Shiga toxin-producing Escherichia coli (STEC) stool multiplex PCR can replace culture for clinical diagnosis and follow-up

Shiga toxin (stx)-producing Escherichia coli (STEC) causes potentially severe gastrointestinal infections. Due to its public health importance, control measures are required, and carriers may need to refrain from work or daycare when the risk of spread to vulnerable people is high. We evaluated the use of direct stool multiplex PCR compared to culture for primary STEC diagnostics and for follow-up in order to update the national guidelines for STEC monitoring. We analyzed primary and follow-up samples of 236 STEC PCR-positive cases at HUSLAB, Helsinki, Finland in 2016-2017, altogether 858 samples. All STEC PCR-positive samples were inoculated on non-selective chromogenic agar plates. Culture positivity was confirmed from culture sweeps by PCR. 211 (89%) of the cases were culture positive in their primary sample. Of all primary and follow-up samples, 499 were PCR positive and of these 450 (90%) were culture positive. PCR-negative follow-up samples were available from 125 cases. Of these, 88 cases were followed for at least three consecutive PCR-negative samples. Two cases (2%) had culture-positive sample(s) after two consecutive PCR-negative samples. The median time for STEC clearance was 22-23 days. The laboratory-developed multiplex PCR test used in this study is a reliable method for STEC diagnostics and follow-up in a clinical laboratory. When non-selective methodology is used, the majority of PCR-positive samples (90%) are also culture positive. Furthermore, only two cases (2%) in our material had two consecutive PCR-negative samples followed by positive samples. Consequently, to demonstrate the clearance from STEC infection, we consider two PCR-negative follow-up samples sufficient. The Finnish national guidelines for STEC monitoring have been updated accordingly.

Rapid molecular detection of pathogenic microorganisms and antimicrobial resistance markers in blood cultures: evaluation and utility of the next-generation FilmArray Blood Culture Identification 2 panel

Rapid detection of pathogens causing bloodstream infections (BSI) directly from positive blood cultures is of highest importance in order to enable an adequate and timely antimicrobial therapy. In this study, the utility and performance of a recently launched next-generation fully automated test system, the Biofire FilmArray® Blood Culture Identification 2 (BCID2) panel, was evaluated using a set of 103 well-characterized microbial isolates including 29 antimicrobial resistance genes and 80 signal-positive and 23 signal-negative clinical blood culture samples. The results were compared to culture-based reference methods, MALDI-TOF, and/or 16S rDNA sequencing. Of the clinical blood culture samples, 68 were monomicrobial (85.0%) and 12 polymicrobial (15.0%). Six samples contained ESBL (bla_CTX-M), two MRSA (mecA), and three MRSE (mecA) isolates. In overall, the FilmArray BCID2 panel detected well on-panel targets and resistance markers from mono- and polymicrobial samples. However, one Klebsiella aerogenes and one Bacteroides ovatus were undetected, and the assay falsely reported one Shigella flexneri as Escherichia coli. Hence, the sensitivity and specificity for detecting microbial species were 98.8% (95%CI, 95.8–99.9%) and 99.9% (95%CI, 99.8–99.9%), respectively. The sensitivity and specificity for detecting of resistance gene markers were 100%. The results were available within 70 min from signal-positive blood cultures with minimal hands-on time. In conclusion, the BCID2 test allows reliable and simplified detection of a vast variety of clinically relevant microbes causing BSI and the most common antimicrobial resistance markers present among these isolates.

Three clusters of carbapenemase-producing Citrobacter freundii in Finland, 2016-20

OBJECTIVES

Carbapenemase-producing Enterobacterales (CPE) have spread widely into health care facilities (HCF) but clusters caused by carbapenemase-producing (CP) Citrobacter freundii have been uncommon until recent years. Here we describe CP C. freundii clusters detected in Finland during 2016-20.

METHODS

As a part of the national CPE surveillance, clinical microbiology laboratories send potential CP C. freundii isolates to the reference laboratory for confirmation and further characterization. Whole genome sequencing (WGS) with Illumina MiSeq sequencer was used to detect clusters. Resistance genes and STs were analysed using SRST2 and typing with core genome (cg) MLST. A case was defined as a patient with a CP C. freundii isolate belonging to one of the detected clusters.

RESULTS

We detected three CP C. freundii clusters: cluster 1 included 16 cases in five HCFs during 2016-20, cluster 2 had two cases in two HCFs during 2018-19 and cluster 3 had two cases in one HCF in 2020. The isolates (11 clinical and 5 screening) in cluster 1 had KPC-2 carbapenemase and were sequence type (ST)18. Cluster 2 (2 clinical isolates) had OXA-181/GES-5 carbapenemases and were ST604 and cluster 3 (two screening isolates) had KPC-3 carbapenemase and were ST116. None of the cases had a history of recent travel abroad.

CONCLUSIONS

CP C. freundii also causes outbreaks and can be a reservoir of carbapenemase genes. The long intervals between successive cases, mostly found in clinical specimens in two clusters, suggest that besides unknown carriers, environmental contamination may play a role in transmission.

Human Protoparvovirus DNA and IgG in Children and Adults with and without Respiratory or Gastrointestinal Infections

Three human protoparvoviruses, bufavirus (BuV), tusavirus (TuV) and cutavirus (CuV), have recently been discovered in diarrheal stool. BuV has been associated with diarrhea and CuV with cutaneous T-cell lymphoma, but there are hardly any data for TuV or CuV in stool or respiratory samples. Hence, using qPCR and IgG enzyme immunoassays, we analyzed 1072 stool, 316 respiratory and 445 serum or plasma samples from 1098 patients with and without gastroenteritis (GE) or respiratory-tract infections (RTI) from Finland, Latvia and Malawi. The overall CuV-DNA prevalences in stool samples ranged between 0-6.1% among our six patient cohorts. In Finland, CuV DNA was significantly more prevalent in GE patients above rather than below 60 years of age (5.1% vs 0.2%). CuV DNA was more prevalent in stools among Latvian and Malawian children compared with Finnish children. In 10/11 CuV DNA-positive adults and 4/6 CuV DNA-positive children with GE, no known causal pathogens were detected. Interestingly, for the first time, CuV DNA was observed in two nasopharyngeal aspirates from children with RTI and the rare TuV in diarrheal stools of two adults. Our results provide new insights on the occurrence of human protoparvoviruses in GE and RTI in different countries.

Molecular epidemiology of carbapenemase-producing Enterobacterales in Finland, 2012-2018

Carbapenemase-producing Enterobacterales (CPE) pose an increasing threat to patient safety and healthcare systems globally. We present molecular epidemiology of CPE in Finland during 2012–2018 with detailed characteristics of CPE strains causing clusters during the same time period. All Finnish clinical microbiology laboratories send Enterobacterales isolates with reduced susceptibility to carbapenems or isolates producing carbapenemase to the reference laboratory for further characterization by whole genome sequencing (WGS). In total, 231 CPE strains from 202 patients were identified during 2012–2018. Of the strains, 59% were found by screening and 32% from clinical specimens, the latter were most commonly urine. Travel and/or hospitalization history abroad was reported for 108/171 strains (63%). The most common species were Klebsiella pneumoniae (45%), Escherichia coli (40%), and Citrobacter freundii (6%), and the most common carbapenemase genes bla_NDM-like (35%), bla_OXA-48-like (33%), and bla_KPC-like (31%). During 2012–2018, the annual number of CPE strains increased from 9 to 70 and different sequence types from 7 to 33, and bla_OXA-48-like genes became the most prevalent. Of the clusters, 3/8 were linked to traveling or hospitalization abroad and 5/8 were caused by K. pneumoniae clone clonal complex 258. Most of the clusters were caused by K. pneumoniae producing KPC. High variety among different sequence types indicates that majority of CPE cases detected in Finland are likely imported from foreign countries. Nearly one-third of the cases are not found by screening suggesting that there is hidden transmission occurring in the healthcare settings.

Outbreak of multiple strains of non-O157 Shiga toxin-producing and enteropathogenic Escherichia coli associated with rocket salad, Finland, autumn 2016

In August 2016, an outbreak of Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) with 237 cases occurred in the Helsinki metropolitan area, Finland. Gastroenteritis cases were reported at 11 events served by one catering company. Microbiological and epidemiological investigations suggested rocket salad as the cause of the outbreak.

STEC ONT

H11 and EPEC O111:H8 strains isolated from food samples containing rocket were identical to the patient isolates. In this outbreak, the reported symptoms were milder than considered before for STEC infection, and the guidelines for STEC control measures need to be updated based on the severity of the illness. Based on our experience in this outbreak, national surveillance criteria for STEC have been updated to meet the practice in reporting laboratories covering both PCR-positive and culture-confirmed findings. We suggest that EPEC could be added to the national surveillance since diagnostics for EPEC are routinely done in clinical laboratories.

Respiratory diphtheria in an asylum seeker from Afghanistan arriving to Finland via Sweden, December 2015

In December 2015, an asylum seeker originating from Afghanistan was diagnosed with respiratory diphtheria in Finland. He arrived in Finland from Sweden where he had already been clinically suspected and tested for diphtheria. Corynebacterium diphtheriae was confirmed in Sweden and shown to be genotypically and phenotypically toxigenic. The event highlights the importance of early case detection, rapid communication within the country and internationally as well as preparedness plans of diphtheria antitoxin availability.

Coincidental detection of the first outbreak of carbapenemase-producing Klebsiella pneumoniae colonisation in a primary care hospital, Finland, 2013

In Finland, occurrence of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-KP) has previously been sporadic and related to travel. We describe the first outbreak of colonisation with KPC-KP strain ST512; it affected nine patients in a 137-bed primary care hospital. The index case was detected by chance when a non-prescribed urine culture was taken from an asymptomatic patient with suprapubic urinary catheter in June 2013. Thereafter, all patients on the 38-bed ward were screened until two screening rounds were negative and extensive control measures were performed. Eight additional KPC-KP-carriers were found, and the highest prevalence of carriers on the ward was nine of 38. All other patients hospitalised on the outbreak ward between 1 May and 10 June and 101 former roommates of KPC-KP carriers since January had negative screening results. Two screening rounds on the hospital's other wards were negative. No link to travel abroad was detected. Compared with non-carriers, but without statistical significance, KPC-KP carriers were older (83 vs 76 years) and had more often received antimicrobial treatment within the three months before screening (9/9 vs 90/133). No clinical infections occurred during the six-month follow-up. Early detection, prompt control measures and repetitive screening were crucial in controlling the outbreak.

Phylogeography of Francisella tularensis subspecies holarctica in Finland, 1993-2011

BACKGROUND

Finland repeatedly reports some of the highest incidences of tularaemia worldwide. To determine genetic diversity of the aetiologic agent of tularaemia, Francisella tularensis, a total of 76 samples from humans (n = 15) and animals (n = 61) were analysed.

METHODS

We used CanSNPs and canINDEL hydrolysis or TaqMan MGB probes for the analyses, either directly from the clinical tissue samples (n = 21) or from bacterial isolates (n = 55).

RESULTS

The genotypes of the strains were assigned to three previously described basal subspecies holarctica clades. The majority of strains (n = 67) were assigned to B.12, a clade reported to dominate in Scandinavia and Eastern Europe. A single strain was assigned to clade B.4, previously reported from North America, Europe and China. The remaining strains (n = 8) were members of clade B.6. Importantly, new diversity was discovered in clade B.6. We describe two newly designed TaqMan MGB probe assays for this new B.6 subclade B.70, and its previously identified sister clade B.11, a clade dominantly found in Western Europe.

CONCLUSIONS

The high genetic diversity of F. tularensis subspecies holarctica present in Finland is consistent with previous findings in Sweden. The results suggest a northern and southern division of the B.6 subclade B.10, where B.11 predominates in Western and Central Europe and B.70 is found in Fennoscandia. Further research is required to define whether the vast diversity of genotypes found is related to different habitats or reservoir species, their different postglacial immigration routes to Fennoscandia, or dynamics of the reservoir species.

Experimental Infection of voles with Francisella tularensis indicates their amplification role in tularemia outbreaks

Tularemia outbreaks in humans have been linked to fluctuations in rodent population density, but the mode of bacterial maintenance in nature is unclear. Here we report on an experiment to investigate the pathogenesis of Francisella tularensis infection in wild rodents, and thereby assess their potential to spread the bacterium. We infected 20 field voles (Microtus agrestis) and 12 bank voles (Myodes glareolus) with a strain of F. tularensis ssp. holarctica isolated from a human patient. Upon euthanasia or death, voles were necropsied and specimens collected for histological assessment and identification of bacteria by immunohistology and PCR. Bacterial excretion and a rapid lethal clinical course with pathological changes consistent with bacteremia and tissue necrosis were observed in infected animals. The results support a role for voles as an amplification host of F. tularensis, as excreta and, in particular, carcasses with high bacterial burden could serve as a source for environmental contamination.

Efficacy of a novel PCR- and microarray-based method in diagnosis of a prosthetic joint infection

BACKGROUND AND PURPOSE

Polymerase chain reaction (PCR) methods enable detection and species identification of many pathogens. We assessed the efficacy of a new PCR and microarray-based platform for detection of bacteria in prosthetic joint infections (PJIs).

METHODS

This prospective study involved 61 suspected PJIs in hip and knee prostheses and 20 negative controls. 142 samples were analyzed by Prove-it Bone and Joint assay. The laboratory staff conducting the Prove-it analysis were not aware of the results of microbiological culture and clinical findings. The results of the analysis were compared with diagnosis of PJIs defined according to the Musculoskeletal Infection Society (MSIS) criteria and with the results of microbiological culture.

RESULTS

38 of 61 suspected PJIs met the definition of PJI according to the MSIS criteria. Of the 38 patients, the PCR detected bacteria in 31 whereas bacterial culture was positive in 28 patients. 15 of the PJI patients were undergoing antimicrobial treatment as the samples for analysis were obtained. When antimicrobial treatment had lasted 4 days or more, PCR detected bacteria in 6 of the 9 patients, but positive cultures were noted in only 2 of the 9 patients. All PCR results for the controls were negative. Of the 61 suspected PJIs, there were false-positive PCR results in 6 cases.

INTERPRETATION

The Prove-it assay was helpful in PJI diagnostics during ongoing antimicrobial treatment. Without preceding treatment with antimicrobials, PCR and microarray-based assay did not appear to give any additional information over culture.

Rapid molecular characterization of Acinetobacter baumannii clones with rep-PCR and evaluation of carbapenemase genes by new multiplex PCR in Hospital District of Helsinki and Uusimaa

Multidrug-resistant Acinetobacter baumannii (MDRAB) is an increasing problem worldwide. Prevalence of carbapenem resistance in Acinetobacter spp. due to acquired carbapenemase genes is not known in Finland. The purpose of this study was to examine prevalence and clonal spread of multiresistant A. baumannii group species, and their carbapenemase genes. A total of 55 Acinetobacter isolates were evaluated with repetitive PCR (DiversiLab) to analyse clonality of isolates, in conjunction with antimicrobial susceptibility profile for ampicillin/sulbactam, colistin, imipenem, meropenem, rifampicin and tigecycline. In addition, a new real-time PCR assay, detecting most clinically important carbapenemase genes just in two multiplex reactions, was developed. The assay detects genes for KPC, VIM, IMP, GES-1/-10, OXA-48, NDM, GIM-1, SPM-1, IMI/NMC-A, SME, CMY-10, SFC-1, SIM-1, OXA-23-like, OXA-24/40-like, OXA-58 and ISAbaI-OXA-51-like junction, and allows confident detection of isolates harbouring acquired carbapenemase genes. There was a time-dependent, clonal spread of multiresistant A. baumannii strongly correlating with carbapenamase gene profile, at least in this geographically restricted study material. The new carbapenemase screening assay was able to detect all the genes correctly suggesting it might be suitable for epidemiologic screening purposes in clinical laboratories.

Rifaximin in the treatment of recurrent Clostridium difficile infection

BACKGROUND

Clostridium difficile can cause severe antibiotic-associated colitis. Conventional treatments with metronidazole and vancomycin improve symptoms, but after discontinuation of treatment, C. difficile infection (CDI) recurs in a number of patients. Rifaximin is a rifamycin-based non-systemic antibiotic that has effect against C. difficile.

AIM

To assess the effectiveness of rifaximin in recurrent C. difficile infection.

METHODS

We retrospectively evaluated the records of 32 patients who were treated with rifaximin for recurrent C. difficile infection. The symptoms were evaluated 12 weeks after the start of treatment and patient records were followed up until 1 year after treatment.

RESULTS

The mean age of the patients was 55 years (median 64, range: 19-84 years). Before the initiation of rifaximin therapy, the patients had undergone, on the average, 4.4 (range: 2-12) antimicrobial courses for C. difficile infection. C. difficile strain typing was performed in 27 patients. Eight (30%) patients had a strain with a DNA profile compatible with the BI/NAP1/027 ribotype. Antibiotic susceptibilities were determined of isolates from 22 patients. Most isolates (68%) had very low MIC-values for rifampin (<0.002 μg/mL) and the highest MIC value was 3.0 μg/mL. Isolates with a DNA profile compatible with the BI/NAP1/027 ribotype had, on the average, higher MICs of rifampin. After 12 weeks 17 (53%) patients had no relapse. The MIC value of rifampin seemed to predict the response to rifaximin treatment.

CONCLUSIONS

Rifaximin is a safe treatment for C. difficile infection. It has a reasonable effect in C. difficile infection and it can be considered as an optional treatment for recurrent C. difficile infection.

Shiga toxin-producing Escherichia coli serotype O78:H(-) in family, Finland, 2009

STEC carrying stx_1c and hlyA genes can invade the human bloodstream.

Shiga toxin–producing Escherichia coli (STEC) is a pathogen that causes gastroenteritis and bloody diarrhea but can lead to severe disease, such as hemolytic uremic syndrome (HUS). STEC serotype O78:H^– is rare among humans, and infections are often asymptomatic. We detected a sorbitol-fermenting STEC O78:H^–stx_1c:hlyA in blood and fecal samples of a 2-week-old boy who had bacteremia and HUS and in fecal samples of his asymptomatic family members. The phenotypic and genotypic characteristics and the virulence properties of this invasive STEC were investigated. Our findings demonstrate that contrary to earlier suggestions, STEC under certain conditions can invade the human bloodstream. Moreover, this study highlights the need to implement appropriate diagnostic methods for identifying the whole spectrum of STEC strains associated with HUS.

Emergence of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae during the years 2000 and 2004 in Helsinki, Finland

The molecular epidemiology of 33 Escherichia coli and 81 Klebsiella pneumoniae extended-spectrum beta-lactamase-producing healthcare-associated and community-acquired isolates collected in the Helsinki district during 2000-2004 was investigated. Clonality studies, antimicrobial susceptibility and genotyping of the isolates were performed. Newly emerging CTX-M-producing E. coli and bla(SHV-12)-producing K. pneumoniae isolates were detected. Clonal clusters of both species persisted throughout the study period.

Type 1 fimbria-mediated adhesion of enteric bacteria to grass roots

Type 1 fimbriae of Klebsiella pneumoniae and Enterobacter agglomerans mediated bacterial adhesion to the roots of bluegrass, Poa pratensis. Purified, radiolabeled fimbriae bound to grass roots in vitro; binding was inhibited by alpha-methyl-d-mannoside or Fab fragments to the fimbriae. Anti-type 1 fimbriae Fab fragments and alpha-methyl-d-mannoside also inhibited adhesion of type 1-fimbriated bacteria to P. pratensis roots. It is proposed that associative nitrogen fixation by Klebsiella and Enterobacter strains also involves type 1 fimbriae, in addition to the type 3 fimbriae of Klebsiella spp. (T. K. Korhonen, E. Tarkka, H. Ranta, and K. Haahtela, J. Bacteriol. 155:860-865, 1983).

A selective broth enrichment combined with real-time nuc-mecA-PCR in the exclusion of MRSA

We analyzed the performance of a selective enrichment broth combined with Taqman-based real-time duplex nuc-mecA-PCR to expedite the screening of methicillin-resistant Staphylococcus aureus (MRSA). We found the broth to be able to select MRSA strains (oxacillin MIC range 4-256 microg/ml) from MSSA strains. A total of 31 MRSA strains were found from 1250 clinical samples screened. The nuc-mecA-PCR was positive from all enrichment broths containing MRSA. From the remaining 1219 samples negative for MRSA on culture/subculture, 138 samples were nuc+/mecA+ in PCR. The sensitivity of the test was 93.5%, specificity 88.6%, positive predictive value 17.3%, and negative predictive value 99.8% as compared to culture. Thus, with this method, the negative MRSA results can be reliably reported within 24-48 h from sampling. The method is a practical additional alternative to those already described for the same purpose.

Accurate and rapid identification of bacterial species from positive blood cultures with a DNA-based microarray platform: an observational study

BACKGROUND

New DNA-based microarray platforms enable rapid detection and species identification of many pathogens, including bacteria. We assessed the sensitivity, specificity, and turnaround time of a new molecular sepsis assay.

METHODS

2107 positive blood-culture samples of 3318 blood samples from patients with clinically suspected sepsis were investigated for bacterial species by both conventional culture and Prove-it sepsis assay (Mobidiag, Helsinki, Finland) in two centres (UK and Finland). The assay is a novel PCR and microarray method that is based on amplification and detection of gyrB, parE, and mecA genes of 50 bacterial species. Operators of the test assay were not aware of culture results. We calculated sensitivity, specificity, and turnaround time according to Clinical and Laboratory Standards Institute recommendations.

FINDINGS

1807 of 2107 (86%) positive blood-culture samples included a pathogen covered by the assay. The assay had a clinical sensitivity of 94.7% (95% CI 93.6-95.7) and a specificity of 98.8% (98.1-99.2), and 100% for both measures for meticillin-resistant Staphylococcus aureus bacteraemia. The assay was a mean 18 h faster than was the conventional culture-based method, which takes an additional 1-2 working days. 34 of 3284 (1.0%) samples were excluded because of technical and operator errors.

INTERPRETATION

Definitive identification of bacterial species with this microarray platform was highly sensitive, specific, and faster than was the gold-standard culture-based method. This assay could enable fast and earlier evidence-based management for clinical sepsis.

Real-time multiplex PCR assay for detection of Yersinia pestis and Yersinia pseudotuberculosis

A multiplex real-time polymerase chain reaction (PCR) assay was developed for the detection of Yersinia pestis and Yersinia pseudotuberculosis. The assay includes four primer pairs, two of which are specific for Y. pestis, one for Y. pestis and Y. pseudotuberculosis and one for bacteriophage lambda; the latter was used as an internal amplification control. The Y. pestis-specific target genes in the assay were ypo2088, a gene coding for a putative methyltransferase, and the pla gene coding for the plasminogen activator. In addition, the wzz gene was used as a target to specifically identify both Y. pestis and the closely related Y. pseudotuberculosis group. The primer and probe sets described for the different genes can be used either in single or in multiplex PCR assays because the individual probes were designed with different fluorochromes. The assays were found to be both sensitive and specific; the lower limit of the detection was 10-100 fg of extracted Y. pestis or Y. pseudotuberculosis total DNA. The sensitivity of the tetraplex assay was determined to be 1 cfu for the ypo2088 and pla probe labelled with FAM and JOE fluorescent dyes, respectively.

First isolation of Clostridium difficile PCR ribotype 027 in Finland

On 18 October 2007, the first case of Clostridium difficile PCR ribotype 027-associated disease was detected in Finland.

Clustering of Serratia marcescens infections in a neonatal intensive care unit

OBJECTIVES

To study clusters of infections caused by Serratia marcescens in a neonatal intensive care unit (NICU) and to determine risk factors for S. marcescens infection or colonization.

DESIGN

Genotyping of S. marcescens isolates was performed by pulsed-field gel electrophoresis (PFGE). A retrospective case-control study was conducted.

SETTING

A tertiary-care pediatric hospital with a 16-bed NICU.

PATIENTS

All neonates with at least one culture positive for S. marcescens in the NICU during December 1999 to July 2002. Case-patients (n = 11) treated in the NICU during December 1999 to February 2000 were included in the case-control study. Neonates treated in the NICU for at least 72 hours during the same period with cultures negative for S. marcescens were used as control-patients (n = 27).

RESULTS

S. marcescens was cultured from 19 neonates; 9 were infected and 10 were colonized. PFGE analysis identified three epidemic strains; each cluster consisted of identical isolates, except one isolate in the first cluster that was different. The risk factors identified were low birth weight, prematurity, prolonged respiratory therapy, prolonged use of antibiotics, and maternal infection prior to delivery. Overcrowding and understaffing were recorded simultaneously with the clusters.

CONCLUSIONS

PFGE analysis showed three independent clusters. Several factors contributed to spread of the epidemic strains: (1) there were many severely premature and susceptible neonates, (2) the NICU was overcrowded during the clusters, and (3) transmission was likely to occur via the hands of staff. Cohorting and improvement of routine infection control measures led to the cessation of each cluster.

Incidence and risk factors for nosocomial infections caused by fluoroquinolone-resistant Escherichia coli

The aim of the retrospective case-control study presented here was to elucidate the incidence, risk factors, and outcomes of nosocomial infections caused by quinolone-resistant Escherichia coli (QREC). During the 3-year period studied, 51 nosocomial QREC infections were found, and the characteristics of these cases were compared with those of 102 control patients with quinolone-susceptible nosocomial infections. In the multivariate analysis, risk factors were identified as prior quinolone therapy (odds ratio [OR], 18.49; 95% confidence interval [CI], 5.53-61.82; P value <0.001), urinary tract abnormalities (OR, 6.69; 95% CI, 1.68-26.63; P=0.007), and prior therapy with other antimicrobial agents (OR, 3.57; 95% CI, 1.38-9.27; P=0.009). No difference in mortality or in length of hospital stay was found. Prudent use of quinolones, especially in patients with urinary tract abnormalities, is probably the best way to avoid an increase in the incidence of QREC infections, but further studies on interventions with restricted use of quinolones are necessary to demonstrate the effectiveness and safety of this strategy.

Etiological diagnosis of childhood pneumonia by use of transthoracic needle aspiration and modern microbiological methods

Childhood pneumonia is usually treated without determining its etiology. The causative organism can be isolated from specimens of blood, empyema fluid, or lung aspirate, but this is rarely done. The potential of transthoracic needle aspiration for identification of causative agents was tested with use of modern microbiological methods. Aspiration was performed for 34 children who had radiological signs compatible with community-acquired pneumonia and had alveolar consolidation. In addition to bacterial and viral cultures and viral antigen detection, nucleic acid detection for common respiratory pathogens was performed on aspirate specimens. Aspiration disclosed the etiology in 20 (59%) of 34 cases overall and in 18 (69%) of 26 patients from whom a representative specimen was obtained. Aspiration's advantages are high microbiological yield and a relatively low risk of a clinically significant adverse event. Aspiration should be used if identification of the causative agent outweighs the modest risk of the procedure.

Clinical "pneumococcal pneumonia" due to Moraxella osloensis: case report and a review

A previously healthy 6-y-old girl presented with a disease very similar to pneumococcal pneumonia. However, Moraxella osloensis was isolated by lung tap. The patient responded well to a course of parenteral penicillin. This is probably the first documented case of community-acquired pneumonia associated with this agent. Clinical isolates of M. osloensis are rare and its pathogenesis has not been delineated; however, a literature review suggests that the organism is more common than is generally recognized.

Characterisation of Eubacterium-like strains isolated from oral infections

The genus Eubacterium currently includes a heterogeneous group of gram-positive, non-spore-forming anaerobic bacilli, many of which are slow growing, fastidious and generally unreactive in biochemical tests. As a consequence, cultivation and identification of isolates are difficult and the taxonomy of the group remains indifferent. In this study, 105 isolates from odontogenic infections, infections associated with dental implants or saliva from healthy subjects and provisionally assigned to the genus Eubacterium were subjected to phenotypic and genotypic analysis. Ninety-one of the isolates were identified as belonging to one of 14 previously described species: Atopobium parvulum (5 isolates), A. rimae (29), Bulleidia extructa (2), Cryptobacterium curtum (1), Dialister pneumosintes (1), Eubacterium saburreum (2), E. sulci (8), E. yurii subsp. yurii (1), Filifactor alocis (3), Lactobacillus uli (1), Mogibacterium timidum (13), M. vescum (6), Pseudoramibacter alactolyticus (6) and Slackia exigua (13). The remaining 14 isolates did not correspond to existing species. This study confirms the diversity of organisms provisionally assigned to the genus Eubacterium by conventional identification methods. This group of organisms is frequently isolated from oral infections but their role in the aetiology of these conditions has yet to be determined.

vanA and vanB incorporate into an endemic ampicillin-resistant vancomycin-sensitive Enterococcus faecium strain: effect on interpretation of clonality

Clonal spread and horizontal transfer in the spread of vancomycin resistance genes were investigated. Multiplex PCR, pulsed-field gel electrophoresis (PFGE), hybridization of enterococcal plasmids with the vanA and vanB probes, and sequencing of a fragment of vanB were used in the analysis. Before May 1996, 12 vancomycin-resistant Enterococcus faecium (VRE) isolates were found in Finland. Between May 1996 and October 1997, 156 VRE isolates were found in the Helsinki area. Between December 1997 and April 1998, fecal samples from 359 patients were cultured for VRE. One new case of colonization with VRE was found. During the outbreak period, 88% (137 of 155) of the VRE isolates belonged to two strains (VRE types I and II), as determined by PFGE. Each VRE type I isolate possessed vanB, and five isolates also had vanA. Of the 34 VRE type II isolates, 27 possessed vanA and 7 possessed vanB. Fifteen of 21 (71%) ampicillin-resistant, vancomycin-sensitive E. faecium (VSE) isolates found during and after the outbreak period in one ward were also of type II. Two VSE type II isolates were found in the hospital before the outbreak in 1995. By PFGE, the three groups (vanA, vanB, or no van gene) of type II shared the same band differences with the main type of VRE type II with vanA. None of the differences was specific to or determinative for any of the groups. Our material suggests that vanA and vanB incorporate into an endemic ampicillin-resistant VSE strain.

Increase of the number of vancomycin resistant enterococci (VRE) isolated in Helsinki, Finland

The emergence of hospital acquired infections with bacteria resistant to antimicrobials such as vancomycin resistant enterococci (VRE) has become a worldwide concern. In hospitals in the United States, VRE have spread quickly and currently account for eve

Escherichia coli and appendicitis: phenotypic characteristics of E. coli isolates from inflamed and noninflamed appendices

Two hundred four appendiceal isolates for Escherichia coli from 146 patients with either inflamed appendices (IA) (110 patients) or noninflamed appendices (NA) (36 patients) were characterized. Strains with P fimbriae were detected in 27% of IA and 31% of NA whereas type 1C-fimbriated strains were found only in IA (13%). Four serotypes, three with K5 antigens (O18:K5, O25:K5:H1, and O75:K5:H-) and one with K1 antigen (O75:K1:H7), were isolated only from IA (20 [18%] of 110); O25:K5:H1 was the most common serotype (isolated from 11 IA [10%]). Fecal isolates from the patients with IA resembled their corresponding appendiceal isolates rather than fecal isolates from patients with NA; this finding suggests that colonization of the gut by virulent E. coli--such as a hemolysin-producing, type 1C-fimbriated, P-fimbriated O25:K5:H1 serotype--may be a prerequisite for the development of appendicitis.

Subtyping of common pediatric pneumococcal serotypes from invasive disease and pharyngeal carriage in Finland

Ninety-nine penicillin-sensitive Streptococcus pneumoniae strains of common pediatric serogroups/types (6, 7, 14, 19, and 23) cultured from the blood of children with invasive disease (n = 49) or asymptomatic oropharyngeal carriage (n = 50) were analyzed by multilocus enzyme electrophoresis and ribotyping; 53 distinctive multilocus enzyme genotypes (ETs) and 53 ribotypes were identified. Multilocus enzyme electrophoresis showed good correlation with ribotying. ETs and ribotypes among invasive and carriage isolates were similar. Within different S. pneumoniae serogroups/types, both clonal (7 and 14) and heterogenous (6, 19, and 23) ET and rRNA hybridization patterns were observed. Greatest diversity was observed among serotypes 6A, 6B, and 19F. Use of 12 additional restriction enzymes besides PvuII and BglII did not increase ribotype discrimination within serotype 7 and 14 isolates. Serotype 7 and 14 strains, which appear clonal by subtyping, are rare among carriers but common causes of invasive disease. Characteristics associated with their clonality may represent an advantage for invasiveness.

Ribotyping as an epidemiologic tool for Escherichia coli

Restriction fragment length polymorphism of ribosomal RNA genes was analysed among 133 Escherichia coli strains predominantly from blood and urine, including 21 isolates from faeces of healthy persons. The strains had also been characterized for their O:K:H serotypes, for the presence of P, S and type 1C fimbriae, non-P, non-S mannose-resistant haemagglutinins and haemolysin production. Hind III-digested genomic DNA was subjected to Southern blot analysis with either plasmid pKK3535 containing E. coli rRNA operon or purified rRNA as a probe. Among the 133 strains 20 ribotypes were obtained. The distribution of strains into different ribotypes generally correlated with their O:K:H serotype. Ribotype variation within serotypes was mainly seen among strains with the K5 capsule. The origin of the strains or the presence of virulence-associated factors did not correlate with the ribotype. In conclusion, ribotyping appears to be a valuable method in epidemiologic studies especially when the serotyping methods are not available.

Incompatibility of outer membrane proteins OmpA and OmpF of Escherichia coli with secretion in Bacillus subtilis: fusions with secretable peptides

The secretion of the outer membrane proteins OmpA and OmpF of Escherichia coli has previously been found to be blocked at an early intracellular step, when these proteins were fused to a bacillar signal sequence and expressed in Bacillus subtilis. We have now fused these proteins to long secretable polypeptides, the amino-terminal portions of alpha-amylase or beta-lactamase. In spite of this, no secretion of the fusion proteins was detected in B. subtilis. With the exception of a small fraction of the beta-lactamase fusion, the proteins were cell-bound with uncleaved signal sequences. Protease accessibility indicated that the fusion proteins were not even partially exposed on the outer surface of the cytoplasmic membrane. Thus there was no change of the location compared to the OmpA or OmpF fused to the signal sequence only. We conclude that, like OmpA and OmpF, the fusion proteins fold into an export-incompatible conformation in B. subtilis before the start of translocation, which we postulate to be a late post-translational event.

High level production of Escherichia coli outer membrane proteins OmpA and OmpF intracellularly in Bacillus subtilis

A high yield of Escherichia coli outer membrane proteins OmpA (about 200 mg/l) and OmpF (about 100 mg/l) was obtained in Bacillus subtilis when produced intracellularly. The yield was more than 100-fold higher than the yield of these proteins by a similar vector containing the complete signal sequence of alpha-amylase of B. amyloliquefaciens. Both proteins isolated after breakage of the B. subtilis cells by low-speed centrifugation were about 70% pure and could be solubilized by Sarkosyl, SDS and guanidine hydrochloride.

Antibody production to a meningococcal outer membrane protein cloned into liv Salmonella typhimurium aroA vaccine strain

We cloned a 28 kDa outer membrane protein (OMP) of Neisseria meningitidis group B into a live Salmonella typhimurium aroA vaccine strain SL3261. The cloned 28 kDa protein was produced in large amounts in the S. typhimurium transformant SH8182 and located in the outer membrane. A mouse-passaged derivative of SH8182 was used as a live vaccine to immunize mice; with antibiotic pressure the strain survived in the mice as well as the parent strain SL3261 and maintained the plasmid carrying the gene encoding the 28 kDa OMP. The mice produced a high titer of antibodies to the 28 kDa OMP, showing that it had been effectively presented to the immune system. The hyperimmune mouse serum bound in an enzyme immunoassay to whole cells of E. coli and group B meningococci expressing the 28 kDa OMP, but its bactericidal activity towards the meningococci was marginal. In a passive protection study, the antiserum did not protect infant rats from meningococcal infection. The results indicate that the antibodies elicited did not bind to intact meningococcal cells, possibly because of inaccessibility of the 28 kDa OMP.

Sero- and subtypes of group B meningococci causing invasive infections in Finland in 1976-87

Neisseria meningitidis group B (MenB) strains isolated from 1976 to 1987 in Finland in 339 patients with invasive infection were sero/subtyped by whole cell enzyme immunoassay using monoclonal antibodies to class 1 and 2/3 outer membrane proteins. 66.7% of the strains could be serotyped (class 2/3) and 70.2% subtyped (class 1). No single phenotype was clearly predominant. The most common serotypes were 4 (18.6%) and 14 (17.4%) and the most common subtypes P1.16 (20.1%) and P1.2 (12.1%). The Norwegian phenotype B:15:P1.16 was seen only rarely (a total of 18 strains). Strains from Northern Finland did not differ from those from Southern Finland: no single phenotype caused the slight increase seen in the incidence of MenB infections in the end of 1970s in the North.

Cloning of an outer membrane protein of Neisseria meningitidis in Escherichia coli

A gene bank of chromosomal DNA of Neisseria meningitidis group B was constructed in phage lambda EMBL3, and screened by rabbit polyclonal antibodies to major outer membrane (OM) proteins of the meningococcus. Several clones expressing a 28 kDa protein were found. The gene coding for the 28 kDa protein was subcloned into plasmid pUC18 in Escherichia coli. The protein was expressed in E. coli and located in the OM. Rabbit antibodies were raised to the 28 kDa protein purified from E. coli and used to localize the protein in the meningococcus. The antiserum recognized a minor protein of similar electrophoretic mobility in the outer membrane complex (OMC) of the meningococcus. The 28 kDa protein was found to be common to different Neisseria species; it was expressed by both pathogenic and nonpathogenic Neisseria.

Type 3 fimbriae of Klebsiella sp.: molecular characterization and role in bacterial adhesion to plant roots

Type 3 fimbriae of Klebsiella were purified and characterized. The fimbriae were 4 to 5 nm in diameter and 0.5 to 2 microns long. In sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the fimbrillin had an apparent molecular weight of 23,500, and it differed from enterobacterial type 1 fimbrillins in its amino acid composition. Hydrophobic amino acids comprised 33.6% of all amino acids in the fimbrillin, which lacked cystine, phenylalanine, and arginine. Serologically, the type 3 fimbriae were also distinct from the type 1 fimbriae. Purified type 3 fimbriae agglutinated tannin-treated human blood group O erythrocytes; this confirms the role of type 3 fimbriae as hemagglutinins. Purified 125I-labeled type 3 fimbriae bound to the roots of Poa pratensis, and this binding could be inhibited by Fab fragments to the purified fimbriae. Anti-type 3 fimbriae Fab fragments also inhibited bacterial adhesion to plant roots. These results demonstrate that type 3 fimbriae mediate adhesion of klebsiellas to plant roots. Eight nitrogen-fixing strains of Klebsiella also produced type 3 fimbriae when grown under anaerobic nitrogen fixation conditions. It is proposed that type 3 fimbriae are involved in the establishment of the plant-bacterium association concerning nitrogen-fixing Klebsiella strains.