Performing under Pressure: Insights into the Diagnostic Testing Burden at a UK National Health Service Clinical Virology Laboratory during the SARS-CoV-2 Pandemic.

UK National Health Service (NHS) Clinical Virology Departments provide a repertoire of tests on clinical samples to detect the presence of viral genomic material or host immune responses to viral infection. In December 2019, a novel coronavirus (SARS-CoV-2) emerged which quickly developed into a global pandemic; NHS laboratories responded rapidly to upscale their testing capabilities. To date, there is little information on the impact of increased SARS-CoV-2 screening on non-SARS-CoV-2 testing within NHS laboratories. This report details the virology test requests received by the Leicester-based NHS Virology laboratory from January 2018 to May 2022. Data show that in spite of a dramatic increase in screening, along with multiple logistic and staffing issues, the Leicester Virology Department was mostly able to maintain the same level of service for non-respiratory virus testing while meeting the new increase in SARS-CoV-2 testing.

Prospective Surveillance of Respiratory Infections in British Antarctic Survey Bases During the COVID-19 Pandemic.

BACKGROUND: The British Antarctic bases offer a semiclosed environment for assessing the transmission and persistence of seasonal respiratory viruses. METHODS: Weekly swabbing was performed for respiratory pathogen surveillance (including SARS-CoV-2), at 2 British Antarctic Survey bases, during 2020: King Edward Point (KEP, 30 June to 29 September, 9 participants, 124 swabs) and Rothera (9 May to 6 June, 27 participants, 127 swabs). Symptom questionnaires were collected for any newly symptomatic cases that presented during this weekly swabbing period. RESULTS: At KEP, swabs tested positive for non-SARS-CoV-2 seasonal coronavirus (2), adenovirus (1), parainfluenza 3 (1), and respiratory syncytial virus B (1). At Rothera, swabs tested positive for non-SARS-CoV-2 seasonal coronavirus (3), adenovirus (2), parainfluenza 4 (1), and human metapneumovirus (1). All bacterial agents identified were considered to be colonizers and not pathogenic. CONCLUSIONS: At KEP, the timeline indicated that the parainfluenza 3 and adenovirus infections could have been linked to some of the symptomatic cases that presented. For the other viruses, the only other possible sources were the visiting ship crew members. At Rothera, the single symptomatic case presented too early for this to be linked to the subsequent viral detections, and the only other possible source could have been a single nonparticipating staff member.

Post-acute COVID-19 associated with evidence of bystander T-cell activation and a recurring antibiotic-resistant bacterial pneumonia.

Here, we describe the case of a COVID-19 patient who developed recurring ventilator-associated pneumonia caused by Pseudomonas aeruginosa that acquired increasing levels of antimicrobial resistance (AMR) in response to treatment. Metagenomic analysis revealed the AMR genotype, while immunological analysis revealed massive and escalating levels of T-cell activation. These were both SARS-CoV-2 and P. aeruginosa specific, and bystander activated, which may have contributed to this patient's persistent symptoms and radiological changes.

Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing.

BACKGROUND: Staphylococci are a major constituent of the nasal microbiome and a frequent cause of hospital-acquired infection. Antibiotic surgical prophylaxis is administered prior to surgery to reduce a patient's risk of postoperative infection. The impact of surgical prophylaxis on the nasal staphylococcal microbiome is largely unknown. Here, we report the species present in the nasal staphylococcal microbiome and the impact of surgical prophylaxis revealed by a novel culture independent technique. Daily nasal samples from 18 hospitalised patients, six of whom received no antibiotics and 12 of whom received antibiotic surgical prophylaxis (flucloxacillin and gentamicin or teicoplanin +/- gentamicin), were analysed by tuf gene fragment amplicon sequencing. RESULTS: On admission to hospital, the species diversity of the nasal staphylococcal microbiome varied from patient to patient ranging from 4 to 10 species. Administration of surgical prophylaxis did not substantially alter the diversity of the staphylococcal species present in the nose; however, surgical prophylaxis did impact on the relative abundance of the staphylococcal species present. The dominant staphylococcal species present in all patients on admission was Staphylococcus epidermidis, and antibiotic administration resulted in an increase in species relative abundance. Following surgical prophylaxis, a reduction in the abundance of Staphylococcus aureus was observed in carriers, but not a complete eradication. CONCLUSIONS: Utilising the tuf gene fragment has enabled a detailed study of the staphylococcal microbiome in the nose and highlights that although there is no change in the heterogeneity of species present, there are changes in abundance. The sensitivity of the methodology has revealed that the abundance of S. aureus is reduced to a low level by surgical prophylaxis and therefore reduces the potential risk of infection following surgery but also highlights that S. aureus does persist.

Antibiotic surgical prophylaxis increases nasal carriage of antibiotic-resistant staphylococci.

Staphylococci are a significant cause of hospital-acquired infection. Nasal carriage of Staphylococcus aureus is an important risk factor for infection in surgical patients and coagulase-negative staphylococci (CNS) are a major cause of prosthetic joint infections. The impact that antibiotic surgical prophylaxis has on the nasal carriage of staphylococci has not been studied. Daily nasal swabs were taken from 63 patients who received antibiotic surgical prophylaxis and 16 patients who received no antibiotics. Total aerobic bacterial count, S. aureus and CNS were enumerated by culture from nasal swabs. Representative isolates were typed by staphylococcal interspersed repeat units (SIRU) typing and PFGE, and MICs to nine antibiotics were determined. After antibiotic administration, there was a reduction in S. aureus counts (median - 2.3 log(10)c.f.u. ml(- 1)) in 64.0 % of S. aureus carriers, compared with only a 0.89 log(10)c.f.u. ml(- 1) reduction in 75.0 % of S. aureus carriers who did not receive antibiotics. A greater increase in the nasal carriage rate of meticillin-resistant CNS was observed after antibiotic surgical prophylaxis compared with hospitalization alone, with increases of 16.4 and 4.6 %, respectively. Antibiotic-resistant S. epidermidis carriage rate increased by 16.6 % after antibiotic administration compared with 7.5 % with hospitalization alone. Antibiotic surgical prophylaxis impacts the nasal carriage of both S. aureus and CNS.

Content validity of the illness perceptions questionnaire--revised among people with type 2 diabetes: a think-aloud study.

OBJECTIVES: to access the cognitions of adults with type 2 diabetes whilst completing items on the Illness Perceptions Questionnaire-Revised (IPQ-R). To determine whether these cognitions are congruent with the meaning of items and subscales as interpreted by researchers and clinicians using the IPQ-R and to identify the nature and extent of problems that individuals experience when completing the IPQ-R. DESIGN: participants (n = 36) were recruited from a primary care diabetes clinic and a hospital diabetes clinic. They were asked to complete the IPQ-R using a 'think-aloud' methodology. MAIN OUTCOME MEASURES: transcripts were analysed to identify instances where participants expressed problems with item completion, or where there was inconsistency between verbal and written responses. RESULTS: the most problematic subscales were those of 'personal control' and 'consequences'. CONCLUSION: generally, participants found the IPQ-R unproblematic. However, participants had problems with the concept of 'cure' and 'symptoms' in the context of type 2 diabetes, and with the negative phrasing used in some items. These findings have important implications for the interpretation of IPQ-R scores, particularly when the IPQ-R is used as the basis for individualised interventions among people with type 2 diabetes.

Regional survey of CTX-M-type extended-spectrum ß-lactamases among Enterobacteriaceae reveals marked heterogeneity in the distribution of the ST131 clone.

OBJECTIVES: To establish the prevalence and diversity of clinically significant extended-spectrum ß-lactamase (ESBL)-producing Enterobacteriaceae harbouring bla(CTX-M) in the West Midlands region of the UK. METHODS: During a 2 month period, 370 consecutive, non-duplicate isolates were collected from 13 laboratories. Isolates were screened for the presence of bla(CTX-M) by multiplex PCR and genotyped using denaturing HPLC (DHPLC). Clonal relationships were studied by PFGE and O25b-ST131 Escherichia coli were identified by PCR. RESULTS: Two hundred and ninety-four out of 345 ESBL-producing isolates (85.2%) carried bla(CTX-M). CTX-M group 1 enzymes were expressed in 284 (96.6%) isolates, with the other 10 carrying group 9, 2 and 25/26 genes. All group 1 isolates had bla(CTX-M-15) DHPLC profiles. The bla(CTX-M) E. coli were split into 23 PFGE clusters. The largest cluster (RE1) was indistinguishable from the previously described strain A and all but one harboured bla(CTX-M-15.) A total of 66% of E. coli were O25b-ST131 positive. CONCLUSIONS: The CTX-M-15-producing RE1 clone (strain A) is the predominant clone in the West Midlands. This clone has spread throughout the region since its emergence in an outbreak 3 years earlier. Most, but not all, RE1 isolates belong to the O25b-ST131 lineage, providing further evidence that this lineage plays a pivotal role in the clonal dispersal of CTX-M-15-producing Enterobacteriaceae. Strain A was found to be considerably more heterogeneous than when first described and has acquired greater resistance to gentamicin. Approximately one-third of CTX-M producers represented a wide variety of unrelated strains. The study shows the rapid spread and diversification of CTX-M-producing Enterobacteriaceae over a 3 year period.

Rapid, automated epidemiological typing of methicillin-resistant Staphylococcus aureus.

The QIAxcel is an accurate, automated DNA sizing system that can be used as an alternative to agarose gel electrophoresis for rapid, high throughput epidemiological typing of methicillin-resistant Staphylococcus aureus using staphylococcal interspersed repeating unit (SIRU) typing.

Reduction in the rate of methicillin-resistant Staphylococcus aureus acquisition in surgical wards by rapid screening for colonization: a prospective, cross-over study.

Identification of patients colonized with methicillin-resistant Staphylococcus aureus (MRSA) and subsequent isolation and decolonization is pivotal to the control of cross infection in hospitals. The aim of this study was to establish if early identification of colonized patients using rapid methods alone reduces transmission. A prospective, cluster, two-period cross-over design was used. Seven surgical wards at a large hospital were allocated to two groups, and for the first 8 months four wards used rapid MRSA screening and three wards used a standard culture method. The groups were reversed for the second 8 months. Regardless of the method of detection, all patients were screened for nasal carriage on admission and then every 4 days. MRSA control measures remained constant. Results were analysed using a log linear Poisson regression model. A total of 12 682/13 952 patient ward episodes (PWE) were included in the study. Admission screening identified 453 (3.6%) MRSA-positive patient ward episodes, with a further 268 (2.2%) acquiring MRSA. After adjusting for other variables, rapid screening was shown to statistically reduce MRSA acquisition, with patients being 1.49 times (p 0.007) more likely to acquire MRSA in wards where they were screened using the culture method. Screening of surgical patients using rapid testing resulted in a statistically significant reduction in MRSA acquisition. This result was achieved in a routine surgical service with high bed occupancy and low availability of isolation rooms, making it applicable to the majority of health-care systems worldwide.

Epidemiological typing of meticillin-resistant Staphylococcus aureus isolates from Pakistan and India.

The levels of meticillin-resistant Staphylococcus aureus (MRSA) in Pakistan and India are known to be high, but few studies have described the epidemiology of the different MRSA clones present. In order to gain an understanding of the epidemiology of MRSA within this region, 60 MRSA isolates from Pakistan (49) and India (11) were genotyped. All isolates were typed using PFGE, staphylococcal interspersed repeat units (SIRUs), a restriction-modification method and staphylococcal cassette chromosome mec (SCCmec) typing. A subset of isolates that were distinct by PFGE and SIRUs were typed using multilocus sequence typing (MLST). Clonal complex (CC) 8 was the dominant clonal complex (57/60) and was present in both Pakistan and India. Within CC8, there were 10 SIRU profiles and 24 PFGE profiles. Two SIRU profiles were present in isolates from both India and Pakistan, whilst seven were distinct for Pakistan and one for India. All PFGE profiles were distinct for each of the two countries. Thirty-four of the 57 isolates carried SCCmec type III/IIIa and the remainder carried type IV SCCmec. MLST analysis of 14 CC8 isolates with diverse SIRU and PFGE profiles showed that all were single-locus variants, with nine belonging to sequence type (ST) 239, three to ST8 and two to ST113. From a single hospital in Pakistan, three isolates belonged to CC30 and all were indistinguishable by PFGE and SIRUs and carried the Panton-Valentine leukocidin gene. Thus, epidemiological typing of strains from three distinct locations in India and Pakistan revealed the predominance of one clonal complex and highly related STs. The ability of SIRUs and PFGE to differentiate within ST239 demonstrates their utility in defining local epidemiology in these countries.