National Reference Laboratory Research Articles

Anti-HMGCR myopathy: estimated five-fold higher incidence in Polynesian compared to European populations in Aotearoa New Zealand.

In 2014 the incidence of anti-HMGCR myopathy in New Zealand was ∼1.7 case/million persons/year. Re-estimate the population incidence and assess ethnic variation in those >40-year -olds. An incidence cohort was defined by seropositivity for immunoprecipitating anti-HMGCR autoantibodies tested at a national reference laboratory between 1 October 2019-30 September 2021.Separately, ethnicity standardized incidence in > 40-year-olds discharged from New Zealand public hospitals for idiopathic and unspecified myopathy (ICD AM codes M60.8/60.9), was examined for concordance. The forty patients identified in the incidence cohort were all >40-years-old and all had a prior history of statin use. Annual incidence was 4 cases/million/year (95%CI 2.8-5.5). In those >40 years the incidence in Polynesians (Māori and Pacific peoples combined) was 25cases/million/year (95% CI 15.9 -40.1), in Asians 5.7cases/million/year (95% CI 0.7 -20.5) and in Europeans 7cases/million/year (95% CI 3.1 -8.4). The risk in statin users aged > 40 years was ∼1/9000 in Polynesians and ∼1/48000 in Europeans.Ethnic difference in incidence of idiopathic and unspecified myopathy (ICD AM codes M60.8/60.9) was also found in hospital discharges. In the past half decade the estimated incidence of anti-HMGCR myopathy in New Zealand has doubled. Polynesian peoples of New Zealand >40-years-old have an estimated 5-fold higher risk compared with European and Asian peoples. The estimated absolute risk in statin users >40-year-olds was 108 cases/million/year in Polynesians vs 21 cases/million/year in Europeans.

European union reference laboratory for feed additives: experience from 11 years organising proficiency testing

Feed additives are individually authorised within the European Union (EU) specifying the conditions of their use under real-world conditions. These criteria often include minimum or maximum level of their content in compound feed. In addition, feed business operators are obliged to indicate on the feed the level of the added content of the feed additive. While it is the task of the EU Member States official laboratories to perform control analyses to establish compliance with these provisions, the European Union Reference Laboratory for Feed Additives (EURL-FA) is organising since 2012 annual proficiency tests (PTs) for Member States’ National Reference Laboratories (NRLs). PTs organised by the EURL-FA are based on the principles that compound feed samples are prepared containing a known content of the target feed additive. These PT samples are then sent to the NRLs for analysis and the results reported back to the EURL-FA are subjected to statistical assessment to establish the laboratory specific proficiency to correctly analyse compound feed samples for the respective feed additive. In the current study, we looked at the outcome of this assessment across different PTs. The topics addressed were (1) the evaluation of the overall measurement capability of NRLs in respect to coccidiostats, trace elements and vitamin D3, (2) the challenge related to the preparation of homogenous test materials with particle-based feed additives, (3) a possible connection between the modified composition of preparations containing vitamin A and analytical results and (4) the impact of a training course on the proficiency of laboratories regarding carotenoid analysis.

Burden and frequency of viral testing of kidney and non-kidney transplant recipients.

Transplant patients are at risk of infections due to long-term immunosuppression contributing to morbidity and mortality in this population. Post-transplant testing guidelines were established to monitor and guide therapeutic interventions in transplant recipients. We hypothesize that there are gaps in adherence to the recommended frequency of laboratory testing in post-transplant patients. We analyzed national reference laboratory data to compare viral post-transplant infection (PTI) testing frequency with their respective published guidelines to understand patient uptake and compliance. We evaluated the ordering patterns, positivity rates, and frequency of molecular infectious disease tests (MIDTs). We included 345 patients with International Classification of Diseases (ICD)-10 codes for transplant (Z940-Z942, Z944, Z9481, Z9483, Z9484) with at least two tests (within 7 days) in January 2019 and at least one test in December 2020 to find patients in the post-transplant period. We analyzed two cohorts: kidney transplant recipients (KTRs; 40%) and non-KTR (60%) then followed them longitudinally for the study period. In KTR cohort, high-to-low proportion of ordered MIDT was blood BK virus (bBKV) followed by cytomegalovirus (CMV); in non-KTR cohort, CMV was followed by Epstein-Barr virus (EBV). KTR cohort positivity was highest for urine BK virus (uBKV; 58%) followed by EBV (46%), bBKV (40%), and CMV (31%). Non-KTR cohort positivity was highest for uBKV (64%), EBV (51%), CMV (30%), bBKV (8%), and adenovirus (7%). All patients were tested at progressively longer intervals from the date of the first post-transplant ICD-10-coded test. More than 40% of the KTR cohort were tested less frequently for EBV and bBKV, and more than 20% of the non-KTR cohort were tested for EBV less frequently than published guidelines 4 months after transplant. Despite regular testing, the results of MIDT testing for KTR and non-KTR patients in the post-transplant period are not aligned with published guidelines.IMPORTANCEGuidance for post-transplant infectious disease testing is established, however, for certain infections it allows for clinician discretion. This leads to transplant center policies developing their own testing/surveillance strategies based on their specific transplant patient population (kidney, stem cell, etc.). The Organ Procurement and Transplant Network (OPTN) has developed a strategic plan to improve and standardize the transplant process in the US to improve outcomes of living donors and recipients. Publishing national reference lab data on the testing frequency and its alignment with the recommended guidelines for post-transplant infectious diseases can inform patient uptake and compliance for these strategic OPTN efforts.

Rapid detection of the source of a Listeria monocytogenes outbreak in Switzerland through routine interviewing of patients and whole-genome sequencing.

Listeriosis is a notifiable disease in Switzerland. In summer 2022, the Swiss Federal Office of Public Health noticed an increase in reports of listeriosis cases, indicating a possible ongoing outbreak. Here we present the approaches applied for rapidly confirming the outbreak, detecting the underlying source of infection and the measures put in place to eliminate it and contain the outbreak. For close surveillance and early detection of outbreak situations with their possible sources, listeriosis patients in Switzerland are systematically interviewed about risk behaviours and foods consumed prior to the infection.Listeria monocytogenesisolates derived from patients in medical laboratories are sent to the National Reference Laboratory for Enteropathogenic Bacteria and Listeria, where they routinely undergo whole-genome sequencing. Interview and whole-genome sequencing data are continuously linked for comparison and analysis. In summer 2022, 20 patient-derivedL. monocytogenesserotype 4b sequence type 388 strains were found to belong to an outbreak cluster (≤10 different alleles between neighbouring isolates) based on core genome multilocus sequence typing analysis. Geographically, 18 of 20 outbreak cases occurred in northeastern Switzerland. The median age of patients was 77.4 years (range: 58.1-89.7), with both sexes equally affected. Rolling analysis of the interview data revealed smoked trout from a local producer as a suspected infection source, triggering an on-site investigation of the production facility and sampling of the suspected products by the responsible cantonal food inspection team on 15 July 2022. Seven of ten samples tested positive forL. monocytogenesand the respective cantonal authority ordered a ban on production and distribution as well as a product recall. The Federal Food Safety and Veterinary Office released a nationwide public alert covering the smoked fish products concerned. Whole-genome sequencing analysis confirmed the interrelatedness of theL. monocytogenessmoked trout product isolates and the patient-derived isolates. Following the ban on production and distribution and the product recall, reporting of new outbreak-related cases rapidly dropped to zero. This listeriosis outbreak could be contained within a relatively short time thanks to identification of the source of contamination through the established combined approach of timely interviewing of every listeriosis patient or a representative and continuous molecular analysis of the patient- and food-derivedL. monocytogenesisolates. These findings highlight the effectiveness of this well-established, joint approach involving the federal and cantonal authorities and the research institutions mandated to contain listeriosis outbreaks in Switzerland.

Evaluation of AAICare®-TB sequence analysis tool for accurate diagnosis of drug-resistant tuberculosis: A comparative study with TB-Profiler and Mykrobe

A rapid and comprehensive drug susceptibility test is essential for eliminating drug resistant tuberculosis. Next generation sequencing (NGS) based susceptibility testing is being explored as a potential substitute for the conventional phenotypic and genotypic testing methods. However, the adoption of NGS based genotypic susceptibility testing depends on the availability of simple, accurate and efficient analysis tools. This preliminary study aimed to evaluate the performance of a Mycobacterium tuberculosis (Mtb) genome analysis pipeline, AAICare®-TB, for susceptibility prediction, in comparison to two widely used gDST prediction tools, TB-Profiler and Mykrobe. This study was performed in a National Reference Laboratory in India on presumptive drug-resistant tuberculosis (DR-TB) isolates. Whole genome sequences of the 120 cultured isolates were obtained through Illumina sequencing on a MiSeq platform. Raw sequences were simultaneously analysed using the three tools. Susceptibility prediction reports thus generated, were compared to estimate the total concordance and discordance. WHO mutation catalogue (1st edition, 2021) was used as the reference standard for categorizing the mutations. In this study, AAICare®-TB was able to predict drug resistance status for First Line (Streptomycin, Isoniazid, Rifampicin, Ethambutol and Pyrazinamide) and Second Line drugs (Fluoroquinolones, Second Line Injectables and Ethionamide) in 93 samples along with lineage and hetero-resistance as per the WHO guidelines.

Development of a graphite pile to produce a neutron thermal field at the CIEMAT - Neutron standards laboratory

The CIEMAT Neutron Standards Laboratory (LPN) is the Spanish national reference laboratory in neutron metrology. Within the framework of the LPN expansion project, it has been planned to incorporate a thermal neutron field based on a graphite pile. A study has been carried out with MCNP 6.2 for a graphite pile with dimensions 180 × 150 × 150 cm3, with a 185 GBq Am–Be source (B = 1.1·107 s−1) and the internal cavity with a section of 40 × 40 cm2 and a depth of 50 cm. The main parameters of the graphite pile and the position and emission rate of the Am–Be neutron source have been varied to determine the fluence rates at several points in the pile, their thermal component and homogeneity. The optimal configuration produces a neutron spectrum with more than 98% of thermal component, fluence rates around 400 cm−2 s−1 inside the cavity and 55 cm−2 s−1 outside, and acceptable homogeneity in this thermal neutron field. From a Radiation Protection point of view it is necessary to incorporate borated high-density polyethylene (HDPE-B) around or at least as a shielding wall, and a Cd window to filter the thermal component.

Use of next generation sequencing for detection of hereditary cancer genes: A shared experience from the UAE national reference laboratory

Use of next generation sequencing for detection of hereditary cancer genes: A shared experience from the UAE national reference laboratory

Isolation of avian influenza virus from backyard poultry population of tehsil Abbottabad, Khyber Pakhtunkhwa, Pakistan

The avian influenza virus is a highly contagious viral disease that predominantly impacts avian species, especially domestic birds like chickens, ducks, and turkeys. The study was conducted to isolate the avian influenza virus from domestic poultry breeds (Desi, Aseel, Fayoumi, and Golden) from backyard poultry population of the Tehsil Abbottabad from January to June 2023. A cross-sectional study was conducted in three rural and five urban areas of Tehsil Abbottabad Using sterile cotton swabs, 128 (tracheal and cloacal) swab samples were collected. The samples were labelled and stored in a brain-heart infusion medium, then transported to the National Reference Laboratory for Poultry Diseases in Islamabad using a thermostat shipment box. The samples were processed using a real-time reverse transcription polymerase chain reaction for avian influenza virus detection. This study concludes with a significant 9.38% prevalence percentage of avian influenza virus in Tehsil Abbottabad backyard poultry. The prevalence percentage of H9 was 83.33%, and that of H5 was 16.66%. The findings reveal the importance of implementing preventative measures to curb avian influenza outbreaks within the poultry population of the district. This study offers vital data for AIV research in 2023, guiding enhanced containment and prevention in backyard poultry to control avian influenza.

Using CHROMagar™ STEC medium exclusively does not recover all clinically relevant Shiga toxin-producing Escherichia coli in Aotearoa, New Zealand.

Diagnostic laboratories in Aotearoa, New Zealand (NZ) refer cultures from faecal samples positive for Shiga toxin genes to the national Enteric Reference Laboratory for isolation of Shiga toxin-producing Escherichia coli (STEC) for epidemiological typing. As there was variation in the culture media being referred, a panel of 75 clinical isolates of STEC, representing 28 different serotypes, was used to assess six commercially available media and provide guidance to clinical laboratories. Recommendations were subsequently tested for a 3-month period, where STEC isolations and confirmations were assessed by whole genome sequencing analysis against the culture media referred. CHROMagar™ STEC (CH-STEC; CHROMagar Microbiology, Paris, France) or CH-STEC plus cefixime-tellurite sorbitol MacConkey agar was confirmed inferior to CH-STEC plus blood agar with vancomycin, cefsulodin, and cefixime (BVCC). The former resulted in fewer STEC types (n=18) being confirmed compared to those from a combination of CH-STEC and BVCC (n=42). A significant (P<.05) association with an STEC's ability to grow on CH-STEC and the presence of the ter gene cluster, and eae was observed. Culturing screen positive STEC samples onto both CH-STEC and BVCC ensures a consistently higher recovery of STEC from all clinical samples in NZ than CH-STEC alone.

Francisella tularensis-specific antibody levels in sera from Swedish patients with suspected tularemia during a 13-year period.

For a majority of tularemia patients, serology is the basis for the diagnosis. The aim of this study was to perform an analysis of the samples analyzed at a Swedish reference laboratory for the presence of Francisella tularensis-specific antibody levels in sera from individuals with suspected tularemia. Annual and monthly variations of the total number of samples and proportions of positive samples were analyzed, as well as the influence of age and gender. We performed a retrospective analysis of the presence of F. tularensis-specific antibodies in serological samples from patients with suspected tularemia analyzed during the period 2010 - 2022 at the University Hospital of Umeå in Sweden, a national reference laboratory, by use of various statistical methods. In total, some 15,100 serum samples had been analyzed for the presence of IgG and IgM antibodies by ELISA during the 13-year period. Overall, there were higher number of samples with IgG positive or borderline titers, 2,522 and 921, respectively, than with IgM positive or borderline titers, 1,802 and 409, respectively. Repeated samples were obtained from some 1,930 individuals and approximately a third of the cases, which were initially seronegative, had seroconverted when resampled. Peak number of monthly samples were recorded in August and September, > 3,000. Annual numbers varied greatly and peak numbers were observed in 2015 and 2019, 1,832 and 2,250, respectively, whereas some other years the numbers were 700 - 800. There was also much variation in the annual and monthly percentages of positive samples and they varied between less than 10% to greater than 20%. The highest percentages of positive samples were recorded in September and October. IgG and IgM titers declined with age and these differences were highly significant for IgG titers, with decreasing average titers for each 20-year interval. Collectively, the data demonstrate the marked annual and seasonal variations in tularemia sampling occurring in Sweden. Also, the proportion of positive samples increased during months and years with peak number of samples. Another notable finding was that average antibody titers decreased with increased age.

Genomic characteristics of clinical non-toxigenic Vibrio cholerae isolates in Switzerland: a cross-sectional study.

Although non-toxigenicVibrio choleraelack thectxABgenes encoding cholera toxin, they can cause diarrhoeal disease and outbreaks in humans. In Switzerland,V. choleraeis a notifiable pathogen and all clinical isolates are analysed at the National Reference Laboratory for Enteropathogenic Bacteria and Listeria. Up to 20 infections are reported annually. In this study, we investigated the population structure and genetic characteristics of non-toxigenicV. choleraeisolates collected over five years. V. choleraeisolates were serotyped and non-toxigenic isolates identified using actxA-specific PCR. Following Illumina whole-genome sequencing, genome assemblies were screened for virulence and antibiotic resistance genes. Phylogenetic analyses were performed in the context of 965 publicly availableV. choleraegenomes. Out of 33V. choleraeinfections reported between January 2017 and January 2022 in Switzerland, 31 were caused byctxA-negative isolates. These non-toxigenic isolates originated from gastrointestinal (n = 29) or extraintestinal (n = 2) sites. They were phylogenetically diverse and belonged to 29 distinct sequence types. Two isolates were allocated to the lineage L3b, actxAB-negative buttcpA-positive clade previously associated with regional outbreaks. The remaining 29 isolates were placed in lineage L4, which is associated with environmental strains. Genes or mutations associated with reduced susceptibility to the first-line antibiotics fluoroquinolones and tetracyclines were identified in 11 and 3 isolates, respectively. One isolate was predicted to be multidrug resistant. V. choleraeinfections in Switzerland are rare and predominantly caused by lowly virulentctxAB-negative andtcpA-negative strains. AsV. choleraeis not endemic in Switzerland, cases are assumed to be acquired predominantly during travel. This assumption was supported by the phylogenetic diversity of the analysed isolates.

Prevalence of oral papillomas in Brazilian children: a retrospectivestudy of biopsied lesions

Introduction: Human papillomavirus (HPV) is an etiologic factor for several diseases of the oralmucosa and skin that can undergo a malignant process. Vaccination is the most important form of prevention, with girls being vaccinated between the ages of 9 and 13 and boys between the ages of 11 and 13. There is still no consensus on the prevalence of the HPV virus in children. Aim: To review the prevalence of HPV in children aged 1 to 13 years based on a database of reports of biopsied lesions diagnosed with papilloma analyzed in a national reference laboratory. Material and methods: Anatomic-pathologic reports of biopsies received at the Oral and Maxillofacial Pathology Laboratory of the Faculty of Dentistry of the College of São Paulo were analyzed over a 20-year period, between 2002 and 2022. Information on gender, lesion location and diagnostic hypotheses was also collected. Results: In a database of 93,950 reports, the age group analyzed accounted for 4,203 and 99 (2.3%) were diagnosed with papilloma. The proportion of male and female reports was similar at 50.5% and 49.5% respectively. The most common location of the lesion found was the lip region (48%). The most frequently cited diagnostic hypotheses were epulis and verruca vulgaris. Conclusion: The prevalence of papillomas in Brazilian children aged 1 to 13 years was 2.3%. Early diagnosis and advice on HPV vaccination can prevent and avoid exacerbation of the disease. Recognizing the clinical features of lesions is essential for correct diagnosis and early intervention and counseling.

Epidemiology of coccidioidomycosis in Argentina, an update.

The National Reference Laboratory in Clinical Mycology of Argentina conducted a retrospective review of human coccidioidomycosis cases diagnosed by the National Mycology Laboratory Network of Argentina between 2010 and 2022 to determine the burden of the disease in the country. A total of 100 human coccidioidomycosis cases were documented, with a higher prevalence in male patients (male-to-female ratio of 1.9:1), with a median age of 41 years. Comparing the number of cases between two 10-year periods (2000-2009 and 2010-2019), the increase was 36.51% (from 63 to 86 cases). Among the 100 recorded cases, 79 tested positive using the double immunodiffusion test. Spherules were observed in 19 cases through histopathology or direct microscopic examination and the fungus was isolated in 39 cases. Thirty-six isolates were identified as Coccidioides posadasii through partial sequencing of the Ag2/PRA gene. Catamarca province had the highest number of cases, comprising 64% of the total, with an incidence rate above 1.0-2.5/100,000 inhabitants until 2018. However, there has been a recent downward trend in the region from 2018 to 2022. It is concerning that more than half of diagnosed cases were chronic pulmonary or disseminated forms, indicating a lack of early disease detection. To rectify this issue, it is imperative to conduct targeted training programs for healthcare personnel and enhance public awareness within the endemic area. This will contribute to a better understanding of the true burden of coccidioidomycosis and enable the implementation of appropriate sanitary control measures.

Quality assessment of malaria microscopic diagnosis at the Aristide Le Dantec University Hospital of Dakar, Senegal, in 2020

BackgroundFollowing WHO guidelines, microscopy is the gold standard for malaria diagnosis in endemic countries. The Parasitology-Mycology laboratory (LPM) is the National Reference Laboratory and is currently undergoing ISO 15189 accreditation. In this context, we assessed the performance of the laboratory by confirming the reliability and the accuracy of results obtained in accordance with the requirements of the ISO 15189 standards. This study aimed to verify the method of microscopic diagnosis of malaria at the LPM, in the Aristide Le Dantec hospital (HALD) in Dakar, Senegal.MethodsThis is a validation/verification study conducted from June to August 2020. Twenty (20) microscopic slides of thick/thin blood smear with known parasite densities (PD) selected from the Cheick Anta Diop University malaria slide bank in Dakar were used for this assessment. Six (6) were used to assess microscopists’ ability to determine PD and fourteen (14) slides were used for detection (positive vs negative) and identification of parasites. Four (4) LPM-HALD microscopists read and recorded their results on prepared sheets. Data analysis was done with Microsoft Excel 2010 software.ResultsA minimum threshold of 50% concordance was used for comparison. Of the twenty (20) slides read, 100% concordance was obtained on eight (8) detection (positive vs negative) slides. Four (4) out of the six (6) parasite density evaluation slides obtained a concordance of less than 50%. Thirteen (13) out of the fourteen (14) identification slides obtained a concordance greater than 50%. Only one (1) identification slide obtained zero agreement from the microscopists. For species identification a concordance greater than 80% was noted and the microscopists obtained scores between 0.20 and 0.4 on a scale of 0 to 1 for parasite density reading. The microscopists obtained 100% precision, sensitivity, specificity and both negative and positive predictive values.ConclusionThis work demonstrated that the microscopic method of malaria diagnosis used in the LPM/HALD is in accordance with the requirements of WHO and ISO 15189. Further training of microscopists may be needed to maintain competency.

Bacteriological culture and direct PCR for detecting the Mycobacterium tuberculosis complex in the Italian eradication campaign: a decade of experience at the National Reference Laboratory.

Our study evaluates the capacity of direct real-time PCR for detecting Mycobacterium tuberculosis complex (MTBC), with a focus on diagnostic performances and the feasibility of implementing this protocol in an eradication campaign. Specifically, we compare the effectiveness of the direct PCR method to various culture systems used by the Italian National Reference Laboratory over the last decade to detect MTBC. Bovine tissue samples were routinely tested and analyzed for bovine tuberculosis (bTB) confirmation using microbiological culture (solid and liquid media), histopathological analysis, and a direct PCR assay targeting IS6110, an insertion sequence specific to the MTBC that is widely used for tuberculosis diagnosis. The direct real-time PCR demonstrated a high concordance (K=0.871) with microbiological culture, as well as good sensitivity (91.84%) and specificity (95.24%). In contrast, histopathology demonstrated lower concordance (K=0.746) and performance levels (sensitivity 91.41%, specificity 82.88%). Liquid media promoted faster and more efficient growth of MTBC than solid media. M. bovis and M. caprae had the comparable ability to respond to the direct real-time PCR test and grow on the microbiological medium. This study confirms that direct real-time PCR can detect MTBC with high diagnostic accuracy within a few days. This study found no significant differences in performance between culture media and direct PCR for M. bovis and M. caprae.

Immunoassay Testing of Alpha-Gal Specific Immunoglobulin-E: Data from a National Reference Laboratory.

Immunoassay measurements of serum alpha-gal (AG) specific IgE (sIgE) enable antibody detection and quantification with high sensitivity and specificity and are essential for AG syndrome diagnosis and patient management. We here present and analyze results from over 15 000 patient serum samples tested using the ImmunoCAP (Thermo/Phadia) assay. AG-sIgE levels and positivity rates were correlated to patient age, gender, geographic location, repeat testing results, sIgE levels to co-tested red meat whole allergen extracts, and Rocky Mountain spotted fever (RMSF) serology performed on a subset of patient samples. Of the tested samples, 36.7% contained detectable (>0.1 KUA/L) AG-sIgE. Antibody levels were higher in patients of older age, in samples submitted from lower midwestern and southern states, and during the June-December period of the year. Specific IgE to co-tested red meat whole allergens showed moderate to strong correlation to AG-sIgE and were of lower levels. Samples with positive RMSF IgG titers (≥1:64) were of overall higher AG-IgE levels. Findings are consistent with the role of lone star ticks in AG syndrome pathogenesis. Levels of measured sIgE to AG are higher than co-tested sIgE to red meat whole allergen, consistent with the improved diagnostic performance of component-resolved testing.

Antimicrobial susceptibility profile of clinically relevant Bacteroides, Phocaeicola, Parabacteroides and Prevotella species, isolated by eight laboratories in the Netherlands.

Recently, reports on antimicrobial-resistant Bacteroides and Prevotella isolates have increased in the Netherlands. This urged the need for a surveillance study on the antimicrobial susceptibility profile of Bacteroides, Phocaeicola, Parabacteroides and Prevotella isolates consecutively isolated from human clinical specimens at eight different Dutch laboratories. Each laboratory collected 20-25 Bacteroides (including Phocaeicola and Parabacteroides) and 10-15 Prevotella isolates for 3 months. At the national reference laboratory, the MICs of amoxicillin, amoxicillin/clavulanic acid, piperacillin/tazobactam, meropenem, imipenem, metronidazole, clindamycin, tetracycline and moxifloxacin were determined using agar dilution. Isolates with a high MIC of metronidazole or a carbapenem, or harbouring cfiA, were subjected to WGS. Bacteroides thetaiotaomicron/faecis isolates had the highest MIC90 values, whereas Bacteroides fragilis had the lowest MIC90 values for amoxicillin/clavulanic acid, piperacillin/tazobactam, meropenem, imipenem and moxifloxacin. The antimicrobial profiles of the different Prevotella species were similar, except for amoxicillin, for which the MIC50 ranged from 0.125 to 16 mg/L for Prevotella bivia and Prevotella buccae, respectively. Three isolates with high metronidazole MICs were sequenced, of which one Bacteroides thetaiotaomicron isolate harboured a plasmid-located nimE gene and a Prevotella melaninogenica isolate harboured a nimA gene chromosomally.Five Bacteroides isolates harboured a cfiA gene and three had an IS element upstream, resulting in high MICs of carbapenems. The other two isolates harboured no IS element upstream of the cfiA gene and had low MICs of carbapenems. Variations in resistance between species were observed. To combat emerging resistance in anaerobes, monitoring resistance and conducting surveillance are essential.

Seek and you shall find: Yersinia enterocolitica in Ireland's drinking water.

Three Yersinia species were identified from samples of drinking water from diverse geographic regions of Ireland. Conventional commercial biochemical identification systems classified them as Yersinia enterocolitica. Since this organism is the most common cause of bacterial gastroenteritis in some countries, further investigation was warranted. The aim of the study was to provide a microbial characterisation of three Yersinia species, to determine their pathogenicity, and to review the incidence rate of Yersinia enterocolitica detection in our region. Organism identification was performed using conventional commercial diagnostic systems MALDI-TOF, API 20E, API 50CHE, TREK Sensititre GNID and Vitek 2 GN, and whole genome sequencing (WGS) was performed. Historical data for detections was extracted from the lab system for 2008 to 2023. All three isolates gave "good" identifications of Yersinia enterocolitica on conventional systems. Further analysis by WGS matched two of the isolates with recently described Yersinia proxima, and the third was a member of the non-pathogenic Yersinia enterocolitica clade 1Aa. Our analysis of these three isolates deemed them to be Yersinia species not known currently to be pathogenic, but determining this necessitated the use of next-generation sequencing and advanced bioinformatics. Our work highlights the importance of having this technology available to public laboratories, either locally or in a national reference laboratory. The introduction of molecular technologies for the detection of Yersinia species may increase the rate of detections. Accurate identification of significant pathogens in environmental, public health and clinical microbiology laboratories is critically important for the protection of society.

Human papillomavirus negative high grade cervical lesions and cancers: Suggested guidance for HPV testing quality assurance

BackgroundSome high-grade cervical lesions and cervical cancers (HSIL+) test negative for human papillomavirus (HPV). The HPV-negative fraction varies between 0.03 % and 15 % between different laboratories. Monitoring and extended re-analysis of HPV-negative HSIL+ could thus be helpful to monitor performance of HPV testing services. We aimed to a) provide a real-life example of a quality assurance (QA) program based on re-analysis of HPV-negative HSIL+ and b) develop international guidance for QA of HPV testing services based on standardized identification of apparently HPV-negative HSIL+ and extended re-analysis, either by the primary laboratory or by a national HPV reference laboratory (NRL). MethodsThere were 116 initially HPV-negative cervical specimens (31 histopathology specimens and 85 liquid-based cytology samples) sent to the Swedish HPV Reference Laboratory for re-testing. Based on the results, an international QA guidance was developed through an iterative consensus process. ResultStandard PCR testing detected HPV in 55.2 % (64/116) of initially “HPV-negative” samples. Whole genome sequencing of PCR-negative samples identified HPV in an additional 7 samples (overall 61.2 % HPV positivity). Reasons for failure to detect HPV in an HSIL+ lesion are listed and guidance to identify cases for extended re-testing, including which information should be included when referring samples to an NRL are presented. ConclusionMonitoring the proportion of and reasons for failure to detect HPV in HSIL+ will help support high performance and quality improvement of HPV testing services. We encourage implementation of QA strategies based on re-analysis of “HPV negative” HSIL+ samples.

Clinical and genomic evaluations of a persistent fatal SARS-CoV-2 infection in a goods syndrome patient: a case report

The coronavirus disease of 2019 (COVID-19) resulted from an infection by severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) which is the main cause of acute respiratory distress syndrome (ARDS) in global population from 2019 on. It may contribute to higher rate of death among the patients with immunodeficiency based on recent reports. In addition, Good syndrome (GS) as a result of thymoma removal might cause in some long-lasting microbial infections. We described clinical aspects and viral mutations on a case of GS suffering from COVID-19. A 46-year-old man with fever, common respiratory disease symptoms and positive COVID-19 polymerase chain reaction (PCR) test, with the history of thymoma removal surgery was admitted to Masih Daneshvari Hospital, Tehran, Iran. Lung radiographs and oxygen saturation measurement disclosed considerable implication resulted in application of several anti-microbial medication. The delta variant (B.1.617.2 (21 J Clade)) was the strain isolated from the patient by sequencing methods done by the COVID-19 National Reference Laboratory (CNRL), Pasteur Institute of Iran, while the dominant strain circulated mostly among population was Omicron (B.1.1.529) at the time of sampling. Unfortunately, the patient had passed away a month later by sudden respiratory failure progressed in refractory septic shock. Despite the fact that opportunistic infections may lead the GS patients to a major health problematic condition, unusual persistent of infections such as non-dominant variant of SARS-Cov-2 could be observed through the disease timeline. Therefore, a fully screening of thymoma plus intra-host evolution monitoring of SARS-CoV-2 is highly recommended in immunocompromised patients.