Panton-Valentine Leukocidin-Positive CC398 MRSA in Urban Clinical Settings, the Netherlands

We report detection of Panton-Valentine leukocidin-positive clonal complex 398 human-origin methicillin-resistant Staphylococcus aureus L2 in the Netherlands. This hypervirulent lineage originated in the Asia-Pacific Region and could become community-acquired in Europe after recurrent travel-related introductions. Genomic surveillance enables early detection to guide control measures and help limit pathogen spread in urban settings.

Livestock-associated methicillin-resistant Staphylococcus aureus epidemiology, genetic diversity, and clinical characteristics in an urban region

Objectives

While Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA), defined as CC398, is a well-known pathogen among those working with livestock, there are indications that LA-MRSA prevalence among the general population is increasing. However, the clinical impact in urban areas remains unknown. The aim of this study was to assess the genetic epidemiology and clinical characteristics of LA-MRSA in an urban area with a limited livestock population.

Methods

In this retrospective study, we evaluated LA-MRSA strains that were collected between 2014 and 2018 from patients who received clinical care in a single urban area in Netherlands. Patient files were assessed for livestock exposure data, clinical findings, and contact tracing information. Next-generation sequencing (NGS) analysis in combination with wgMLST was conducted to assess genetic diversity and relatedness and to detect virulence and resistance genes.

Results

LA-MRSA strains were cultured from 81 patients, comprising 12% of all the MRSA strains found in seven study laboratories between 2014 and 2018. No livestock link was found in 76% of patients (n = 61), and 28% of patients (n = 23) had an infection, mostly of the skin or soft tissue. Contact tracing had been initiated in 14 cases, leading to the identification of two hospital transmissions: a cluster of 9 cases and one of 2 cases. NGS data were available for 91% (n = 75) of the patients. wgMLST confirmed the clusters detected via contact tracing (n = 2) and identified 5 additional clusters without a known epidemiological link. Relevant resistance and virulence findings included the PVL virulence gene (3 isolates) and tetracycline resistance (79 isolates).

Conclusion

LA-MRSA may cause a relevant burden of disease in urban areas. Surprisingly, most infections in the present study occurred in the absence of a livestock link, suggesting inter-human transmission. These findings and the presence of PVL and other immune evasive complex virulence genes warrant future surveillance and preventative measures.

Hospital transmission of borderline oxacillin-resistant Staphylococcus aureus evaluated by whole-genome sequencing

Introduction

Staphylococcus aureus is a major cause of hospital infections worldwide. Awareness towards methicillin-resistant S. aureus (MRSA) infections is high but attention towards borderline oxacillin-resistant S. aureus (BORSA) is limited, possibly due to an underestimated clinical relevance, presumption of low incidence and diagnostic limitations.

Gap statement

BORSA surveillance has not been routinely implemented, and thus consensus with regard to a definition and infection control measures is lacking.

Aim

Our goals were to investigate the occurrence, molecular characteristics and clinical manifestations of BORSA infections in the hospital setting.

Methodology

Following an increased incidence in 2016, BORSA cases in 2014/2016 (in our institution) were more specifically evaluated. Medical records were reviewed to investigate epidemiological links, clinical characteristics and outcomes. Resistance and virulence markers were assessed by whole genome sequencing (WGS). Conventional methods: amplified fragment length polymorphism (AFLP) ; multilocus sequence typing (MLST) and multiple locus variable-number tandem repeat analysis (MLVA) were compared with core genome MLST (cgMLST) and whole-genome single nucleotide polymorphism (wgSNP) analysis to confirm genetic clusters.

Results

From 2009 to 2013, BORSA comprised 0.1 % of all clinical S. aureus strains. In 2016, the incidence was six-fold higher in comparison to the baseline. Whole-genome SNP and cgMLST confirmed two BORSA clusters among patients with dermatological conditions. Patients with BORSA presented with skin infections, and one case developed a severe invasive infection with a fatal outcome. Infection control measures successfully prevented further transmission in both clusters. WGS findings showed that BORSA strains carried multiple resistance and virulence genes with increased pathogenic potential.

Conclusion

WGS and cgMLST effectively characterized and confirmed BORSA clusters among at-risk patients with clinical manifestations ranging from mild skin infections to life-threatening bacteraemia. Clinical awareness and active monitoring are therefore warranted for the timely implementation of infection control measures to prevent BORSA transmission in high-risk patients.

Chlamydia caviae Causing Community-Acquired Pneumonia: An Emerging Zoonosis

We describe a case of community-acquired pneumonia due to Chlamydia caviae in a patient with no direct animal exposure, raising questions about the zoonotic reservoirs and potential transmission routes. Genotyping of Chamydia isolates that cause pneumonia should be performed for a precise diagnosis and to initiate adequate infection control measures.

First case of severe pneumonic tularemia in an immunocompetent patient in the Netherlands

Tularemia is a zoonosis caused by different subspecies of the Gram-negative bacterium Francisella tularensis. We report the first case in the Netherlands of pneumonic tularemia caused by the F. tularensis subspecies holarctica after probable occupational inhalation of contaminated aerosols. Notification of cases of tularemia has been mandatory by law in the Netherlands since 1 November 2016.

Clinical evaluation of viral acute respiratory tract infections in children presenting to the emergency department of a tertiary referral hospital in the Netherlands

Background

The relative incidence and clinical impact of individual respiratory viruses remains unclear among children presenting to the hospital emergency department with acute respiratory tract infection (ARTI).

Methods

During two winter periods, respiratory virus real-time multiplex PCR results were evaluated from children (< 18 years) presenting to the emergency department of a tertiary referral hospital with ARTI that had been sampled within 48 hours of hospital presentation. In an attempt to identify virus-specific distinguishing clinical features, single virus infections were correlated with presenting signs and symptoms, clinical findings and outcomes using multivariate logistic regression.

Results

In total, 274 children with ARTI were evaluated and most were aged < 3 years (236/274, 86%). PCR detected respiratory viruses in 224/274 (81.8%) children and included 162 (59%) single and 62 (23%) mixed virus infections. Respiratory syncytial virus (RSV) and human rhinovirus (HRV) single virus infections were common among children aged < 3 years, but proportional differences compared to older children were only significant for RSV (95% CI 1.3–15). Clinical differentiation between viral ARTIs was not possible due to common shared presenting signs and symptoms and the high frequency of mixed viral infections. We observed virus-associated outcome differences among children aged < 3 years. Oxygen treatment was associated with RSV (OR 3.6) and inversely correlated with FLU (OR 0.05). Treatment with steroids (OR 3.4) or bronchodilators (OR 3.4) was associated with HRV. Severe respiratory complications were associated with HRV (OR 3.5) and inversely correlated with RSV (OR 0.24).

Conclusions

Respiratory viruses are frequently detected in young children presenting to the hospital emergency department with ARTI and require PCR diagnosis since presenting signs and symptoms are not discriminant for a type of virus. RSV and HRV bear a high burden of morbidity in the pediatric clinical setting.

Mass spectrometry-based comparative sequence analysis for the genetic monitoring of influenza A(H1N1)pdm09 virus

The pandemic influenza A (H1N1) 2009 virus (pH1N1) contains novel gene segments of zoonotic origin that lack virulence and antiviral resistance markers. We aimed to evaluate the applicability and accuracy of mass spectrometry-based comparative sequence analysis (MSCSA) to detect genetic mutations associated with increased virulence or antiviral resistance in pH1N1. During the 2009 H1N1 pandemic, routine surveillance specimens and clinical antiviral resistance monitoring specimens were analyzed. Routine surveillance specimens obtained from 70 patients with pH1N1 infection were evaluated for mutations associated with increased virulence (PB1-F2, PB2 and NS1 genes) or antiviral resistance (neuraminidase gene, NA) using MSCSA and Sanger sequencing. MSCSA and Sanger sequencing results revealed a high concordance (nucleotides >99%, SNPs ∼94%). Virulence or resistance markers were not detected in routine surveillance specimens: all identified SNPs encoded for silent mutations or non-relevant amino acid substitutions. In a second study population, the presence of H275Y oseltamivir resistant virus was identified by real-time PCR in 19 of 35 clinical antiviral resistance monitoring specimens obtained from 4 immunocompromised patients with ≥14 days prolonged pH1N1 excretion. MSCSA detected H275Y in 24% (4/19) of positive specimens and Sanger sequencing in 89% (17/19). MSCSA only detected H275Y when the mutation was dominant in the analyzed specimens. In conclusion, MSCSA may be used as a rapid screening tool during molecular surveillance of pH1N1. The low sensitivity for the detection of H275Y mutation in mixed viral populations suggests that MSCSA is not suitable for antiviral resistance monitoring in the clinical setting.

Morbidity and mortality associated with nosocomial transmission of oseltamivir-resistant influenza A(H1N1) virus

CONTEXT

The sudden emergence and rapid spread of oseltamivir-resistant influenza A(H1N1) viruses with neuraminidase (NA) gene H274Y amino acid substitution is the hallmark of global seasonal influenza since January 2008. Viruses carrying this mutation are widely presumed to exhibit attenuated pathogenicity, compromised transmission, and reduced lethality.

OBJECTIVE

To investigate nosocomial viral transmission in a cluster of patients with influenza A(H1N1) virus infection.

DESIGN, SETTING, AND PATIENTS

Descriptive outbreak investigation of 2 hematopoietic stem cell transplant recipients and an elderly patient who developed hospital-acquired influenza A virus infection following exposure to an index patient with community-acquired H274Y-mutated influenza A(H1N1) virus infection in a medical ward at a Dutch university hospital in February 2008. The investigation included a review of the medical records, influenza virus polymerase chain reaction and culture, phenotypic oseltamivir and zanamivir susceptibility determination, and hemagglutinin chain 1 (HA(1)) gene and NA gene sequence analysis.

MAIN OUTCOME MEASURE

Phylogenetic relationship of patient cluster influenza A(H1N1) viruses and other 2007-2008 seasonal influenza A(H1N1) viruses.

RESULTS

Viral HA(1) and NA gene sequence analysis from the 4 patients revealed indistinguishable nucleotide sequences and phylogenetic clustering of H274Y-mutated, oseltamivir-resistant influenza A(H1N1) virus, confirming nosocomial transmission. Influenza virus pneumonia (3 patients) and attributable mortality (2 patients) during active infection was observed in patients with lymphocytopenia at onset.

CONCLUSION

Seasonal oseltamivir-resistant influenza A(H1N1) viruses with NA gene H274Y mutation are transmitted and retain significant pathogenicity and lethality in high-risk patients.

Severe influenza resembling hemorrhagic shock and encephalopathy syndrome

Influenza-associated encephalopathy is a clinically diverse syndrome and severe cases are not well documented outside Japan. Clinical, pathological and molecular aspects are described of two fatal cases presenting during 2004 and 2005 winter seasons in The Netherlands. Results showed that severe influenza can resemble hemorrhagic shock and encephalopathy syndrome, and proper testing for influenza virus should be considered in similar cases. The failure to detect viral replication in non-pulmonary organs including the brain would support the pathogenesis of this syndrome is based on proinflammatory cytokine responses.

Quantitative detection of herpes simplex virus DNA in the lower respiratory tract

Quantitation of herpes simplex virus (HSV) DNA in bronchoalveolar lavage specimens could indicate an infectious role in the lower respiratory tract. The aim of this study was to compare quantitative HSV DNA results from adult bronchoalveolar lavage specimens to clinical outcome. Quantitative real-time PCR assays targeting HSV and other herpes viruses were performed on adult bronchoalveolar lavage specimens obtained from a largely immunocompromised population during a 1-year period. The results were compared to patient characteristics and outcome. HSV DNA was detected in 11 (19%) of 57 bronchoalveolar lavage specimens with a mean viral level of 5.6 log genome equivalents/ml (range, 2.9-8.1 log). A threshold of HSV DNA levels equal or higher than 5.0 log (n = 7) was associated with mortality within 28 days following hospital admission (odds ratio [OR], 6.8; 95% confidence interval [CI], 1.2-39.2). A threshold level of 5.5 log was associated with mortality within 28 days of sampling (OR 8.5; 95% CI 1.2-62.1), only after excluding patients receiving specific antiviral medication. Patients with HSV DNA levels equal or higher than 7.5 log had severe respiratory failure. Viral pneumonia was histologically proven in one patient with 8.0 log at autopsy. No patient with HSV DNA levels below 5.5 log (n = 5) or DNA levels higher than 5.0 log of cytomegalovirus (CMV) (n = 3), Epstein-Barr virus (EBV) (n = 9), varicella-zoster virus (VZV) (n = 1), or human herpesvirus 6 (HHV-6) (n = 0) died within 28 days of hospital admission. We conclude that quantitative detection of HSV DNA in bronchoalveolar lavage fluid is a potential diagnostic tool for detection of relevant viral infection of the lower respiratory tract.

Evaluation of an internally controlled real-time PCR targeting the ospA gene for detection of Borrelia burgdorferi sensu lato DNA in cerebrospinal fluid

This study reports the development and evaluation of an internally controlled real-time PCR targeting the ospA gene for detection of Borrelia burgdorferi sensu stricto, Borrelia garinii, Borrelia afzelii and Borrelia valaisiana. DNA was extracted using QIAamp DNA Blood Mini kit columns. DNA from 33 B. burgdorferi sensu lato strains reacted in the assay, whereas no reactivity was observed with DNA from four relapsing fever Borrelia spp., 11 unrelated spirochaetes, and 31 unrelated microorganisms. The quantitative sensitivity of the assay was 1-10 fg of Borrelia DNA and one to five cultured Borrelia spirochaetes. Cerebrospinal fluid (CSF) specimens from 70 patients sent for routine testing for neuroborreliosis, and three CSF specimens containing B. garinii were also tested. Positive PCR results were obtained with all three culture-confirmed neuroborreliosis specimens, five of ten neuroborreliosis specimens with specific antibodies in CSF and pleocytosis, none of nine specimens from possible cases of early neuroborreliosis (antibodies in serum, CSF pleocytosis, no antibodies in CSF), one of 15 specimens from patients with active or past Lyme disease with neurological signs (antibodies in serum, no pleocytosis or antibodies in CSF), and none of 36 specimens from patients without Lyme borreliosis (no antibodies in serum or CSF). Overall, the real-time PCR assay enabled sensitive and specific detection of all B. burgdorferi sensu lato species tested. The PCR had a sensitivity of 50% in patients with neuroborreliosis. The main diagnostic role of the assay could be to confirm neuroborreliosis in patients for whom the diagnosis is doubtful.

Streptococcal toxic shock syndrome by an iMLS resistant M type 77 Streptococcus pyogenes in the Netherlands

An increasing number of group A streptococci (GAS) with constitutive or inducible resistance to macrolide-lincosamide-streptogramin B antibiotics (cMLS or iMLS phenotype) is observed in Europe, but MLS resistant GAS associated with streptococcal toxic shock syndrome (STSS) has not been reported. We describe a patient admitted with STSS caused by an iMLS resistant T28 M77 Streptococcus pyogenes carrying the ermA [subclass TR] gene. A 2-y retrospective analysis among 701 nationwide collected GAS strains revealed an incidence of 3.1% of this M type 77 GAS. Analysis of 17 available M77 strains (12 T28 and 5 T13) indicated that 2 (12%) were MLS resistant due to the ermA [TR] gene. Both MLS resistant strains were cultured from blood and belonged to T28 serotype. Multilocus sequence typing (MLST) showed that all M77 isolates belonged to sequence type 63. We conclude that 17 M77 GAS collected in the Netherlands in a 2-y period were associated with invasive disease and belonged to the same clonal complex. Since only 12% carried the ermA [TR] resistance gene, it is very likely that the gene has been acquired by horizontal transmission rather than from spread of a resistant circulating clone.

Simple dipstick assay for the detection of Salmonella typhi-specific IgM antibodies and the evolution of the immune response in patients with typhoid fever

Application of a dipstick assay for the detection of Salmonella typhi-specific IgM antibodies on samples collected from S. typhi or S. paratyphi culture-positive patients at the day of admission to the hospital revealed the presence of specific IgM antibodies in 43.5%, 92.9%, and 100% for samples collected 4-6 days, 6-9 days, and > 9 days after the onset of fever, respectively. The mean sensitivity for samples collected an average of 6.6 days after the onset of fever was 65.3%. Culture was positive in 65.9% of the cases with a final clinical diagnosis of typhoid fever. Testing of paired serum samples from culture negative patients with a final clinical diagnosis of typhoid fever resulted in staining of the dipstick in 4.3% of the samples collected at the day of admission to the hospital and in 76.6% of the samples collected one week later, thereby provided strong supporting evidence of typhoid fever by demonstrating seroconversion in a large proportion of the patients. The dipstick assay may thus also be useful for the serodiagnosis of culture-negative patients with clinical signs and symptoms consistent with typhoid fever. The advantages of the dipstick assay are that the result can be obtained on the same day allowing a prompt treatment, that only a small volume of serum is needed, and that no special laboratory equipment is needed to perform the assay. The stability of the reagents of the dipstick and the simplicity of the assay allows its use in places that lack laboratory facilities.

Introduction of a rapid dipstick assay for the detection of Leptospira-specific immunoglobulin m antibodies in the laboratory diagnosis of leptospirosis in a hospital in Makassar, Indonesia

An easy, rapid and robust dipstick assay for detection of leptospira-specific immunoglobulin M (IgM) antibodies was evaluated on 403 patients admitted for hospitalization because of fever. The clinical symptoms and signs of 35 patients were consistent with leptospirosis. The final diagnosis for the remaining patients was as follows: 136 with typhoid fever, 82 with hepatitis, 74 with malaria, 48 with infections of the respiratory tract, and 20 with fever of unknown origin. The clinical diagnosis of leptospirosis was confirmed for 24 (68.6%) patients by the combined results of the microscopic agglutination test (MAT), the reference test for leptospirosis, and of IgM ELISA, a standard laboratory test for the serodiagnosis of leptospirosis. In addition, serum specimens from 8 (2.2%) patients with a final clinical diagnosis other than leptospirosis were found to be positive in MAT and/or IgM ELISA. Compared with the results of MAT and IgM ELISA a sensitivity of 91.6% and specificity of 93.6% was calculated for the dipstick assay. Most of the serum samples from the laboratory confirmed patients gave a moderate to strong staining intensity of the antigen band of the dipstick and were easy to read. The results demonstrate that the dipstick assay is convenient to use and allows the rapid and accurate confirmation of patients with clinical suspicion of leptospirosis in areas where the disease is endemic.