Influenza-associated mortality in hospital care: a retrospective cohort study of risk factors and impact of oseltamivir in an English teaching hospital, 2016 to 2017.

BackgroundEvidence of an oseltamivir treatment effect on influenza A(H3N2) virus infections in hospitalised patients is incomplete.AimsThis cohort study aimed to evaluate risk factors for death among PCR-confirmed hospitalised cases of seasonal influenza A(H3N2) of all ages and the impact of oseltamivir.MethodsParticipants included all 332 PCR-confirmed influenza A(H3N2) cases diagnosed between 30 August 2016 and 17 March 2017 in an English university teaching Hospital. Oseltamivir treatment effect on odds of inpatient death was assessed by backward stepwise multivariable logistic regression analysis.ResultsThe odds of death were reduced by two thirds (odds ratio (OR): 0.32; 95% confidence interval (CI): 0.11-0.93), in inpatients treated with a standard course of oseltamivir 75 mg two times daily for 5 days - compared with those untreated with oseltamivir, after adjustment for age, sex, current excess alcohol intake, receipt of 2016/17 seasonal influenza vaccine, serum haemoglobin and hospital vs community attribution of acquisition of influenza.ConclusionsOseltamivir treatment given according to National Institutes of Clinical Excellence (NICE); United States Centres for Disease Control and Prevention (CDC); Infectious Diseases Society of America (IDSA) and World Health Organization (WHO) guidelines was shown to be effective in reducing the odds of mortality in inpatients with PCR-confirmed seasonal influenza A(H3N2) after adjustment in a busy routine English hospital setting. Our results highlight the importance of hospitals complying with relevant guidelines for prompt seasonal influenza PCR testing and ensuring standard oseltamivir treatment to all PCR-confirmed cases of seasonal influenza.

Emergence of OXA-162 Carbapenemase- and DHA-1 AmpC Cephalosporinase-Producing Sequence Type 11 Klebsiella pneumoniae Causing Community-Onset Infection in Greece.

OXA-48-like carbapenemases have only recently emerged in Europe. OXA-162 is a rare OXA-48 variant usually coexpressed with extended-spectrum ß-lactamases. Here, we report the identification of the first OXA-162 carbapenemase-producing Klebsiella pneumoniae isolates, which coexpressed an AmpC cephalosporinase (DHA-1), retrieved from a patient in Greece. They belonged to a single sequence type (ST11) and caused the first documented community-onset urinary tract infections attributable to an OXA-48-like-producing Enterobacteriaceae strain.

Linezolid dependence in Staphylococcus epidermidis bloodstream isolates.

We document linezolid dependence among 5 highly linezolid-resistant (LRSE) Staphylococcus epidermidis bloodstream isolates that grew substantially faster at 32 µg/mL linezolid presence. These isolates carried the mutations T2504A and C2534T in multiple 23S rRNA copies and 2 mutations leading to relevant amino acid substitutions in L3 protein. Linezolid dependence could account for increasing LRSE emergence.

Outbreak of OXA-48 carbapenemase-producing Klebsiella pneumoniae in Greece involving an ST11 clone.

OBJECTIVES: First detected in Enterobacteriaceae isolates in Turkey, the OXA-48 carbapenemase has gradually disseminated in the wider Mediterranean area and Europe. Despite reports from other European regions, until now no such isolates have been detected in Greece. We describe the characteristics of the first outbreak caused by OXA-48-producing Klebsiella pneumoniae in Greece. METHODS: From December 2011 to March 2012, 13 ertapenem-resistant K. pneumoniae isolates, which were positive by the modified Hodge test while remaining negative by phenotypic screening for metallo-ß-lactamase (MBL) and KPC production, were recovered from nine patients. Patient records were retrieved to access patterns of acquisition. Resistance genes were identified by PCR and sequencing. ompK35, ompK36 and the genetic environment of the bla(OXA-48) gene were investigated. Plasmid profiling, conjugation experiments, PFGE and multilocus sequence typing (MLST) were performed. RESULTS: All isolates harboured the bla(OXA-48) gene along with the bla(CTX-M-15) and bla(OXA-1) genes. The bla(OXA-48) gene was located on a self-transferable IncL/M-type plasmid of ~62 kb, which harboured no other resistance genes. IS1999 was located upstream of the bla(OXA-48) gene. Genetic disruptions of the ompK35 and ompK36 genes were not detected. The isolates belonged to a unique PFGE clone and MLST assigned them to sequence type ST11. All cases were characterized as hospital acquired and none of them was linked to immigration or history of travel in endemic areas. CONCLUSIONS: Carbapenem resistance due to MBL and KPC carbapenemases is currently on an endemic scale in Greece and this report highlights the wider undetected dissemination of yet another carbapenemase in this region.

Oseltamivir is protective for in-patient mortality in PCR confirmed influenza B and influenza A(H3N2) infections in an historic cohort of 1,048 patients hospitalised during the 2016-17 and 2017-18 influenza seasons.

Standard course oseltamivir 75mg two times daily for five days was associated with an 82% reduction of odds of in-patient death (OR 0.18 (0.07,0.51)) compared to no oseltamivir treatment (OR 1.0 Reference) in a final multivariable logistic regression model of a retrospective cohort of PCR confirmed influenza B and influenza A (H3N2) infected patients admitted to a large UK teaching hospital in influenza seasons 2016-17 and 2017-18. No difference of protective odds for standard course oseltamivir was observed between influenza B and influenza A (H3N2) nor between influenza seasons. These observations strongly support clinical guidelines for molecular testing for respiratory viruses on admission to hospital and prompt treatment of confirmed seasonal influenza B and A with oseltamivir 75mg twice daily for five days.

Comparative evaluation of a prototype chromogenic medium (ChromID CARBA) for detecting carbapenemase-producing Enterobacteriaceae in surveillance rectal swabs.

Carbapenemase-producing Enterobacteriaceae (CPE) are an increasing problem worldwide, and rectal swab surveillance is recommended as a component of infection control programs. The performance of a prototype chromogenic medium (chromID CARBA) was evaluated and compared with media tested by four other screening methods: (i) overnight selective enrichment in 5 ml tryptic soy broth with a 10-µg ertapenem disk followed by plating onto MacConkey agar (CDC-TS), (ii) short selective enrichment in 9 ml brain heart infusion broth with a 10-µg ertapenem disk followed by plating onto chromID ESBL medium (ESBL-BH), (iii) direct plating onto chromID ESBL, and (iv) direct plating onto MacConkey agar supplemented with meropenem (1 µg/ml) (MCM). The screening methods were applied to detect CPE in 200 rectal swab specimens taken from different hospitalized patients. Identification and antimicrobial susceptibility were performed by the Vitek 2 system. Carbapenem MICs were checked by Etest. Carbapenemase production was confirmed using the modified Hodge test, combined-disk tests, and PCR assays. In total, 133 presumptive CPE strains were detected. Phenotypic and genotypic assays confirmed 92 strains to be CPE (56 KPC-positive Klebsiella pneumoniae, 29 VIM-positive K. pneumoniae, and 7 KPC-positive Enterobacter aerogenes strains) recovered from 73 patients, while the remaining 41 strains were confirmed to be CPE negative (19 ESBL producers and 22 nonfermenters). chromID CARBA, ESBL-BH, and chromID ESBL exhibited the highest sensitivity (92.4%), followed by CDC-TS and MCM (89.1%) (P = 0.631). The specificity was greater for chromID CARBA (96.9%) and ESBL-BH (93.2%) than for CDC-TS (86.4%), MCM (85.2%), and chromID ESBL (84.7%) (P = 0.014). In conclusion, chromID CARBA was found to be a rapid and accurate culture screening method for active CPE surveillance.

Detection of Pseudomonas aeruginosa isolates of the international clonal complex 11 carrying the blaPER-1 extended-spectrum ß-lactamase gene in Greece.

OBJECTIVES: The extended-spectrum ß-lactamase (ESBL) PER-1 initially disseminated among Pseudomonas aeruginosa strains in Turkey. Despite reports from other European countries, such strains have not been detected in Greece until now. We describe the first bla(PER-1)-positive P. aeruginosa isolates from Greece and their genetic environment. METHODS: From January 2008 to December 2009, 287 consecutive non-duplicate P. aeruginosa isolates with reduced susceptibility or resistance to ceftazidime (MIC >8 mg/L) were screened for ESBL production with a modified boronic acid-based double-disc synergy test. Phenotypically ESBL-positive isolates were subjected to agar dilution, PFGE and multilocus sequence typing (MLST). Broad-spectrum bla genes were identified by PCR and sequencing. Plasmid analysis and conjugation experiments were performed. The location of the bla(PER-1) gene was detected by Southern blotting and its genetic environment was characterized using inverse PCR. RESULTS: Five isolates were phenotypically positive for ESBL production, exhibited resistance to cefepime, ceftazidime, aztreonam and meropenem, and carried the bla(PER-1) gene. MLST showed that they belonged to sequence type (ST) 235, which belongs to the international clonal complex 11. Four isolates had the same PFGE pattern. Southern blotting revealed the chromosomal location of the bla(PER-1) gene. Analysis of the bla(PER-1) flanking regions showed identity to transposon Tn1213 downstream and 1406 bp upstream of bla(PER-1). Further upstream, an orfA gene and ISPa12 were identified; both were truncated by the insertion of IS6100. CONCLUSIONS: This study confirmed the presence of PER-1-producing P. aeruginosa strains in Greece. The chromosomal location of bla(PER-1), as part of a truncated transposon, suggests clonal expansion rather than horizontal gene transfer.

Antibody Response Following a Two-Dose mRNA Vaccination Regimen, in Health Care Workers of a Tertiary Hospital in Athens, Greece.

We analyzed the antibody responses of 564 hospital workers in Athens, Greece, after vaccination with two doses of the BNT162b2 (Comirnaty®; BioNTech and Pfizer) mRNA COVID-19 vaccine. A greater antibody increase was observed in women, younger age groups, previously infected individuals and personnel working in COVID-19 clinics. Notably, individuals with a prior COVID-19 infection mounted a significantly higher antibody titer following the first dose than the rest of the population; the same was true for those working in COVID-19 clinics, even without history of previous infection.

In vivo acquisition of a plasmid-mediated bla(KPC-2) gene among clonal isolates of Serratia marcescens.

Three patients admitted to a Greek hospital were infected with Serratia marcescens isolates that exhibited reduced susceptibility to carbapenems and harbored Klebsiella pneumoniae carbapenemase (KPC) enzymes. In two of these cases, the patients were initially infected by carbapenem-susceptible S. marcescens isolates. Molecular typing and plasmid analysis suggested that all three patients had clonally indistinguishable isolates of S. marcescens that acquired a plasmid-mediated bla(KPC-2) gene during the hospitalization.

Recurrent healthcare-associated community-onset infections due to Klebsiella pneumoniae producing VIM-1 metallo-beta-lactamase.

OBJECTIVES: To investigate the extrahospital dissemination of carbapenem-resistant Klebsiella pneumoniae isolates and the mechanisms of acquired resistance. METHODS: Patients who were referred to the outpatient department of Serres General Hospital with community-onset infections due to carbapenem-resistant K. pneumoniae isolates during August 2007-October 2008 were included in the study. The selected isolates were tested by determination of agar dilution MICs, phenotypic carbapenemase testing and PFGE. PCR and sequencing analyses were employed for identification of bla genes and mapping of the integron carrying the metallo-ß-lactamase (MBL) gene. The location of the MBL allele was investigated by mating experiments, plasmid analysis and PCR assays. RESULTS: Twenty-four carbapenem-resistant K. pneumoniae isolates causing urinary tract infections were recovered from 12 outpatients. Six of the patients presented with recurrent infections within a period of 1-6 months after the initial extrahospital isolation. All patients reported prior hospitalization within the preceding 4 months, whilst two were infected by carbapenem-resistant K. pneumoniae isolates during their previous hospitalization. Imipenem, meropenem and ertapenem MICs ranged from 8 to 64 mg/L, 4 to 32 mg/L and 8 to 128 mg/L, respectively. All studied isolates as well as those obtained from prior hospitalization belonged to a single PFGE clone. They harboured a plasmid-mediated bla(VIM-1) gene in an integron structure that has been previously described among K. pneumoniae isolates causing hospital-acquired infections in Greece. CONCLUSIONS: This is the first study to document the dissemination of an MBL-producing K. pneumoniae strain in the community. The successful strain caused recurrent community-onset infections and was most likely acquired during patients' previous hospitalization.

Adenovirus pseudo-outbreak in a large UK neonatal intensive care unit.

An unusually high number of positive adenovirus stool antigen tests were observed in neonatal samples from a large tertiary referral unit over a 10-week period, prompting the declaration of an outbreak and escalation of infection control precautions. Subsequent testing of original samples by alternative methods revealed a series of false-positive results. This is the first adenovirus pseudo-outbreak to be reported in the United Kingdom and the first to involve the Proflow Rotavirus-Adenovirus Combi test.

UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis.

Background: Human parainfluenza viruses type 3 (HPIV3) are a prominent cause of respiratory infection with a significant impact in both pediatric and transplant patient cohorts.  Currently there is a paucity of whole genome sequence data that would allow for detailed epidemiological and phylogenetic analysis of circulating strains in the UK. Although it is known that HPIV3 peaks annually in the UK, to date there are no whole genome sequences of HPIV3 UK strains available.  Methods: Clinical strains were obtained from HPIV3 positive respiratory patient samples collected between 2011 and 2015.  These were then amplified using an amplicon based method, sequenced on the Illumina platform and assembled using a new robust bioinformatics pipeline. Phylogenetic analysis was carried out in the context of other epidemiological studies and whole genome sequence data currently available with stringent exclusion of significantly culture-adapted strains of HPIV3. Results: In the current paper we have presented twenty full genome sequences of UK circulating strains of HPIV3 and a detailed phylogenetic analysis thereof.  We have analysed the variability along the HPIV3 genome and identified a short hypervariable region in the non-coding segment between the M (matrix) and F (fusion) genes. The epidemiological classifications obtained by using this region and whole genome data were then compared and found to be identical. Conclusions: The majority of HPIV3 strains were observed at different geographical locations and with a wide temporal spread, reflecting the global distribution of HPIV3. Consistent with previous data, a particular subcluster or strain was not identified as specific to the UK, suggesting that a number of genetically diverse strains circulate at any one time. A small hypervariable region in the HPIV3 genome was identified and it was shown that, in the absence of full genome data, this region could be used for epidemiological surveillance of HPIV3.

Complete Genome Sequences of BK Polyomavirus Strains from Two Patients with Urinary Tract Infection, Sequenced Using the Ion Torrent Platform.

BK polyomavirus is an important pathogen in kidney transplant patients. We report here two complete genome sequences, those of isolates CAMB-1035 and CAMB-1055, identified in two urine samples tested for urinary tract infection at a hospital in eastern England, United Kingdom. Variation and phylogenetic analyses indicate that both isolates belong to subtype Ib-1.

Polymorphisms in prothrombotic genes in young stroke patients in Greece: a case-controlled study.

Mechanisms of ischemic stroke in young adults are poorly understood. The aim of the study was to investigate and compare the frequency of common variations in prothrombotic genes between young patients with ischemic stroke and controls. Fifty-one cases of first-ever ischemic stroke and 70 community-based controls aged below 50 years were studied. In both groups, the insertion/deletion 4G/5G variation (-675 4G/5G PAI-1) as well as the single-nucleotide polymorphism-844 G/A of the PAI-1 (-844 G/A PAI-1) gene promoter, factor V Leiden (FVL) G1691Α, the prothrombin variant (allele 20210A, FIIG20210A), factor XIII-A Val34Leu polymorphism (FXIII-AVal34Leu) and C677T methylenotetrahydrofolate reductase (C677T MTHFR) polymorphism have been assessed. The -675 4G/5G PAI-1 allele distribution differed significantly between patients and controls (P = 0.020), but no difference was found regarding the distribution of -844 G/A PAI-1 (P = 0.493), FVL (P = 0.199), FIIG20210A (P = 0.410), FXIII-AVal34leu (P = 0.160) and C677T MTHFR (P = 0.788). A lower frequency of 5G/5G genotype and a higher frequency of the 4G/5G genotype of the PAI -675 4G/5G polymorphism was found in young ischemic stroke patients compared to healthy controls. Further epidemiological studies are needed to investigate the differences between different geographic areas, and prospective cohort studies are needed to investigate the possible protective role of 5G/5G polymorphism.

Emergence of VIM-1 metallo-ß-lactamase-producing Escherichia coli in a neonatal intensive care unit.

A carbapenem-resistant Escherichia coli isolate was recovered from rectal swab of a 12-day-old female neonate, which was admitted to a Greek neonatal intensive care unit (NICU). Phenotypic testing, polymerase chain reaction assays with sequencing, and plasmid analysis revealed that the isolate harbored a plasmid-mediated bla(VIM-1) metallo-ß-lactamase gene. The appearance of a metallo-ß-lactamase-producing E. coli in NICU is worrisome. Further surveys are needed to determine whether such Enterobacteriaceae may also be spreading in other NICUs.