPEC).

Methods

Using clinical CREC isolates detected in a Japanese university hospital over 4 years, carbapenemase production was screened with phenotypic methods. Carbapenemase genes were analysed by PCR and sequencing. Molecular epidemiological analyses were conducted with repetitive extragenic palindromic (REP)-PCR and multilocus sequence typing (MLST). CRECs were identified to the subspecies level by hsp60 sequencing. Whole-genome sequencing of plasmids was conducted. A case-control study was performed to identify risk factors for acquisition of CPEC among patients with CREC.

Results

Thirty-nine CRECs including 20 CPECs carrying bla _IMP-1 were identified. Patients with CPEC had longer hospital stay before detection (26.5 days vs. 12 days, p = 0.008), a urinary catheter (odds ratio [OR], 5.36; 95% confidence interval [CI], 1.14-30.9; p = 0.023), or intubation (OR, 7.53; 95% CI, 1.47-53.8; p = 0.008) compared to patients without CPEC. Four genetically closely related CPEC clusters were observed, which showed that three of four CPEC clusters corresponded to E. asburiae (ST 53), E. hormaechei subsp. steigerwaltii (ST 113 and ST 1047) and E. cloacae subsp. cloacae (ST 513) by MLST and hsp60 sequencing. Seven representative plasmids shared structures with class I integron containing bla _IMP-1 and IncHI2A replicon type.

Conclusions

A longer hospital stay, presence of a urinary catheter, and intubation are risk factors for CPEC acquisition. In addition to horizontal transmission of genetically indistinguishable CPECs, IncHI2A plasmid carrying bla _IMP-1 appeared to be transferred among genetically different ECs.

Bacteria-Instructed Click Chemistry between Functionalized Gold Nanoparticles for Point-of-Care Microbial Detection

Bacterial infections pose mounting public health concerns and cause an enormous medical and financial burden today. Rapid and sensitive detection of pathogenic bacteria at the point of care (POC) remains a paramount challenge. Here, we report a novel concept of bacteria-instructed click chemistry and employ it for POC microbial sensing. In this concept of bacteria-instructed click chemistry, we demonstrate for the first time that pathogenic bacteria can capture and reduce exogenous Cu²⁺ to Cu⁺ by leveraging their unique metabolic processes. The produced Cu⁺ subsequently acts as a catalyst to trigger the click reaction between gold nanoparticles (AuNPs) modified with azide and alkyne functional molecules, resulting in the aggregation of nanoparticles with a color change of the solution from red to blue. In this process, signal amplification from click chemistry is complied with the aggregation of functionalized AuNPs, thus presenting a robust colorimetric strategy for sensitive POC sensing of pathogenic bacteria. Notably, this colorimetric strategy is easily integrated in a smartphone app as a portable platform to achieve one-click detection in a mobile way. Moreover, with the help of the magnetic preseparation process, this smartphone app-assisted platform enables rapid (within 1 h) detection of Escherichia coli with high sensitivity (40 colony-forming units/mL) in the complex artificial sepsis blood samples, showing great potential for clinical early diagnosis of bacterial infections.

Nosocomial outbreak of extended-spectrum β-lactamase-producing Enterobacter cloacae among cardiothoracic surgical patients: causes and consequences

BACKGROUND

Enterobacteriaceae are recognized as leading pathogens of healthcare-associated infections.

AIM

To report the investigation of a nosocomial outbreak of extended-spectrum β-lactamase-producing Enterobacter cloacae affecting cardiothoracic surgery patients in a Belgian academic hospital.

METHODS

Cases were defined based on epidemiological and microbiological investigations, including molecular typing using repetitive element-based polymerase chain reaction and multi-locus sequence typing. Case-control studies followed by field evaluations allowed the identification of a possible reservoir, and the retrospective assessment of human and financial consequences.

FINDINGS

Over a three-month period, 42 patients were infected or colonized by CTX-M-15-producing E. cloacae strains that belonged to the same clonal lineage. Acquisition mainly occurred in the intensive care unit (N = 23) and in the cardiothoracic surgery ward (N = 16). All but one patient had, prior to acquisition, undergone a cardiothoracic surgical procedure, monitored by the same transoesophageal echocardiography (TOE) probe in the operating room. Despite negative microbiological culture results, the exclusion of the suspected probe resulted in rapid termination of the outbreak. Overall, the outbreak was associated with a high mortality rate among infected patients (40%) as well as significant costs (€266,550).

CONCLUSION

The outbreak was indirectly shown to be associated with the contamination of a manually disinfected TOE probe used per-operatively during cardiothoracic surgery procedures, because withdrawal of the putative device led to rapid termination of the outbreak.

Discovery of mcr-1-Mediated Colistin Resistance in a Highly Virulent Escherichia coli Lineage

Resistance to last-line polymyxins mediated by the plasmid-borne mobile colistin resistance gene (mcr-1) represents a new threat to global human health. Here we present the complete genome sequence of an mcr-1-positive multidrug-resistant Escherichia coli strain (MS8345). We show that MS8345 belongs to serotype O2:K1:H4, has a large 241,164-bp IncHI2 plasmid that carries 15 other antibiotic resistance genes (including the extended-spectrum β-lactamase bla _CTX-M-1) and 3 putative multidrug efflux systems, and contains 14 chromosomally encoded antibiotic resistance genes. MS8345 also carries a large ColV-like virulence plasmid that has been associated with E. coli bacteremia. Whole-genome phylogeny revealed that MS8345 clusters within a discrete clade in the sequence type 95 (ST95) lineage, and MS8345 is very closely related to the highly virulent O45:K1:H4 clone associated with neonatal meningitis. Overall, the acquisition of a plasmid carrying resistance to colistin and multiple other antibiotics in this virulent E. coli lineage is concerning and might herald an era where the empirical treatment of ST95 infections becomes increasingly more difficult.IMPORTANCE Escherichia coli ST95 is a globally disseminated clone frequently associated with bloodstream infections and neonatal meningitis. However, the ST95 lineage is defined by low levels of drug resistance amongst clinical isolates, which normally provides for uncomplicated treatment options. Here, we provide the first detailed genomic analysis of an E. coli ST95 isolate that has both high virulence potential and resistance to multiple antibiotics. Using the genome, we predicted its virulence and antibiotic resistance mechanisms, which include resistance to last-line antibiotics mediated by the plasmid-borne mcr-1 gene. Finding an ST95 isolate resistant to nearly all antibiotics that also has a high virulence potential is of major clinical importance and underscores the need to monitor new and emerging trends in antibiotic resistance development in this important global lineage.

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.

Methicillin-Resistant Staphylococcus aureus: Molecular Characterization, Evolution, and Epidemiology

Staphylococcus aureus, a major human pathogen, has a collection of virulence factors and the ability to acquire resistance to most antibiotics. This ability is further augmented by constant emergence of new clones, making S. aureus a "superbug." Clinical use of methicillin has led to the appearance of methicillin-resistant S. aureus (MRSA). The past few decades have witnessed the existence of new MRSA clones. Unlike traditional MRSA residing in hospitals, the new clones can invade community settings and infect people without predisposing risk factors. This evolution continues with the buildup of the MRSA reservoir in companion and food animals. This review focuses on imparting a better understanding of MRSA evolution and its molecular characterization and epidemiology. We first describe the origin of MRSA, with emphasis on the diverse nature of staphylococcal cassette chromosome mec (SCCmec). mecA and its new homologues (mecB, mecC, and mecD), SCCmec types (13 SCCmec types have been discovered to date), and their classification criteria are discussed. The review then describes various typing methods applied to study the molecular epidemiology and evolutionary nature of MRSA. Starting with the historical methods and continuing to the advanced whole-genome approaches, typing of collections of MRSA has shed light on the origin, spread, and evolutionary pathways of MRSA clones.

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.

High Genetic Diversity among Stenotrophomonas maltophilia Isolates from Single Hospital: Nosocomial Outbreaks or Genotypic Profile Changes during Subcultures

Background

Stenotrophomonas maltophilia is a non-fermentative gram-negative bacillus which is widely recognised as an important nosocomial pathogen causing pneumonia, blood-stream, wound and urinary tract infections, particularly in immunosuppressed patients. The aim of this study was to evaluate a nosocomial outbreak of by S. maltophilia in an intensive care unit of a tertiary hospital and evaluate unexpected multiclonality.

Methods

A total of 11 isolates from respiratory cultures in intensive care unit of a 24 bed tertiary hospital obtained over a one months period and one isolate obtained from the nebuliser during environmental screening were investigated. The bacteria were identified by Phoenix 100 system. The clonal relatedness was evaluated by PFGE and semi-automated repetitive sequence-based PCR. Genotyping tests were repeated for 10 serial subcultures.

Results

PFGE and DiversiLab yielded 10 genotypic profiles for 12 isolates. Four to eight different genotypes were observed from 10 subcultures of the same isolate.

Conclusion

We conclude that, high genetic diversity and supposed multiclonal appearance of the outbreak isolates may be due to changing profiles during subcultures most probably depending on hypermutation.

Molecular epidemiology of Klebsiella pneumoniae K1 and K2 isolates in Japan

Although severe infections caused by hypervirulent Klebsiella pneumoniae isolates, such as K1 isolates belonging to sequence type (ST) 23, have been a significant problem in Asian countries, epidemiology of these isolates in Japan remains unclear. We performed a nationwide molecular epidemiological study of K. pneumoniae K1 and K2 isolates in Japan. Of the 259K. pneumoniae isolates collected, 14 and 16 isolates were identified as capsular genotypes K1 and K2, respectively. All K1 isolates were ST23 or its closely related clones and showed high genetic similarity by pulsed-field gel electrophoresis (PFGE) and the DiversiLab system (DL). K2 isolates, belonging to ST14, ST25, ST65, ST86, and ST110, were more genetically diverse than K1 isolates. Isolates belonging to a specific ST showed identical virulence gene profiles with a few exceptions. PFGE and DL results using K1 and K2 isolates were generally in agreement.

Diagnostics and laboratory role in outbreaks

PURPOSE OF REVIEW

The review describes the investigative benefits of traditional and novel molecular epidemiology techniques, while acknowledging the limitations faced by clinical laboratories seeking to implement these methods.

RECENT FINDINGS

Pulse-field gel electrophoresis and other traditional techniques remain powerful tools in outbreak investigations and continue to be used by multiple groups. Newer techniques such as matrix-assisted laser desorption/ionization-time of flight mass-spectrometry and whole genome sequencing show great promise. However, there is a lack of standardization regarding definitions for genetic relatedness, nor are there established criteria for accuracy and reproducibility. There are also challenges regarding availability of trained bioinformatics staff, and concerns regarding reimbursement.

SUMMARY

There are many tools available for molecular epidemiologic investigation. Epidemiologists and clinical laboratorians should work together to determine which testing methods are best for each institution.

Impact of single room design on the spread of multi-drug resistant bacteria in an intensive care unit

Background

Cross-transmission of nosocomial pathogens occurs frequently in intensive care units (ICU). The aim of this study was to investigate whether the introduction of a single room policy resulted in a decrease in transmission of multidrug-resistant (MDR) bacteria in an ICU.

Methods

We performed a retrospective study covering two periods: between January 2002 and April 2009 (old-ICU) and between May 2009 and March 2013 (new-ICU, single-room). These periods were compared with respect to the occurrence of representative MDR Gram-negative bacteria. Routine microbiological screening, was performed on all patients on admission to the ICU and then twice a week. Multi-drug resistance was defined according to a national guideline. The first isolates per patient that met the MDR-criteria, detected during the ICU admission were included in the analysis. To investigate the clonality, isolates were genotyped by DiversiLab (bioMérieux, France) or Amplified Fragment Length Polymorphism (AFLP). To guarantee the comparability of the two periods, the ‘before’ and ‘after’ periods were chosen such that they were approximately identical with respect to the following factors: number of admissions, number of beds, bed occupancy rate, per year and month.

Results

Despite infection prevention efforts, high prevalence of MRD bacteria continue to occur in the original facility. A marked and sustained decrease in the prevalence of MDR-GN bacteria was observed after the migration to the new ICU, while there appear to be no significant changes in the other variables including bed occupancy and numbers of patient admissions.

Conclusion

Single room ICU design contributes significantly to the reduction of cross transmission of MRD-bacteria.

Infection control in the new age of genomic epidemiology

With the growing importance of infectious diseases in health care and communicable disease outbreaks garnering increasing attention, new technologies are playing a greater role in helping us prevent health care-associated infections and provide optimal public health. The microbiology laboratory has always played a large role in infection control by providing tools to identify, characterize, and track pathogens. Recently, advances in DNA sequencing technology have ushered in a new era of genomic epidemiology, where traditional molecular diagnostics and genotyping methods are being enhanced and even replaced by genomics-based methods to aid epidemiologic investigations of communicable diseases. The ability to analyze and compare entire pathogen genomes has allowed for unprecedented resolution into how and why infectious diseases spread. As these genomics-based methods continue to improve in speed, cost, and accuracy, they will be increasingly used to inform and guide infection control and public health practices.

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.

Validation of Minim typing for fast and accurate discrimination of extended-spectrum, beta-lactamase-producing Klebsiella pneumoniae isolates in tertiary care hospital

Minim typing is derived from the multi-locus sequence typing (MLST). It targets the same genes, but sequencing is replaced by high resolution melt analysis. Typing can be performed by analysing six loci (6MelT), four loci (4MelT) or using data from four loci plus sequencing the tonB gene (HybridMelT). The aim of this study was to evaluate Minim typing to discriminate extended-spectrum beta-lactamase producing Klebsiella pneumoniae (ESBL-KLPN) isolates at our hospital. In total, 380 isolates were analyzed. The obtained alleles were assigned according to both the 6MelT and 4MelT typing scheme. In 97 isolates, the tonB gene was sequenced to enable HybridMelT typing. We found that the presented method is suitable to quickly monitor isolates of ESBL-KLPN; results are obtained in less than 2 hours and at a lower cost than MLST. We identified a local ESBL-KLPN outbreak and a comparison of colonizing and invasive isolates revealed a long term colonization of patients with the same strain.

High Prevalence of New Delhi Metallo-β-Lactamase-1 (NDM-1) Producers among Carbapenem-Resistant Enterobacteriaceae in Kuwait

The aim of the study was to determine the prevalence of New Delhi metallo-β lactamase-1 (NDM-1) producing Enterobacteriaceae in Kuwait over a one year period. Consecutive Enterobacteriaceae isolates with reduced susceptibility to carbapenems were collected from four government hospitals in Kuwait from January–December 2014. Their susceptibility to 18 antibiotics was performed by determining the minimum inhibitory concentration. Isolates resistant to carbapenems were tested by PCR for resistant genes. Finger printing of the positive isolates was done by DiversiLab^®. Clinical data of patients harboring NDM-1 positive isolates were analyzed. A total of 764 clinically significant Enterobacteriaceae isolates were studied. Of these, 61 (8%) were carbapenem-resistant. Twenty one out of these 61 (34.4%) were NDM-1-producers. All patients positive for NDM-1-carrying bacteria were hospitalized. About half were females (11/21 [52.3%]), average age was 53.3 years and the majority were Kuwaitis (14/21 [66.6%]). Six patients (28.5%) gave a history of travel or healthcare contact in an endemic area. Mortality rate was relatively high (28.6%). The predominant organism was Klebsiella pneumoniae (14 [66.6%]) followed by E. coli (4 [19%]). All NDM-1-positive isolates were resistant to meropenem, ertapenem, cefotaxime, cefoxitin and ampicillin, while 95.2% were resistant to imipenem, cefepime, and piperacillin-tazobactam. They were multidrug resistant including resistance to tigecycline, but 90% remained susceptible to colistin. About two-thirds of isolates (61.9%) co-produced-extended spectrum β-lactamases. During the study period, an outbreak of NDM-1 positive K. pneumoniae occurred in one hospital involving 3 patients confirmed by DiversiLab^® analysis. In conclusion, NDM-1-producing Enterobacteriaceae is a growing healthcare problem with increasing prevalence in Kuwait, especially in hospitalized patients, leaving few therapeutic options. A high prevalence of NDM-1 necessitates the implementation of strict infection control to prevent the spread of these organisms.

Isolation of Enterobacter aerogenes carrying blaTEM-1 and blaKPC-3 genes recovered from a hospital Intensive Care Unit

Enterobacter aerogenes has recently emerged as an important hospital pathogen. In this study, we showed the emergence of E. aerogenes isolates carrying the blaKPC gene in patients colonized by carbapenem-resistant Klebsiella pneumoniae strains. Two multiresistant E. aerogenes isolates were recovered from bronchial aspirates of two patients hospitalized in the Intensive Care Unit at the "Santa Maria della Scaletta" Hospital, Imola. The antimicrobial susceptibility test showed the high resistance to carbapenems and double-disk synergy test confirmed the phenotype of KPC and AmpC production. Other investigation revealed that ESBL and blaKPC genes were carried on the conjugative pKpQIL plasmid. This is a relevant report in Italy that describes a nosocomial infection due to the production of KPC beta-lactamases by an E. aerogenes isolate in patients previously colonized by K. pneumoniae carbapenem-resistant. In conclusion, it's necessary a continuous monitoring of multidrug-resistant strains for the detection of any KPC-producing bacteria that could expand the circulation of carbapenem-resistant pathogens.

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.

Molecular Subtyping of Shiga Toxin-Producing Escherichia coli Using a Commercial Repetitive Sequence-Based PCR Assay

PCR-based typing methods, such as repetitive sequence-based PCR (rep-PCR), may facilitate the identification of Shiga toxin-producing Escherichia coli (STEC) by serving as screening methods to reduce the number of isolates to be processed for further confirmation. In this study, we used a commercial rep-PCR typing system to generate DNA fingerprint profiles for STEC O157 (n = 60) and non-O157 (n = 91) isolates from human, food, and animal samples and then compared the results with those obtained from pulsed-field gel electrophoresis (PFGE). Fifteen serogroups were analyzed using the Kullback Leibler or extended Jaccard statistical method, and the unweighted pair group method of averages algorithm was used to create dendrograms. Among the 151 STEC isolates tested, all were typeable by rep-PCR. Among the non-O157 isolates, rep-PCR clustered 79 (88.8%) of 89 isolates according to serogroup status, with peak differences ranging from 1 (96.4% similarity) to 12 (58.7% similarity). The genetic relatedness of the non-O157 serogroups mirrored the branching of distinct clonal groups elucidated by other investigators. Although the discriminatory power of rep-PCR (Simpson's index of diversity [SID] = 0.954) for the O157 isolates was less than that of PFGE (SID = 0.993), rep-PCR was able to identify 29 pattern types, suggesting that this method can be used for strain typing, although not to the same level as PFGE. Similar results were obtained from analysis of the non-O157 isolates. With rep-PCR, we assigned non-O157 isolates to 46 pattern types with a SID of 0.977. By PFGE, non-O157 STEC strains were divided into 77 pattern types with a SID of 0.996. Together, these results indicate the ability of the rep-PCR typing system to distinguish between and within O157 and non-O157 STEC groups. Rapid PCR-based typing methods could be invaluable tools for use in outbreak investigations by excluding unrelated STEC isolates within 24 h.

An overview of various typing methods for clinical epidemiology of the emerging pathogen Stenotrophomonas maltophilia

Typing of bacterial isolates has been used for decades to study local outbreaks as well as in national and international surveillances for monitoring newly emerging resistant clones. Despite being recognized as a nosocomial pathogen, the precise modes of transmission of Stenotrophomonas maltophilia in health care settings are unknown. Due to the high genetic diversity observed among S. maltophilia clinical isolates, the typing results might be better interpreted if also environmental strains were included. This could help to identify preventative measures to be designed and implemented for decreasing the possibility of outbreaks and nosocomial infections. In this review, we attempt to provide an overview on the most common typing methods used for clinical epidemiology of S. maltophilia strains, such as PCR-based fingerprinting analyses, pulsed-field gel electrophoresis, multilocus variable number tandem repeat analysis, and multilocus sequence type. Application of the proteomic-based mass spectrometry by matrix-assisted laser desorption ionization-time of flight is also described. Improvements of typing methods already in use have to be achieved to facilitate S. maltophilia infection control at any level. In the near future, when novel Web-based platforms for rapid data processing and analysis will be available, whole genome sequencing technologies will likely become a highly powerful tool for outbreak investigations and surveillance studies in routine clinical practices.

Pseudo-outbreak of Actinomyces graevenitzii associated with bronchoscopy

Outbreaks and pseudo-outbreaks of infection related to bronchoscopy typically involve Gram-negative bacteria, Mycobacterium species or Legionella species. We report an unusual bronchoscopy-related pseudo-outbreak due to Actinomyces graevenitzii. Extensive epidemiological and microbiological investigation failed to identify a common source. Strain typing revealed that the cluster was comprised of heterogeneous strains of A. graevenitzii. A change in laboratory procedures for Actinomyces cultures was coincident with the emergence of the pseudo-outbreak, and we determined that A. graevenitzii isolates more readily adopted a white, dry, molar tooth appearance on anaerobic colistin nalidixic acid (CNA) agar which likely facilitated its detection and identification in bronchoscopic specimens. This unusual pseudo-outbreak was related to frequent requests of bronchoscopists for Actinomyces cultures combined with a change in microbiology laboratory practices.

Comparison of a semiautomated commercial repetitive-sequence-based PCR method with spoligotyping, 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing, and restriction fragment length polymorphism-based analysis of IS6110 for Mycobacterium tuberculosis typing

Fifty-two multidrug-resistant isolates of Mycobacterium tuberculosis representative of the currently predominant lineages in France were analyzed using repetitive-sequence-based PCR (rep-PCR) DiversiLab (DL), spoligotyping, 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing (MIRU-VNTR), and restriction fragment length polymorphism of IS6110 (IS6110-RFLP). DL, as opposed to MIRU-VNTR and IS6110-RFLP analysis, did not allow discrimination among half of the isolates, an indication of comparatively lower resolving power.

Evaluation of repetitive element polymerase chain reaction for surveillance of methicillin-resistant Staphylococcus aureus at a large academic medical center and community hospitals

Repetitive element polymerase chain reaction (rep-PCR) typing has been used for methicillin-resistant Staphylococcus aureus (MRSA) strain characterization. The goal of this study was to determine if a rapid commercial rep-PCR system, DiversiLab™ (DL; bioMérieux, Durham, NC, USA), could be used for MRSA surveillance at a large medical center and community hospitals. A total of 1286 MRSA isolates genotyped by the DL system were distributed into 84 distinct rep-PCR patterns: 737/1286 (57%) were clustered into 6 major rep-PCR patterns. A subset of 220 isolates was further typed by pulsed-field gel electrophoresis (PFGE), spa typing, and SCCmec typing. The 220 isolates were distributed into 80 rep-PCR patterns, 94 PFGE pulsotypes, 27 spa, and 3 SCCmec types. The DL rep-PCR system is sufficient for surveillance, but the DL system alone cannot be used to compare data to other institutions until a standardized nomenclature is established and the DL MRSA reference library is expanded.

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.

Design of clone-specific probes from genome sequences for rapid PCR-typing of outbreak pathogens

The genome sequence of one OXA-48-producing Klebsiella pneumoniae belonging to sequence type (ST) 405, and three belonging to ST11, were used to design and test ST-specific PCR assays for typing OXA-48-producing K. pneumoniae. The approach proved to be useful for in-house development of rapid PCR typing assays for local outbreak surveillance.

Comparison of pulsed-gel electrophoresis and a commercial repetitive-element PCR method for assessment of methicillin-resistant Staphylococcus aureus clustering in different health care facilities

Pulsed-field gel electrophoresis (PFGE) is a common method used to type methicillin-resistant Staphylococcus aureus (MRSA) in nosocomial investigations and epidemiological studies but is time-consuming and methodologically challenging. We compared typing results obtained using a commercial repetitive-element PCR (rep-PCR) system with PFGE in a sample of 86 unique MRSA isolates recovered from subjects in an academic referral hospital and two nursing homes in the same geographic region. Both methods reliably assigned isolates to the same Centers for Disease Control and Prevention (CDC) pulsotype. PFGE was significantly more discriminatory (Simpson's index of diversity, 0.92 at the 95% strain similarity threshold) than the commercial rep-PCR system (Simpson's index of diversity, 0.58). The global (adjusted Rand coefficient, 0.10) and directional congruence (adjusted Wallace coefficient(repPCR→PFGE) = 0.06; adjusted Wallace coefficient(PFGE → repPCR) = 0.52) between the two methods was low. MRSA strains recovered from study nursing homes that were clonal when typed by the commercial rep-PCR method were frequently noted to be genetically distinct when typed using PFGE. These data suggest that the commercial rep-PCR has less utility than PFGE in small-scale epidemiological assessments of MRSA in health care settings.

Genetic diversity and antibiotic resistance profiles of Campylobacter jejuni isolates from poultry and humans in Turkey

In this study, the investigation of clonal relations between human and poultry Campylobacter jejuni isolates and the determination of susceptibilities of isolates to various antibiotics were aimed. A total of 200 C. jejuni isolates concurrently obtained from 100 chicken carcasses and 100 humans were genotyped by the Pulsed-Field Gel Electrophoresis (PFGE) and automated Repetitive Extragenic Palindromic PCR (Rep-PCR, DiversiLab system) methods and were tested for their susceptibility to six antibiotics with disk diffusion method. The minimum inhibitory concentration (MIC) values of ciprofloxacin (CI), enrofloxacin (EF) and erythromycin (EM) were evaluated by E-test. By using PFGE 174 of (87.0%) the isolates were able to be typed. The clonally related strains were placed in 35 different clusters and 115 different genotypes were obtained. All of the two hundred isolates could be typed by using Rep-PCR and were divided into 133 different genotypes. One hundred and fourteen clonally related isolates (57.0%) were included in 47 clusters. In disk diffusion test, while the susceptibility rates of AMC and S to human and chicken derived C. jejuni isolates were 84.0%-96.0% and 96.0%-98.0%, respectively, all isolates were susceptible to gentamicin. The resistance rates of human isolates to AMP, NA and TE were detected as 44.0%, 84.0% and 38.0% of the resistances of chicken isolates to these antibiotics were 34.0%, 95.0% and 56.0%, respectively. The MIC values of human and chicken isolates to CI, EF and EM were detected as 81.0-93.0%, 85.0-88.0% and 6.0-7.0%, respectively. The clonal proximity rates were detected between human and poultry origin C. jejuni isolates. The discriminatory power of PFGE and Rep-PCR was similar, with Simpson's diversity indexes of 0.993 and 0.995, respectively. Concordance of the two methods as determined by Adjusted Rand coefficient was 0.198 which showed the low congruence between Rep-PCR and PFGE. High rates of quinolone resistance were detected in C. jejuni isolates. This study demonstrated that chicken meat played an important role for infections caused by C. jejuni in Turkey and erythromycin, amoxicillin clavulanic acid and gentamicin are recommended for the treatment of Campylobacteriosis in humans.

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.

International multicenter evaluation of the DiversiLab bacterial typing system for Escherichia coli and Klebsiella spp

Successful multidrug-resistant clones are increasing in prevalence globally, which makes the ability to identify these clones urgent. However, adequate, easy-to-perform, and reproducible typing methods are lacking. We investigated whether DiversiLab (DL), an automated repetitive-sequence-based PCR bacterial typing system (bioMérieux), is suitable for comparing isolates analyzed at different geographic centers. A total of 39 Escherichia coli and 39 Klebsiella species isolates previously typed by the coordinating center were analyzed. Pulsed-field gel electrophoresis (PFGE) confirmed the presence of one cluster of 6 isolates, three clusters of 3 isolates, and three clusters of 2 isolates for each set of isolates. DL analysis was performed in 11 centers in six different countries using the same protocol. The DL profiles of 425 E. coli and 422 Klebsiella spp. were obtained. The DL system showed a lower discriminatory power for E. coli than did PFGE. The local DL data showed a low concordance, as indicated by the adjusted Rand and Wallace coefficients (0.132 to 0.740 and 0.070 to 1.0 [E. coli] and 0.091 to 0.864 and 0.056 to 1.0 [Klebsiella spp.], respectively). The central analysis showed a significantly improved concordance (0.473 to 1.0 and 0.290 to 1.0 [E. coli] and 0.513 to 0.965 and 0.425 to 1.0 [Klebsiella spp.], respectively). The misclassifications of profiles for individual isolates were mainly due to inconsistent amplification, which was most likely due to variations in the quality and amounts of the isolated DNA used for amplification. Despite local variations, the DL system has the potential to indicate the occurrence of clonal outbreaks in an international setting, provided there is strict adherence to standardized, reproducible DNA isolation methods and analysis protocols, all supported by a central database for profile comparisons.

Otitis externa following aural irrigation linked to instruments contaminated with Pseudomonas aeruginosa

BACKGROUND

The incidence of acute otitis externa, an infection of the external auditory canal, in general practitioners' (GP) practices in The Netherlands is about 14 per 1000 patients per year. In early 2010, one of the authors noted that some of the otitis externa patients in his GP practice had undergone cerumen removal by ear syringing a few weeks earlier. Bacterial cultures of samples taken from the instruments used showed contamination of an ear syringe by Pseudomonas aeruginosa. From then on, P. aeruginosa isolates from patients' ears were stored in the laboratory.

AIM

It was assessed whether cross-contamination with P. aeruginosa between patients in the same GP practice could occur through the use of contaminated ear lavage instruments.

METHODS

From 17 GP practices, the otolaryngology Outpatient Department and the Out-of-Hours GP Service, instruments used for examining and cleaning the outer ear were swabbed. Strains of P. aeruginosa cultured from the instruments were genotyped together with isolates of patients registered in the same practice.

FINDINGS

In four practices where contaminated instruments were found, genotyping showed similarity between P. aeruginosa strains isolated from a patient and the ear syringe, and/or between strains of different patients in the same practice.

CONCLUSIONS

Transmission of P. aeruginosa from ear lavage instruments to patients appears to occur with otitis externa as a result. Together with the Infection Control Unit of our hospital we have formulated recommendations for the appropriate cleaning, disinfection and storage of re-usable ear lavage instruments for the GP practices to implement.

Applicability of DiversiLab repetitive sequence-based PCR method in epidemiological typing of enterohemorrhagic Escherichia coli (EHEC)

Enterohemorrhagic Escherichia coli (EHEC) causes diarrhea, often with severe complications. Rapid and discriminatory typing of EHEC using advanced molecular methods is needed for determination of the genetic relatedness of clones responsible for foodborne outbreaks and for finding out the transmission sources of the outbreaks. This study evaluated the potential of DiversiLab, a semiautomated repetitive sequence-based polymerase chain reaction method for the genotyping of EHEC strains. A set of 52 EHEC strains belonging to 15 O:H serotypes was clustered into 10 DiversiLab groups. All of the O157 strains and one O55 strain were classified into the same group based on a 90% similarity threshold. The other serotypes were classified to their own DiversiLab group, with the exception of one R:H(-) strain that was grouped with O5:H(-) strains. In addition, O26 and O111 strains were grouped together but ultimately subdivided according to their O-serotypes based on a 95% similarity threshold. The O104 strain, which was associated with a major outbreak of hemolytic uremic syndrome in Germany in May 2011, was also classified independently. The DiversiLab performed well in identifying isolates, but the discriminatory power of the repetitive sequence-based polymerase chain reaction method was lower than that of pulsed-field gel electrophoresis. Analysis of 15 enteropathogenic E. coli (EPEC) strains revealed that some EPEC strains clustered together with EHEC strains. Therefore, the DiversiLab system cannot be used to discriminate between these pathogroups. In conclusion, DiversiLab is a rapid and easy system for the primary exclusion of unrelated EHEC strains based on their serotypes, but more discriminatory methods, such as pulsed-field gel electrophoresis, are needed for accurate typing of the EHEC strains.

Good performance of the SpectraCellRA system for typing of methicillin-resistant Staphylococcus aureus isolates

Typing of methicillin-resistant Staphylococcus aureus (MRSA) remains necessary in order to assess whether transmission of MRSA occurred and to what extent infection prevention measures need to be taken. Raman spectroscopy (SpectraCellRA [SCRA]; RiverD International, Rotterdam, The Netherlands) is a recently developed tool for bacterial typing. In this study, the performance (typeability, discriminatory power, reproducibility, workflow, and costs) of the SCRA system was evaluated for typing of MRSA strains isolated from patients and patients' household members who were infected with or colonized by MRSA. We analyzed a well-documented collection of 113 MRSA strains collected from 54 households. The epidemiological relationship between the MRSA strains within one household was used as the gold standard. Pulsed-field gel electrophoresis (PFGE) was used for discrepancy analysis. The results of SCRA analysis on the strain level corresponded with epidemiological data for 108 of 113 strains, a concordance of 95.6%. When analyzed at the household level, the results of SCRA were correct for 49 out of 54 households, a concordance of 90.7%. Concordance on the strain level with epidemiological data for PFGE was 93.6% (103/110 isolates typed). Concordance on the household level with epidemiological data for PFGE was 93.5% (49/53 households analyzed). With PFGE regarded as the reference standard, the conclusions reached with Raman spectroscopy were identical to those reached with PFGE in 100 of 105 cases (95.2%). The reproducibility of SCRA was found to be 100%. We conclude that the SpectraCellRA system is a fast, easy-to-use, and highly reproducible typing platform for outbreak analysis that can compete with the currently used typing techniques.

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.

Population distribution of Beta-lactamase conferring resistance to third-generation cephalosporins in human clinical Enterobacteriaceae in the Netherlands

There is a global increase in infections caused by Enterobacteriaceae with plasmid-borne β-lactamases that confer resistance to third-generation cephalosporins. The epidemiology of these bacteria is not well understood, and was, therefore, investigated in a selection of 636 clinical Enterobacteriaceae with a minimal inhibitory concentration >1 mg/L for ceftazidime/ceftriaxone from a national survey (75% E. coli, 11% E. cloacae, 11% K. pneumoniae, 2% K. oxytoca, 2% P. mirabilis). Isolates were investigated for extended-spectrum β-lactamases (ESBLs) and ampC genes using microarray, PCR, gene sequencing and molecular straintyping (Diversilab and multi-locus sequence typing (MLST)). ESBL genes were demonstrated in 512 isolates (81%); of which 446 (87%) belonged to the CTX-M family. Among 314 randomly selected and sequenced isolates, bla_CTX-M-15 was most prevalent (n = 124, 39%), followed by bla_CTX-M-1 (n = 47, 15%), bla_CTX-M-14 (n = 15, 5%), bla_SHV-12 (n = 24, 8%) and bla_TEM-52 (n = 13, 4%). Among 181 isolates with MIC ≥16 mg/L for cefoxitin plasmid encoded AmpCs were detected in 32 and 27 were of the CMY-2 group. Among 102 E. coli isolates with MIC ≥16 mg/L for cefoxitin ampC promoter mutations were identified in 29 (28%). Based on Diversilab genotyping of 608 isolates (similarity cut-off >98%) discriminatory indices of bacteria with ESBL and/or ampC genes were 0.994, 0.985 and 0.994 for E. coli, K. pneumoniae and E. cloacae, respectively. Based on similarity cut-off >95% two large clusters of E. coli were apparent (of 43 and 30 isolates) and 21 of 21 that were typed by belonged to ST131 of which 13 contained bla_CTX-M-15. Our findings demonstrate that bla_CTX-M-15 is the most prevalent ESBL and we report a larger than previously reported prevalence of ampC genes among Enterobacteriaceae responsible for resistance to third-generation cephalosporins.

Colistin resistance in gram-negative bacteria during prophylactic topical colistin use in intensive care units

PURPOSE

Topical use of colistin as part of selective digestive decontamination (SDD) and selective oropharyngeal decontamination (SOD) has been associated with improved patient outcome in intensive care units (ICU), yet little is known about the risks of colistin resistance. We quantified effects of selective decontamination on acquisition of colistin-resistant gram-negative bacteria (GNB) using data from a cluster-randomized study and a single-centre cohort.

METHODS

Acquisition of colistin-resistant GNB and conversion from susceptible to resistance in GNB was determined in respiratory samples [from patients receiving SDD (n = 455), SOD (n = 476), or standard care (SC) (n = 315)], and in rectal swabs from 1,840 SDD-patients. Genotyping of converting isolates was performed where possible.

RESULTS

The respiratory tract acquisition rates of colistin-resistant GNB were comparable during SDD, SOD, and SC and ranged from 0.7 to 1.1/1,000 patient-days at risk. Rectal acquisition rates during SDD were <3.3/1,000 days at risk. In patients with respiratory tract GNB carriage, conversion rates were 3.6 and 1.1/1,000 patient-days at risk during SDD and SC, respectively, (p > 0.05). In patients with rectal GNB carriage conversion rates during SDD were 5.4 and 3.2/1,000 days at risk and 15.5 and 12.6/1,000 days at risk when colonized with tobramycin-resistant GNB.

CONCLUSIONS

Acquisition rates with colistin-resistant GNB in the respiratory tract were low and comparable with and without topical use of colistin. Rates of acquisition of colistin-resistant GNB during SDD were--in ICUs with low endemicity of antibiotic resistance--<2.5/1,000 days at risk, but were fivefold higher during persistent GNB colonization and 15-fold higher during carriage with tobramycin-resistant GNB.

Typing of nosocomial outbreaks of Acinetobacter baumannii by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been evaluated for the identification of multidrug-resistant Acinetobacter baumannii nosocomial outbreaks in comparison with the repetitive sequence-based PCR DiversiLab system. The results suggest that MALDI-TOF MS can be used for real-time detection of Acinetobacter outbreaks before results from DNA-based systems are available.

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.

In vivo emergence of tigecycline resistance in multidrug-resistant Klebsiella pneumoniae and Escherichia coli

Although resistance to tigecycline has been reported in surveillance studies, very few reports have described the emergence of resistance in vivo. We report two cases of patients with infections due to SHV-12-producing Klebsiella pneumoniae and K. pneumoniae carbapenemase-3 (KPC-3)-producing Escherichia coli, which developed tigecycline resistance in vivo after treatment. The reported limited experience underlines the risk of occurrence of a tigecycline MIC increase under treatment pressure.