Targeted amplification and MinION nanopore sequencing of key azole and echinocandin resistance determinants of clinically relevant Candida spp. from blood culture bottles

The objective of the study was to evaluate the use of targeted multiplex Nanopore MinION amplicon re-sequencing of key Candida spp. from blood culture bottles to identify azole and echinocandin resistance associated SNPs. Targeted PCR amplification of azole (ERG11 and ERG3) and echinocandin (FKS) resistance-associated loci was performed on positive blood culture media. Sequencing was performed using MinION nanopore device with R9.4.1 Flow Cells. Twenty-eight spiked blood cultures (ATCC strains and clinical isolates) and 12 prospectively collected positive blood cultures with candidaemia were included. Isolate species included Candida albicans, Candida glabrata, Candida krusei, Candida parapsilosis, Candida tropicalis and Candida auris. SNPs that were identified on ERG and FKS genes using Snippy tool and CLC Genomic Workbench were correlated with phenotypic testing by broth microdilution (YeastOne™ Sensititre). Illumina whole-genome-sequencing and Sanger-sequencing were also performed as confirmatory testing of the mutations identified from nanopore sequencing data. There was a perfect agreement of the resistance-associated mutations detected by MinION-nanopore-sequencing compared to phenotypic testing for acquired resistance (16 with azole resistance; 3 with echinocandin resistance), and perfect concordance of the nanopore sequence mutations to Illumina and Sanger data. Mutations with no known association with phenotypic drug resistance and novel mutations were also detected.

Clinical evaluation of serological IgG antibody response on the Abbott Architect for established SARS-CoV-2 infection

OBJECTIVE

This study aimed to evaluate the diagnostic performance of the Abbott Architect SARS-CoV-2 IgG assay in COVID-19 patients.

METHODS

Residual sera from 177 symptomatic SARS-CoV-2-positive patients and 163 non-COVID-19 patients were tested for antibody with the Abbott SARS-CoV-2 IgG assay (Abbott Diagnostics, Chicago, USA). Clinical records for COVID-19 patients were reviewed to determine the time from onset of clinical illness to testing.

RESULTS

Specificity of the assay was 100.0% (95%CI: 97.1-100.0%). The clinical sensitivity of the assay varied depending on time from onset of symptoms, increasing with longer periods from the onset of clinical illness. The clinical sensitivity at ≤6 days was 8.6% (7/81; 95%CI: 3.8-17.5%), at 7-13 days 43.6% (17/39; 95%CI: 28.2-60.2%), at 14-20 days 84.0% (21/25; 95%CI: 63.1-94.7%), and at ≥21 days 84.4% (27/32; 95%CI: 66.5-94.1%). Clinical sensitivity was higher in the ≥14-day group compared to <14 days. There were no differences between the 14-20-day and ≥21-days groups; the combined clinical sensitivity for these groups (≥14 days) was 84.2% (49/57; 71.6-92.1%).

CONCLUSION

The Abbott SARS-CoV-2 IgG test has high specificity. Clinical sensitivity was limited in the early stages of disease but improved from 14 days after the onset of clinical symptoms.

Rapidly growing mycobacteria in Singapore, 2006-2011

Nontuberculous mycobacteria infection is a growing global concern, but data from Asia are limited. This study aimed to describe the distribution and antibiotic susceptibility profiles of rapidly growing mycobacterium (RGM) isolates in Singapore. Clinical RGM isolates with antibiotic susceptibility tests performed between 2006 and 2011 were identified using microbiology laboratory databases and minimum inhibitory concentrations of amikacin, cefoxitin, clarithromycin, ciprofloxacin, doxycycline, imipenem, linezolid, moxifloxacin, sulfamethoxazole or trimethoprim-sulfamethoxazole, tigecycline and tobramycin were recorded. Regression analysis was performed to detect changes in antibiotic susceptibility patterns over time. A total of 427 isolates were included. Of these, 277 (65%) were from respiratory specimens, 42 (10%) were related to skin and soft tissue infections and 36 (8%) were recovered from blood specimens. The two most common species identified were Mycobacterium abscessus (73%) and Mycobacterium fortuitum group (22%), with amikacin and clarithromycin being most active against the former, and quinolones and trimethoprim-sulfamethoxazole against the latter. Decreases in susceptibility of M. abscessus to linezolid by 8.8% per year (p 0.001), M. fortuitum group to imipenem by 9.5% per year (p 0.023) and clarithromycin by 4.7% per year (p 0.033) were observed. M. abscessus in respiratory specimens is the most common RGM identified in Singapore. Antibiotic options for treatment of RGM infections are increasingly limited.

Sustained meticillin-resistant Staphylococcus aureus control in a hyper-endemic tertiary acute care hospital with infrastructure challenges in Singapore

Background

Meticillin-resistant Staphylococcus aureus (MRSA) has been entrenched in Singapore hospitals since the 1980s, with an excess of 600 non-duplicate cases of infections (120 bacteraemia episodes) each year in our 995-bed university hospital. Approximately 5% of our hospital beds are used as isolation facilities.

Aim

To study the impact of an MRSA control bundle that was implemented via gradual geographic extension across hospital wards.

Methods

The bundle included active surveillance on admission and transfer/discharge to identify ward-based acquisition of MRSA, isolation and cohorting of MRSA-infected patients, enhanced hand hygiene initiatives, and publicly displayed feedback of MRSA acquisition and hand hygiene compliance rates. Implementation was between October 2006 and June 2010 in order to provide lead-time for the incremental development of infrastructural capacity, and to develop an ethic of infection prevention among staff. Results were analysed via interrupted time-series analysis.

Findings

MRSA infections fell midway through the implementation, with MRSA bacteraemia declining from 0.26 [95% confidence interval (CI): 0.18–0.34] cases per 1000 inpatient-days in the first quarter of 2004 to 0.11 (95% CI: 0.07–0.19) cases per 1000 inpatient-days in the first quarter of 2012. MRSA acquisition rates fell a year after the programme had been fully implemented, whereas hand hygiene compliance rose significantly from 47% (95% CI: 44–49) in the first quarter of 2009 to 69% (95% CI: 68–71) in the first quarter of 2012.

Conclusion

Successful staged implementation of an MRSA bundle in a hyper-endemic setting is sustainable and represents a model that may be adapted for similar settings.

Bad design, bad practices, bad bugs: frustrations in controlling an outbreak of Elizabethkingia meningoseptica in intensive care units

BACKGROUND

Elizabethkingia meningoseptica is a nosocomial-adapted Gram-negative bacillus intrinsically resistant to antibiotics commonly used in the intensive care setting. An outbreak investigation commenced when five patients developed E. meningoseptica infection in two intensive care units (ICUs).

METHODS

Analysis of laboratory data, case reviews, ICU workflows and extensive environmental sampling were undertaken. Molecular typing was performed using repetitive element palindromic polymerase chain reaction. Follow-up studies after interventions included environmental monitoring and a survey of staff compliance with interventions.

FINDINGS

Laboratory data revealed increasing incidence of E. meningoseptica colonization or infection in ICU patients compared with preceding years. E. meningoseptica was cultured from 44% (35/79) of taps, but not from other sources. Hand hygiene sinks were used for disposal of patient secretions and rinsing re-usable patient care items. Sinks misused in this way were contaminated more often than sinks that were not misused (odds ratio 4.38, 95% confidence interval 1.68-11.39; P = 0.004). Molecular typing revealed that patient isolates had identical patterns to several isolates from hand hygiene taps. An urgent education programme was instituted to change these practices. Taps were cleaned systematically and aerators were changed. A temporary reduction in case numbers was achieved. Recolonization of taps was demonstrated on follow-up environmental screening, and cases recurred after two months. A survey revealed that 77.3% (163/213) of nursing staff still misused sinks due to time constraints or other problems adhering to the interventions.

CONCLUSION

Introduction of non-sanctioned practices due to suboptimal unit design may have unintentional consequences for ICU patients. Room design and staff workflows must be optimized for patient safety as lapses in procedure can inadvertently put patients at risk.

Emergence of Klebsiella pneumoniae co-producing NDM-type and OXA-181 carbapenemases

The emergence of carbapenemase-producing Enterobacteriaceae is a rapidly evolving threat worldwide. Here, we report the molecular characterization of two Klebsiella pneumoniae isolates carrying both bla(OXA -181) and bla(NDM -1) or bla(NDM -5) isolated from epidemiologically unrelated patients in Singapore. The bla(OXA -181) genes were found existing in different genetic environments.

Prospective audit and feedback on antibiotic prescription in an adult hematology-oncology unit in Singapore

We evaluated the impact of a prospective audit and feedback antimicrobial stewardship program (ASP) on antibiotic prescription and resistance trends in a hematology-oncology unit in a university hospital (National University Cancer Institute, Singapore [NCIS]). A prospective interrupted time-series study comprising 11-month pre-intervention (PIP) and intervention evaluation phases (IEP) flanking a one-month implementation phase was carried out. Outcome measures included defined daily dose per 100 (DDD/100) inpatient-days of ASP-audited and all antibiotics (encompassing audited and non-audited antibiotics), and the incidence-density of antibiotic-resistant microorganisms at the NCIS. Internal and external controls were DDD/100 inpatient-days of paracetamol at the NCIS and DDD/100 inpatient-days of antibiotics prescribed in the rest of the hospital. There were 580 ASP recommendations from 1,276 audits, with a mean monthly compliance of 86.9%. Significant reversal of prescription trends towards reduced prescription of audited (coefficient = -2.621; 95% confidence interval [CI]: -4.923, -0.319; p = 0.026) and all evaluated antibiotics (coefficient = -4.069; 95% CI: -8.075, -0.063; p = 0.046) was observed. No changes were seen for both internal and external controls, except for the reversal of prescription trends for cephalosporins hospital-wide. Antimicrobial resistance did not change over the time period of the study. Adverse outcomes-the majority unavoidable-occurred following 5.5% of accepted ASP recommendations. Safe and effective ASPs can be implemented in the complex setting of hematology-oncology inpatients.

Aspergillus vertebral osteomyelitis and epidural abscess

We present the first reported case of Aspergillus vertebral osteomyelitis and epidural abscess in Singapore in a 50-year-old man with post-tuberculous bronchiectasis. The patient presented with acute urinary retention and flaccid paraplegia. Despite surgical debridement and treatment with voriconazole, the patient developed multiorgan failure and died two weeks after presentation. Early diagnosis and prompt initiation of treatment are emphasised in the hope of improving the outcome of this aggressive condition.

Colon cancer presenting as Streptococcus gallolyticus infective endocarditis

A 58-year-old Chinese man presented with a three-week history of fever. He had a background history of rheumatic heart disease, hypertension, and thalassaemia. He was found to have infective endocarditis of the aortic valve due to Streptococcus gallolyticus. During the hospital stay, he developed a few episodes of haematochaezia and was subsequently found to have colonic carcinomain- situ. He completed appropriate antibiotic treatment for his infective endocarditis and underwent a left hemicolectomy with primary anastomosis. The association between Streptococcus gallolyticus infective endocarditis and colonic neoplasm is well documented. This case report stresses the importance of performing routine colonoscopy to look for colonic neoplastic change in patients diagnosed to have Streptococcus gallolyticus infective endocarditis. The early diagnosis of the colonic neoplasm has enabled our patient to have a curative surgery without compromising his quality of life.

Role of penicillin-binding protein 5 C-terminal amino acid substitutions in conferring ampicillin resistance in Norwegian clinical strains of Enterococcus faecium

The importance of amino acid sequence differences in the C-terminal part and levels of mRNA expression of penicillin-binding protein 5 (PBP5) for ampicillin resistance in Enterococcus faecium was investigated. Seventeen isolates from Norwegian hospitalized patients (ampicillin MIC 0.064->256 mg/L) with different C-terminal pbp5 DNA sequences encoding 11 different amino acid sequences were analyzed with a 14C-radiolabeled penicillin- binding assay to PBP5 and with real-time PCR quantification of pbp5 mRNA expression. Using multiple logistic regression analysis the amino acid substitution Met 485 was linked to ampicillin MIC and levels of 14C-radiolabeled penicillin bound to PBP5; however, there were isolates with identical PBP5 alleles and different ampicillin MICs. There was no relation between the quantity of pbp5 mRNA transcripts and ampicillin resistance. The results cannot explain ampicillin resistance in Norwegian clinical strains of E. faecium and indicate that other factors besides the properties of the C-terminal part of PBP5 are most likely involved.

Outbreak of infection with high-level gentamicin-resistant Enterococcus faecalis (HLGRE) in a Norwegian hospital

OBJECTIVES

To examine and characterize a suspected outbreak of high-level gentamicin-resistant Enterococcus (HLGRE) infection.

METHODS

Eighty-nine patients with clinical infection diagnosed during hospital stay or within 30 days after discharge in the period from June 1995 to 31 December 1999 were included in the study. One control patient was assigned for each HLGRE patient according to localization in the hospital (same ward), time of admission (+/-3 months), and age (+/-10 years). Unadjusted risk analysis and multivariate logistic regression analysis were performed. Sixty-nine HLGRE strains were subjected to PCR amplification of the genes coding for aminoglycoside-3'-O-phosphoryltransferase-III (APH(3')-III) and aminoglycoside-6'-N-acetyltransferase/2"-O-phosphoryltransferase-III (AAC(6')/APH(2")).

RESULTS

The gene aacA/aphD, associated with HLGRE, was detected by PCR in all isolates, and the gene aphA3, associated with high-level streptomycin, kanamycin and amikacin resistance, was detected in 56 of the 69 isolates. None of the 69 isolates was resistant to glycopeptides or ampicillin. Resistance to ciprofloxacin was found in 57 (82.6%). Pulsed-field gel electrophoresis analysis revealed 12 different genotypes, among which two major clusters dominated.

CONCLUSIONS

Both clonal expansion and the emergence of unique strains contributed to the increased number of infections caused by HLGRE. Urinary catheterization, duration of hospital stay and antibiotic therapy were significant risk factors for HLGRE infection.

The prevalence of faecal carriage of ampicillin-resistant and high-level gentamicin-resistant enterococci among inpatients at 10 major Norwegian hospitals

From March to October 1999, 854 patients hospitalized at 10 major Norwegian hospitals were screened for rectal carriage of ampicillin-resistant enterococci (ARE) and high-level gentamicin-resistant enterococci (HLGRE). A total of 59 ARE carriers (prevalence 6.9%, range 0-22% among hospitals) and 28 HLGRE carriers (prevalence 3.3%, range 1-11%) were detected. All ARE or HLGRE strains were susceptible to vancomycin, whereas 77% of the ARE isolates were resistant to ciprofloxacin. All the ARE strains were identified as Enterococcus faecium, and 48% of these were genomically closely related as shown by PFGE. Specific point mutations in the pbp5 gene were associated with reduced susceptibility to ampicillin. The adjusted risk of becoming a carrier of ARE was related to the use of glycopeptides [odds ratio (OR) = 4.8], the use of any antimicrobial agent (OR = 3.1) and more than one hospital admission during the last six months (OR = 2.0). Twenty-five of 28 HLGRE isolates were Enterococcus faecalis. The aacA/aphD genes were detected in 26 (93%) and the aphA3 in 19 (68%) of the HLGRE isolates. Sixty-four percent of the HLGRE isolates belonged to two PFGE clusters. Consumption of antimicrobial agents was also a significant risk factor for HLGRE colonization (OR = 5.4), while prescription of penicillins was associated with reduced risk (OR = 0.28).

Comparative evaluation of a commercial test for rapid identification of methicillin-resistant Staphylococcus aureus

The performance and ease of use of the recently introduced MRSA screen test (Denka Seiken Co. Ltd., Japan) for the identification of methicillin-resistant Staphylococcus aureus was evaluated in comparison with the BBL Crystal MRSA ID System (Becton Dickinson Europe, France). A total of 109 strains of S. aureus, consisting of 57 strains of MecA-negative S. aureus and 52 strains of MecA-positive S. aureus, were tested. With MecA PCR as the gold standard, the MRSA screen test had 98% sensitivity and 98% specificity, whereas the BBL Crystal MRSA ID System had 98% sensitivity and 95% specificity. The simplicity of use and rapid result make the MRSA screen test a valuable tool in the clinical microbiology laboratory pending demonstration of the MecA gene that should still always be done.

Antibiotic sensitivity still prevails in Norwegian blood culture isolates

We describe the antimicrobial susceptibility of bacteraemia isolates from Norway. From March 1998 to February 1999, four university hospitals covering all parts of Norway collected their first 10 isolates each month. Minimal inhibitory concentrations were determined for: Enterobacteriaceae (n=192), staphylococci (n=89) and Streptococcus pneumoniae (n=69) using the Etest. NCCLS breakpoints were used. About 20% of all blood culture isolates in Norway in this period were investigated. Compared with countries outside Scandinavia antibiotic sensitivity still prevails. Only minor differences in resistance were found between participating hospitals, between hospital departments and between hospital- and community-acquired pathogens. The prudent use of antibiotics in Norway may contribute to the fact that antibiotic resistance still remains low in the most common bacterial pathogens causing bloodstream infections.

Diagnostic and biological significance of anti-p41 IgM antibodies against Borrelia burgdorferi

We performed a prospective study to investigate the biological significance and diagnostic specificity of anti-p41 immunoglobulin (Ig)M antibodies against Borrelia burgdorferi. During a 1-year interval 2403 patients were referred to our department for B. burgdorferi serology. Sixty-three patients had repetitive positive tests for IgM anti-p41 antibodies and negative tests for anti-p41 IgG antibodies. Ten of the 63 patients recently had symptoms of erythema migrans. A confirmatory IgM Western blot gave a positive reaction in 5 patients out of 53 patients with little or no clinical evidence of B. burgdorferi infection. The remaining 48 patients were negative in this test and were considered as false-positives. Two whole cell enzyme-linked immunosorbent assay (ELISAs), two immunofluorescence assays and Western blotting were not useful as confirmatory tests. Sera from 330 blood donors and 72 cord sera were also screened for anti-p41 IgM. Five blood donor sera and five cord sera showed an IgM reactivity against p41. Based on our data we hypothesize that up to 1.5% of the population may have natural IgM antibodies against p41 in their sera. We observed that six out of nine sera with such antibodies could immobilize a B. afzelii reference strain in vitro. Whether anti-p41 IgM antibodies are capable of inactivating infective spirochetes and thereby prevent infection in vivo is, however, not yet clarified. The paradoxical conclusion that anti-p41 IgM antibodies may be a sign of resistance to infection rather than a sign of infection should be given consideration.

[Immunological investigation of hypogammaglobulinemia]

Immunoglobulin deficiency syndromes should be considered in patients with recurrent respiratory tract infections or in patients with infections caused by agents of low virulence. We present two patients with a clinical history of recurrent respiratory tract infections. Both patients had a humoral immunodeficiency characterised as common variable immunodeficiency (CVID). We give a brief survey of CVID with emphasis on the immunological investigation of hypogamma-globulinaemia. Analysis of serum, immunoglobulins should be performed in patients with recurrent infections Patients with humoral immuno-deficiency often have false negative serology for infectious agents despite obvious infections.