Primary splenic abscess in an adult female patient: a case report

BACKGROUND

Primary splenic abscess is rare and typically presents in patients who are immunocompromised. We present a case of a 47-year-old apparently immunocompetent female patient who was diagnosed with primary splenic abscess from a Salmonella Typhimurium infection following emergency laparotomy.

CASE PRESENTATION

A 47-year-old female patient presented with subjective fever and severe epigastric and left flank pain. She was treated empirically with intravenous piperacillin/tazobactam and gentamicin and was resuscitated with intravenous crystalloid infusion. A radiological diagnosis of splenic infarct secondary to splenic artery aneurysm superimposed with splenic abscess was presumed, however at emergency laparotomy, primary splenic abscess was identified. This abscess had eroded the left hemidiaphragm and had ruptured the splenic capsule leading to intra-abdominal pus in the pelvis which on culture grew Salmonella Typhimurium. A splenectomy and primary repair of the left hemidiaphragm were performed, with postoperative pancreatitis diagnosed following the procedure. After intensive care treatment, this patient made a full recovery.

CONCLUSION

This case of primary splenic abscess was treated successfully with a combination of surgery (i.e.: splenectomy and surgical drainage), prolonged antimicrobial therapy, and intensive care in the perioperative period.

Indwelling central venous catheter infection with Chryseobacterium shandongense - successful eradication in a 5-year-old with cystic fibrosis

Introduction

Chryseobacterium shandongense is a Gram-negative Flavobacterium bacillus with intrinsic multidrug-resistant properties.

Case Presentation

Herein, we present the first case report of human C. shandongense infection, relating to an implantable portal and catheter (port-a-cath) central line in a 5-year-old female with cystic fibrosis. The infection was identified using a Bruker MALDI-TOF Biotyper with BDAL (v12) of blood, which was cultured due to pyrexia and rigour following port-a-cath access. This report details the effective eradication of C. shandongense infection from the port-a-cath device using initial empirical gentamicin followed by targeted ciprofloxacin locks and systemic antibiotics.

Conclusion

We demonstrated successful eradication of C. shandongense from a port-a-cath device, including the minimum inhibitory concentrations (MICs) required in this case. The result was eradication of central access infection, preventing progression to bacteraemia/septicaemia and preserving central access in a child with cystic fibrosis and established respiratory disease.

Whole genome sequencing of increased number of azithromycin-resistant Shigella flexneri 1b isolates in Ontario

Azithromycin (AZM) resistance among Shigella is a major public health concern. Here, we investigated the epidemiology of Shigella flexneri serotype 1b recovered during 2016-2018 in Ontario, to describe the prevalence and spread of AZM resistance. We found that 72.3% (47/65) of cases were AZM-resistant (AZMR), of which 95.7% (45/47) were among males (P < 0.001). Whole-genome based phylogenetic analysis showed three major clusters, and 56.9% of isolates grouped within a single closely-related cluster (0-10 ∆SNP). A single AZMR clonal population was persistent over 3 years and involved 67.9% (36/53) of all male cases, and none reported international travel. In 2018, a different AZMR cluster appeared among adult males not reporting travel. A proportion of isolates (10.7%) with reduced susceptibility to ciprofloxacin (CIP) due to S83L mutation in gyrA were AZM susceptible, and 71.4% reported international travel. Resistance to AZM was due to the acquisition of mph gene-bearing incFII plasmids having > 95% nucleotide similarity to pKSR100. Plasmid-borne resistance limiting treatment options to AZM, ceftriaxone (CRO) and CIP was noted in a single isolate. We characterized AZMR isolates circulating locally among males and found that genomic analysis can support targeted prevention and mitigation strategies against antimicrobial-resistance.

Whole-genome sequencing to investigate transmission of SARS-CoV-2 in the acute healthcare setting: a systematic review

BACKGROUND

Whole-genome sequencing (WGS) has been used widely to elucidate transmission of SARS-CoV-2 in acute healthcare settings, and to guide infection, prevention, and control (IPC) responses.

AIM

To systematically appraise available literature, published between January 1st, 2020 and June 30th, 2022, describing the implementation of WGS in acute healthcare settings to characterize nosocomial SARS-CoV-2 transmission.

METHODS

Searches of the PubMed, Embase, Ovid MEDLINE, EBSCO MEDLINE, and Cochrane Library databases identified studies in English reporting the use of WGS to investigate SARS-CoV-2 transmission in acute healthcare environments. Publications involved data collected up to December 31st, 2021, and findings were reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement.

FINDINGS

In all, 3088 non-duplicate records were retrieved; 97 met inclusion criteria, involving 62 outbreak analyses and 35 genomic surveillance studies. No publications from low-income countries were identified. In 87/97 (90%), WGS supported hypotheses for nosocomial transmission, while in 46 out of 97 (47%) suspected transmission events were excluded. An IPC intervention was attributed to the use of WGS in 18 out of 97 (18%); however, only three (3%) studies reported turnaround times ≤7 days facilitating near real-time IPC action, and none reported an impact on the incidence of nosocomial COVID-19 attributable to WGS.

CONCLUSION

WGS can elucidate transmission of SARS-CoV-2 in acute healthcare settings to enhance epidemiological investigations. However, evidence was not identified to support sequencing as an intervention to reduce the incidence of SARS-CoV-2 in hospital or to alter the trajectory of active outbreaks.

Outcomes of implementation of the FilmArray meningoencephalitis panel in a tertiary hospital between 2017 and 2020

Background

Acute meningoencephalitis is encountered commonly in the acute hospital setting and is associated with significant morbidity and mortality, in addition to significant healthcare costs. Multiplex PCR panels now allow syndromic testing for central nervous system infection. The BioFire® FilmArray® Meningoencephalitis (ME) allows testing of 14 target pathogens using only 0.2mls of cerebrospinal fluid (CSF). We conducted a retrospective observational study to assess the performance of the assay and secondarily to observe the clinical utility of negative results by comparing clinical outcomes of aseptic meningitis to bacterial and viral meningoencephalitis.

Methods

Data for CSF samples tested using the FilmArray ME panel from October 2017 to October 2020 were analysed. Detection of bacterial and viral targets was analysed. Admission to critical care area, 90-day readmission rates, average length of stay and 30-day and 90-day mortality were analysed for three groups with following diagnoses: bacterial meningitis, viral meningoencephalitis, or aseptic meningitis.

Results

From October 2017 to October 2020, 1926 CSF samples were received in the Clinical Microbiology laboratory. Of those, 543 CSF samples from 512 individual patients were tested using the FilmArray ME panel. Twenty-one bacterial targets and 56 viral targets were detected during the study period. For viral targets, the cumulative specificity was 98.9% (95% confidence interval: 93.1–99.9) when compared to the reference laboratory methods. The outcomes for 30- and 90-day mortality of the aseptic meningitis group were non-inferior relative to the viral meningoencephalitis and bacterial meningitis group. Patients with bacterial meningitis had a longer average length of stay. Aseptic meningitis was associated with a higher 90-day readmission rate than the other 2 groups, but without statistical significance.

Conclusion

In our hands, implementation of the FilmArray ME panel was relatively straightforward. We experienced a transition in our workflow processes that enabled streamlining of CSF diagnostics and the safe removal of Gram staining in those samples being tested by this molecular assay. Coupled to this improvement, there was a positive clinical impact on patient care due to rapid turnaround time to results.

Tinea capitis with multiple isolates: The interaction of nature, animal and child

Tinea capitis is an infection of the scalp and hair commonly seen in the pediatric population. Detection of multiple dermatophytes is unusual, and true mixed infections have been rarely reported. Herein, we describe an 8-year-old girl with tinea capitis revealing three different dermatophyte isolates that highlight the clinical challenge posed by this phenomenon.

Effect of Pseudomonas colonisation on lower limb venous ulcer healing: a systematic review

OBJECTIVE

Pseudomonas aeruginosa is a Gram-negative bacillus that commonly colonises lower limb venous ulcers. Its effects on venous ulcer healing are widely debated. It produces exotoxins and elastase, as well as forming biofilms in hard-to-heal wounds. It is postulated that these virulence factors lead to slower healing times in patients with lower limb venous ulcers colonised with Pseudomonas. This review aimed to summarise the available evidence pertaining to this topic.

METHOD

A systematic review was performed in August 2019, where the Pubmed, Cochrane and Embase databases were searched for relevant literature according to PRISMA guidelines. Retrospective and prospective studies examining the effect of Pseudomonas colonisation on any measure of ulcer healing were included.

RESULTS

Some 282 articles were screened, of which seven studies including 491 patients were ultimately included for analysis. Of these, no study demonstrated a significant association between Pseudomonas colonisation and delayed healing of venous ulcers. In five of the seven studies, the effect of Pseudomonas aeruginosa on initial ulcer size at presentation was recorded.

CONCLUSION

All the studies demonstrated an association between ulcer size and the presence of Pseudomonas aeruginosa. While Pseudomonas aeruginosa may colonise larger ulcers or those with a worse prognosis, no evidence was found to support the hypothesis that this colonisation had a negative impact on lower limb venous ulcer healing.

Evaluation of digital dispense-assisted broth microdilution antimicrobial susceptibility testing for Pseudomonas aeruginosa isolates

Antimicrobial susceptibility testing (AST) is essential for detecting resistance in Pseudomonas aeruginosa and other bacterial pathogens. Here we evaluated the performance of broth microdilution (BMD) panels created using a semi-automated liquid handler, the D300e Digital Dispenser (Tecan Group Ltd., CH) that relies on inkjet printing technology. Microtitre panels (96-well) containing nine twofold dilutions of 12 antimicrobials from five classes (β-lactams, β-lactam/β-lactamase inhibitors, aminoglycosides, fluoroquinolones, polymyxins) were prepared in parallel using the D300e Digital Dispenser and standard methods described by CLSI/ISO. To assess performance, panels were challenged with three well characterized quality control organisms and 100 clinical P. aeruginosa isolates. Traditional agreement and error measures were used for evaluation. Essential (EA) and categorical (CA) agreements were 92.7% and 98.0% respectively for P. aeruginosa isolates with evaluable on-scale results. The majority of minor errors that fell outside acceptable EA parameters (≥ ± 1 dilution, 1.9%) were seen with aztreonam (5%) and ceftazidime (4%), however all antimicrobials displayed acceptable performance in this situation. Differences in MIC were often log₂ dilution lower for D300e dispensed panels. Major and very major errors were noted for aztreonam (2.6%) and cefepime (1.7%) respectively. The variable performance of D300e panels suggests that further testing is required to confirm their diagnostic utility for P. aeruginosa.

Pseudomonas aeruginosa strain sharing in early infection among children with cystic fibrosis

BACKGROUND

We previously identified Pseudomonas aeruginosa isolates with characteristics typical of chronic infection in some early infections in children with Cystic Fibrosis (CF), suggesting these isolates may have been acquired from other patients. Our objective was to define the extent of P. aeruginosa strain sharing in early CF infections and its impact on antibiotic eradication treatment failure rates.

METHODS

We performed whole genome sequencing on isolates from early pediatric CF pulmonary infections and from comparator groups in the same hospital: chronic CF infection, sink drains, sterile site infections and asymptomatic carriage. Univariate logistic regression was used to assess factors associated with treatment failure.

RESULTS

In this retrospective observational study, 1,029 isolates were sequenced. The CF clones Strain B and Clone C were present. In 70 CF patients with early infections, 14 shared strains infected 29 (41%) patients over five years; 16% (n=14) of infections had mixed-strains. In the 70 children, approximately one third of shared strain infections were likely due to patient-to-patient transmission. Mixed-strain infections were associated with strain sharing (odds ratio 8.50; 95% confidence interval 2.2 - 33.4, P = 0.002). Strain sharing was not associated with antibiotic eradication treatment failure; however, nosocomial strain transmission was associated with establishment of chronic infection in a CF sibling pair.

CONCLUSIONS

Although early P. aeruginosa CF infection is thought to reflect acquisition of diverse strains from community reservoirs, we identified frequent early CF strain sharing which was associated with the presence of mixed-strains and instances of possible patient-to-patient transmission.

Dual RNA-Seq characterization of host and pathogen gene expression in liver cells infected with Crimean-Congo Hemorrhagic Fever Virus

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne virus that can cause a hemorrhagic fever in humans, with a case fatality rate of up to 40%. Cases of CCHFV have been reported in Africa, Asia, and southern Europe; and recently, due to the expanding range of its vector, autochthonous cases have been reported in Spain. Although it was discovered over 70 years ago, our understanding of the pathogenesis of this virus remains limited. We used RNA-Seq in two human liver cell lines (HepG2 and Huh7) infected with CCHFV (strain IbAr10200), to examine kinetic changes in host expression and viral replication simultaneously at 1 and 3 days post infection. Through this, numerous host pathways were identified that were modulated by the virus including: antiviral response and endothelial cell leakage. Notably, the genes encoding DDX60, a cytosolic component of the RIG-I signalling pathway and OAS2 were both shown to be dysregulated. Interestingly, PTPRR was induced in Huh7 cells but not HepG2 cells. This has been associated with the TLR9 signalling cascade, and polymorphisms in TLR9 have been associated with poor outcomes in patients. Additionally, we performed whole-genome sequencing on CCHFV to assess viral diversity over time, and its relationship to the host response. As a result, we have demonstrated that through next-generation mRNA deep-sequencing it is possible to not only examine mRNA gene expression, but also to examine viral quasispecies and typing of the infecting strain. This demonstrates a proof-of-principle that CCHFV specimens can be analyzed to identify both the virus and host biomarkers that may have implications for prognosis.

Evaluating the use of whole genome sequencing for the investigation of a large mumps outbreak in Ontario, Canada

In 2017 Ontario experienced the largest mumps outbreak in the province in 8 years, at a time when multiple outbreaks were occurring across North America. Of 259 reported cases, 143 occurred in Toronto, primarily among young adults. Routine genotyping of the small hydrophobic gene indicated that the outbreak was due to mumps virus genotype G. We performed a retrospective study of whole genome sequencing of 26 mumps virus isolates from early in the outbreak, using a tiling amplicon method. Results indicated that two of the cases were genetically divergent, with the remaining 24 cases belonging to two major clades and one minor clade. Phylogeographic analysis confirmed circulation of virus from each clade between Toronto and other regions in Ontario. Comparison with other genotype G strains from North America suggested that the presence of co-circulating major clades may have been due to separate importation events from outbreaks in the United States. A transmission network analysis performed with the software program TransPhylo was compared with previously collected epidemiological data. The transmission tree correlated with known epidemiological links between nine patients and identified new potential clusters with no known epidemiological links.

Application of whole genome sequencing to query a potential outbreak of Elizabethkingia anophelis in Ontario, Canada

Bioinformatic analysis of whole genome sequence (WGS) data is emerging as a tool to provide powerful insights for clinical microbiology. We used WGS data to investigate the genetic diversity of clinical isolates of the bacterial pathogen Elizabethkingia anophelis to query the existence of a single-strain outbreak in Ontario, Canada. The Public Health Ontario Laboratory (PHOL) provides reference identification of clinical isolates of bacteria for Ontario and prior to 2016 had not identified E. anophelis. In the wake of the Wisconsin outbreak of 2015–2016 for which a source was never elucidated, the identification of E. anophelis from clinical specimens from five Ontario patients gave reason to question the presence of an outbreak. Genomic comparisons based on core genome multi-locus sequence typing conclusively refuted the existence of an outbreak, since the 5 Ontario isolates were genetically dissimilar, representing at least 3 distinct sub-lineages scattered among a set of 39 previously characterized isolates. Further interrogation of the genomic data revealed multiple antimicrobial resistance genes. Retrospective reidentification via rpoB sequence analysis of 22 clinical isolates of Elizabethkingia spp. collected by PHOL from 2010 to 2018 demonstrated that E. anophelis was isolated from clinical specimens as early as 2010. The uptick in E. anophelis in Ontario was not due to an outbreak or increased incidence of the pathogen, but rather enhanced laboratory identification techniques and improved sequence databases. This study demonstrates the usefulness of WGS analysis as a public health tool to quickly rule out the existence of clonally related case clusters of bacterial pathogens indicative of single-strain outbreaks.

Antibiotic resistance patterns of Escherichia coli urinary isolates and comparison with antibiotic consumption data over 10 years, 2005-2014

INTRODUCTION

Escherichia coli is a common cause of urinary tract infections (UTI). Reviews of antibiotic resistance of this organism can inform choice of empiric treatment of UTI and other infections and strategies for combating antimicrobial resistance. We reviewed laboratory and hospital pharmacy records to assess trends in non-susceptibility rates and the effect of antimicrobial stewardship interventions.

METHODS

A retrospective observational study of isolates of E. coli from MSU samples at a Dublin teaching hospital from inpatients and community, obtained from January 2005 to December 2014. Susceptibility to a panel of antibiotics was determined using the disc diffusion method, as well as extended-spectrum beta-lactamase (ESBL) production status. Trends in resistance were plotted graphically and analysed in a descriptive manner.

RESULTS

Except for nitrofurantoin and gentamicin, non-susceptibility increased for all antimicrobials tested. Co-amoxiclav non-susceptibility reached 48% in hospital and 32.6% in the community by 2014. Piperacillin-tazobactam non-susceptibility increased from 6.8 to 23.8% in hospital and from <1 to 12.5% in community, with similar increases for ESBL producing isolates. Ciprofloxacin non-susceptibility peaked at 25.5% in hospital in 2012 and 11.44% in the community in 2014.

CONCLUSION

Escherichia coli isolates from community MSU samples have high rates of non-susceptibility to trimethoprim and co-amoxiclav. Nitrofurantoin remains the best empiric therapy for cystitis. Increasing non-susceptibility to co-amoxiclav and piperacillin-tazobactam in hospital isolates is concerning. Ciprofloxacin non-susceptibility is increasing faster in the community than in hospital. A sharp reduction in hospital fluoroquinolone consumption did not result in a significant reduction in ciprofloxacin non-susceptibility of hospital E. coli isolates.

Intravenous midazolam: a study of the degree of oxygen desaturation occurring during upper gastrointestinal endoscopy

Intravenous midazolam (mean dose of 6.3 mg) was given to 100 consecutive patients coming to endoscopy. All patients had an ear oximeter attached throughout the procedure to record continuously their levels of oxygen saturation. Eighty-five of the 100 patients had pre-endoscopy respiratory function tests measured, and 82 wore an induction plethysmograph vest to get a continuous qualitative estimate of respiratory rate and excursion throughout the procedure. Following intravenous midazolam a reduction in respiratory excursion was observed in 80% of patients. The initial baseline oxygen saturation of 95.4% fell 3.3% (P less than 0.0005) following intravenous midazolam to 92.1%. During the endoscopic procedure there was a further 3.1% decrease in oxygen saturation to 89.0% (P less than 0.0005) and in 7% the level fell to below 80%. Age, sex, dose of midazolam given and pre-endoscopy respiratory function tests failed to identify those patients at risk of hypoxia during the endoscopy.

No association between malignant melanoma and acne or psoriasis: results from the Western Canada Melanoma Study

In a study of 651 patients with cutaneous malignant melanoma and matched controls, no association was found with a history of acne vulgaris or psoriasis. Examination of the severity, age at onset and treatment for acne or psoriasis, and analysis by age, sex and site distribution of melanoma, revealed no evidence of any association.

Malignant melanoma in relation to moles, pigmentation, and exposure to fluorescent and other lighting sources

Interviews were performed on 83 patients with malignant melanoma, being 74% of all new NHS patients over a 33 month period who were resident in a defined area of Nottingham, and on age and sex matched controls chosen from all outpatients and inpatients of the same hospitals with the same area of residence. Significantly increased risks of melanoma were found in subjects with 3 or more raised moles on the upper arms (relative risk = 17.0), in association with heavy freckling of the face and arms, and with a tendency to sunburn easily and tan poorly, these factors having independent effects. While no significant and consistent association with exposure to fluorescent light was seen, the observed risks were higher in subjects with greater exposure, and higher in association with exposure to undiffused than to diffused light. Cases had a significantly greater number of hours' exposure to undiffused light than did controls. The associations with fluorescent light exposure were stronger when based on interview data than on a subsequent postal questionnaire. Twenty-one cases and 11 controls reported exposure to unusual occupational lighting sources which may have had an ultraviolet component; these included various intense lighting sources and lamps used in printing and dyeline copying.