Whole genome sequencing of Salmonella Chester reveals geographically distinct clusters, Norway, 2000 to 2016.

IntroductionDuring summer 2016, Norway observed an increase in Salmonella enterica subsp. enterica serovar Chester cases among travellers to Greece.AimOur aim was to investigate genetic relatedness of S. Chester for surveillance and outbreak detection by core genome multilocus sequence typing (cgMLST) and compare the results to genome mapping.MethodsWe included S. Chester isolates from 51 cases of salmonellosis between 2000 and 2016. Paired-end sequencing (2 × 250 bp) was performed on Illumina MiSeq. Genetic relatedness by cgMLST for Salmonella enterica subsp. enterica, including 3,002 genes and seven housekeeping genes, was compared by reference genome mapping with CSI Phylogeny version 1.4 and conventional MLST.ResultsConfirmed travel history was available for 80% of included cases, to Europe (n = 13), Asia (n = 12) and Africa (n = 16). Isolates were distributed into four phylogenetic clusters corresponding to geographical regions. Sequence type (ST) ST411 and a single-locus variant ST5260 (n = 17) were primarily acquired in southern Europe, ST1954 (n = 15) in Africa, ST343 (n = 11) and ST2063 (n = 8) primarily in Asia. Part of the European cluster was further divided into a Greek (n = 10) and a Cypriot (n = 4) cluster. All isolates in the African cluster displayed resistance to ≥ 1 class of antimicrobials, while resistance was rare in the other clusters.ConclusionWhole genome sequencing of S. Chester in Norway showed four geographically distinct clusters, with a possible outbreak occurring during summer 2016 related to Greece. We recommend public health institutes to implement cgMLST-based real-time Salmonella enterica surveillance for early and accurate detection of future outbreaks and further development of cluster cut-offs.

Massive parallel sequencing provides new perspectives on bacterial brain abscesses.

Rapid development within the field of massive parallel sequencing (MPS) is about to bring this technology within reach for diagnostic microbiology laboratories. We wanted to explore its potential for improving diagnosis and understanding of polymicrobial infections, using bacterial brain abscesses as an example. We conducted a prospective nationwide study on bacterial brain abscesses. Fifty-two surgical samples were included over a 2-year period. The samples were categorized as either spontaneous intracerebral, spontaneous subdural, or postoperative. Bacterial 16S rRNA genes were amplified directly from the specimens and sequenced using Ion Torrent technology, with an average of 500,000 reads per sample. The results were compared to those from culture- and Sanger sequencing-based diagnostics. Compared to culture, MPS allowed for triple the number of bacterial identifications. Aggregatibacter aphrophilus, Fusobacterium nucleatum, and Streptococcus intermedius or combinations of them were found in all spontaneous polymicrobial abscesses. F. nucleatum was systematically detected in samples with anaerobic flora. The increased detection rate for Actinomyces spp. and facultative Gram-negative rods further revealed several species associations. We suggest that A. aphrophilus, F. nucleatum, and S. intermedius are key pathogens for the establishment of spontaneous polymicrobial brain abscesses. In addition, F. nucleatum seems to be important for the development of anaerobic flora. MPS can accurately describe polymicrobial specimens when a sufficient number of reads is used to compensate for unequal species concentrations and principles are defined to discard contaminant bacterial DNA in the subsequent data analysis. This will contribute to our understanding of how different types of polymicrobial infections develop.

Primary vitrectomy or intravitreal antibiotics followed by early vitrectomy for acute endophthalmitis: A prospective observational study.

BACKGROUND/AIMS: To compare outcomes of acute endophthalmitis (EO) managed with either primary vitrectomy (PV) or primary intravitreal antibiotics (vancomycin and ceftazidime) followed by early vitrectomy (PIAEV) combined with polymerase chain reaction (PCR)-based diagnostics. METHODS: This was a prospective, comparative observational study of acute EO cases admitted to a regional vitreoretinal service over 18 months. Depending on whether immediate vitrectomy (within 6 h) was achievable, the EO cases were treated with either (1) PV or (2) PIAEV. Microbiology samples were collected either (A) before or (B) after administration of intravitreal antibiotics. The samples were analysed with broad-range 16S PCR and culture. RESULTS: The study included 41 EO cases. There were 19 post-injection EO, 18 post-cataract EO, three post-vitrectomy EO, and one blebitis-related EO. Fifteen of 19 PV cases and 15 of 21 PIAEV had a clinically meaningful improvement in best-corrected visual acuity (BCVA) of at least 15 letters at 3 months (p = 0.58). One patient was lost to follow-up. Twenty-three cases were culture- and PCR-positive, and seven additional cases were culture-negative but PCR-positive (p = 0.02). PCR increased the diagnostic yield for samples collected both before and after administration of intravitreal antibiotics. CONCLUSION: Primary vitrectomy or PIAEV allowed for vitrectomy for all cases of acute EO in a large region. Most eyes in both groups achieved a clinically meaningful improvement in BCVA. By combining culture with PCR in connection with the vitrectomy procedure, intravitreal antibiotics could be injected before microbiological sampling, thereby improving the door-to-treatment time without sacrificing microbial identification.

A 15-month-old girl with fever and pancytopenia.

A 15 month-old girl was admitted after a couple of months' history of illness with remittent fever, increasing pallor and a swollen abdomen. On admission she was highly febrile, with palpably enlarged liver and spleen. Blood tests revealed pancytopenia, a high CRP level and a high serum ferritin level. We describe the diagnostic evaluation, interpretation and treatment.

Late onset periprosthetic infection of the hip caused by the fish pathogen Lactococcus garvieae in a patient not associated with fish exposure.

Lactococcus garvieae is a fish pathogen, rarely causing opportunistic infections in humans. There are only a few cases reported in the literature, mainly endocarditis, suggesting an association with raw fish consumption. We report a case of a periprosthetic hip infection successfully treated with a two-stage revision surgery.

Fatal primary amoebic meningoencephalitis in a Norwegian tourist returning from Thailand.

INTRODUCTION: Primary amoebic meningoencephalitis (PAM) is a rare disease caused by the free-living amoeba Naegleria fowleri. Infection occurs by insufflation of water containing amoebae into the nasal cavity, and is usually associated with bathing in freshwater. Nasal irrigation is a more rarely reported route of infection. CASE PRESENTATION: A fatal case of PAM in a previously healthy Norwegian woman, acquired during a holiday trip to Thailand, is described. Clinical findings were consistent with rapidly progressing meningoencephalitis. The cause of infection was discovered by chance, owing to the unexpected detection of N. fowleri DNA by a PCR assay targeting fungi. A conclusive diagnosis was established based on sequencing of N. fowleri DNA from brain biopsies, supported by histopathological findings. Nasal irrigation using contaminated tap water is suspected as the source of infection. CONCLUSION: The clinical presentation of PAM is very similar to severe bacterial meningitis. This case is a reminder that when standard investigations fail to identify a cause of infection in severe meningoencephalitis, it is of crucial importance to continue a broad search for a conclusive diagnosis. PAM should be considered as a diagnosis in patients with symptoms of severe meningoencephalitis returning from endemic areas.

[Typhoid and paratyphoid fever in children]. / Tyfoid- og paratyfoidfeber hos barn.

BACKGROUND: Febrile illness without focal symptoms in a child who has visited tropical or sub-tropical areas is an increasing health problem in western countries. In the department of paediatrics at Ullevaal University Hospital, malaria, typhoid and paratyphoid fever are the most frequent infectious diseases acquired in tropical or sub-tropical areas. MATERIALS AND METHODS: We describe all 31 children under 16 admitted between 1998 and 2003 who had blood cultures positive for Salmonella typhi or Salmonella paratyphi A or B. RESULTS: Nearly all the children were second or third generation immigrants from the Indian subcontinent. Fever was the main symptom at onset. Out of 31 salmonella strains, 8 showed reduced sensitivity to quinolones, which are the drugs of choice. Clinical poor response to treatment is associated with reduced sensitivity to nalidixic acid in vitro. CONCLUSION: Blood cultures prior to administration of antibiotics are important in providing correct diagnosis and appropriate treatment. Before visiting endemic areas, groups at risk should be informed that there are vaccines available against typhoid fever.

Investigation of the algT operon sequence in mucoid and non-mucoid Pseudomonas aeruginosa isolates from 115 Scandinavian patients with cystic fibrosis and in 88 in vitro non-mucoid revertants.

Pseudomonas aeruginosa is the dominant pathogen causing chronic lung infections in patients with cystic fibrosis (CF). After an initial phase characterized by intermittent colonizations, a chronic infection is established upon conversion of P. aeruginosa from the non-mucoid to the mucoid, alginate-overproducing phenotype. During the chronic infection the isolation of both mucoid and non-mucoid isolates in CF sputum samples is very common. The purpose of the present study was to establish, by sequence analysis, the types of mutations present in the algTmucABD operon in a large number of mucoid and non-mucoid P. aeruginosa isolates from Scandinavian CF patients and in in vitro-derived non-mucoid revertants. Mucoid (83) and non-mucoid isolates (103) from 91 Scandinavian patients with chronic P. aeruginosa infection and 24 non-mucoid isolates from intermittently colonized CF patients were investigated. In addition, 88 spontaneous non-mucoid revertants obtained in vitro from nine mucoid CF isolates were also included in the study. Mutations in mucA were found in 92 % of the mucoid and in up to 70 % of the non-mucoid isolates from chronically infected patients, indicating that the majority of non-mucoid isolates are revertants. None of the non-mucoid isolates from intermittently colonized CF patients harboured mucA mutations. Although algT has been considered an important gene for secondary-site mutations responsible for reversion to non-mucoidy, only 30 % of the mucA-mutated non-mucoid CF isolates had mutations in algT. In contrast, 83 % of the in vitro-derived spontaneous non-mucoid revertants had mutations in algT, showing that in the CF lung there is a selection for non-mucoid revertants with secondary-site mutations in genes other than algT. In addition, we report, to our knowledge for the first time, loss-of-function mutations in the negative regulators mucB and mucD in CF clinical isolates. In some of the CF isolates these mutations are associated with moderate alginate production. In conclusion, most non-mucoid isolates from chronically infected CF patients are revertants and the mechanism of revertance is algT-independent in the CF lung.

In vitro formation of ethanol in autopsy samples containing fluoride ions.

We present a case of a death of a diabetic man where the concentration of ethanol in post-mortem blood rose from 0.4 g/l 2 days after autopsy to 3.5 g/l 10 days after autopsy. The presence of fluoride ions in this blood sample was determined with ion chromatography and verified that fluoride ions were added to the vials. The concentrations of free fluoride, corresponding to 0.21 and 0.25% w/v potassium fluoride in blood and urine, respectively, were somewhat lower than the recommended 1% w/v. However, the amount of fluoride ions bound to calcium, proteins and other compounds in the samples is unknown. The blood sample was also subject to microbiological examination, which revealed growth of bacteria. In addition, a very high concentration of glucose was found in vitreous humour from the deceased. To determine whether the ethanol detected at the first analysis was of ante-mortem origin, ethyl glucuronide was analysed. Its absence, in the blood as well as the urine sample, strongly supported the theory that, in this case, all the ethanol detected was formed post-mortem. This case showed that ethanol may be formed in vitro at a very high concentration, despite the verified presence of fluoride ions. Possible reasons for this unusual formation of ethanol were the abundant presence of bacteria, a high level of glucose and, possibly, an insufficient amount of fluoride added to the vials.