Rapid Detection of Emerging Pathogens and Loss of Microbial Diversity Associated with Severe Lung Disease in Cystic Fibrosis.

Respiratory infection in cystic fibrosis (CF) is polymicrobial, but standard sputum microbiology does not account for the lung microbiome or detect changes in microbial diversity associated with disease. As a clinically applicable CF microbiome surveillance scheme, total sputum nucleic acids isolated by a standard high-throughput robotic method for accredited viral diagnosis were profiled for bacterial diversity using ribosomal intergenic spacer analysis (RISA) PCR. Conventional culture and RISA were performed on 200 paired sputum samples from 93 CF adults; pyrosequencing of the 16S rRNA gene was applied to 59 patients to systematically determine bacterial diversity. Compared to the microbiology data, RISA profiles clustered into two groups: the emerging nonfermenting Gram-negative organisms (eNFGN) and Pseudomonas groups. Patients who were culture positive for Burkholderia, Achromobacter, Stenotrophomonas, and Ralstonia clustered within the eNFGN group. Pseudomonas group RISA profiles were associated with Pseudomonas aeruginosa culture-positive patients. Sequence analysis confirmed the abundance of eNFGN genera and Pseudomonas within these respective groups. Low bacterial diversity was associated with severe lung disease (P < 0.001) and the presence of Burkholderia (P < 0.001). An absence of Streptococcus (P < 0.05) occurred in individuals with lung function in the lowest quartile. In summary, nucleic acids isolated from CF sputum can serve as a single template for both molecular virology and bacteriology, with a RISA PCR rapidly detecting the presence of dominant eNFGN pathogens or P. aeruginosa missed by culture (11% of cases). We provide guidance for how this straightforward CF microbiota profiling scheme may be adopted by clinical laboratories.

Viral capture sequencing detects unexpected viruses in the cerebrospinal fluid of adults with meningitis.

OBJECTIVES: Many patients with meningitis have no aetiology identified leading to unnecessary antimicrobials and prolonged hospitalisation. We used viral capture sequencing to identify possible pathogenic viruses in adults with community-acquired meningitis. METHODS: Cerebrospinal fluid (CSF) from 73 patients was tested by VirCapSeq-VERT, a probe set designed to capture viral targets using high throughput sequencing. Patients were categorised as suspected viral meningitis - CSF pleocytosis, no pathogen identified (n = 38), proven viral meningitis - CSF pleocytosis with a pathogen identified (n = 15) or not meningitis - no CSF pleocytosis (n = 20). RESULTS: VirCapSeq-VERT detected virus in the CSF of 16/38 (42%) of those with suspected viral meningitis, including twelve individual viruses. A potentially clinically relevant virus was detected in 9/16 (56%). Unexpectedly Toscana virus, rotavirus and Saffold virus were detected and assessed to be potential causative agents. CONCLUSION: VirCapSeq-VERT increases the probability of detecting a virus. Using this agnostic approach we identified Toscana virus and, for the first time in adults, rotavirus and Saffold virus, as potential causative agents in adult meningitis. Further work is needed to determine the prevalence of atypical viral candidates as well as the clinical impact of using sequencing methods in real time. This knowledge can help to reduce antimicrobial use and hospitalisations leading to both patient and health system benefits.

An Outbreak of Pseudomonas Aeruginosa Infection Linked to a "Black Friday" Piercing Event.

INTRODUCTION: Outbreaks linked to cosmetic piercing are rare, but can cause significant illness. We report the investigation and management of a point-source outbreak that occurred during a Black Friday promotional event in North West England. METHODS: Outbreak investigation was led by Public Health England, and included active case finding among individuals pierced at a piercing premises between 25/11/2016 (Black Friday) and 7/12/2016. Detailed epidemiological, environmental (including inspection and sampling), and microbiological investigation was undertaken. RESULTS: During the Black Friday event (25/11/2016), 45 people were pierced (13 by a newly-appointed practitioner). Eleven cases were identified (7 microbiologically-confirmed, 2 probable, and 2 possible). All cases had clinical signs of infection around piercing sites, and five required surgical intervention, with varying degrees of post-operative disfigurement. All confirmed and probable cases had a scaffold piercing placed with a guide bar by the newly-appointed practitioner. Pseudomonas aeruginosa, indistinguishable at nine-locus variable-number tandem repeat loci, was isolated from four of the confirmed cases, and from pre- and post-flush samples from five separate water taps (three sinks) in the premises. Water samples taken after remedial plumbing work confirmed elimination of Pseudomonas contamination. DISCUSSION: Although high levels of Pseudomonas water contamination and some poor infection control procedures were identified, infection appeared to require additional exposure to an inexperienced practitioner, and the more invasive scaffold piercing. A proactive collaborative approach between piercers and health and environmental officials is required to reduce outbreak risk, particularly when unusually large events are planned.

Increased prevalence of Pneumocystis jirovecii colonisation in acute pulmonary exacerbations of cystic fibrosis.

OBJECTIVES: This study examined the prevalence of Pneumocystis jirovecii in the sputum of adults with cystic fibrosis during clinical stability and acute pulmonary exacerbation. METHODS: This was a prospective, longitudinal observational study of patients attending the Manchester Adult Cystic Fibrosis Centre. Sputum samples were analysed for P. jirovecii DNA using PCR at enrolment and up to 5 follow-up visits. Patients were classified as stable or exacerbating using a modified Fuch's pulmonary exacerbation score. RESULTS: 226 samples were tested from 111 patients. P. jirovecii was more likely to be detected in samples at acute pulmonary exacerbation (7/76 (9.2%)) compared with stable visits (3/150 (2%)), p = 0.03. P. jirovecii was detected less frequently if patients had received co-trimoxazole within 3 months of sample collection (0% versus 29.7%, p = 0.03). CONCLUSIONS: Prevalence of P. jirovecii in stable patients is low, but P. jirovecii is detected in approximately 1 in 10 patients experiencing an acute pulmonary exacerbation.

Chronic mould exposure as a risk factor for severe community acquired pneumonia in a patient requiring extra corporeal membrane oxygenation.

A previously fit and well man developed acute respiratory failure due to environmental mould exposure from living in damp rental accommodation. Despite aggressive intensive care management he rapidly deteriorated and required respiratory and cardiac Extracorporeal Membrane Oxygenation. We hypothesize that poor domiciliary conditions may make an underestimated contribution to community respiratory disease. These conditions may present as acute and severe illness with non-typical pathogens identified.

Identification, investigation and management of patient-to-patient hepatitis B transmission within an inpatient renal ward in North West England.

BACKGROUND: Transmission of hepatitis B virus (HBV) is rare within healthcare settings in developed countries. The aim of the article is to outline the process of identification and management of transmission of acute hepatitis B in a renal inpatient ward. METHODS: The case was identified through routine reporting to public health specialists, and epidemiological, virological and environmental assessment was undertaken to investigate the source of infection. An audit of HBV vaccination in patients with chronic kidney disease was undertaken. RESULTS: Investigations identified inpatient admission to a renal ward as the only risk factor and confirmed a source patient with clear epidemiological, virological and environmental links to the case. Multiple failures in infection control leading to a contaminated environment and blood glucose testing equipment, failure to isolate a non-compliant, high-risk patient and incomplete vaccination for patients with chronic kidney disease may have contributed to the transmission. CONCLUSIONS: Patient-to-patient transmission of hepatitis B was shown to have occurred in a renal ward in the UK, due to multiple failures in infection control. A number of policy changes led to improvements in infection control, including reducing multi-function use of wards, developing policies for non-compliant patients, improving cleaning policies and implementing competency assessment for glucometer use and decontamination. HBV vaccination of renal patients may prevent patient-to-patient transmission of HBV. Consistent national guidance should be available, and clear pathways should be in place between primary and secondary care to ensure appropriate hepatitis B vaccination and follow-up testing.

Widespread dissemination in England of a stable and persistent hepatitis B virus variant.

BACKGROUND: Outbreaks of acute hepatitis B among inmates of 6 prisons in 3 regions of northern England occurring from 1992 through 1994 were found to be associated with a single hepatitis B virus (HBV) variant, which was carried by 20 of the 24 case patients. We instigated a study of cases of acute hepatitis B to trace the spread and prevalence of this variant. METHODS: A denaturing gradient gel electrophoresis assay was optimized to detect the HBV variant, and cases of acute HBV infection in 3 regions in England occurring from 1990 through 1996 were screened for its presence. Samples from HBV-transmission incidents that were received for molecular investigation were also tested. RESULTS: The variant was identified in 117 (41%) of the 266 cases of acute hepatitis examined in representative regions in England. In North Humberside, but not in southeast England or the West Midlands, a trend toward an increase in the prevalence of the variant was observed. Furthermore, the same variant was identified in the case patients or the individuals implicated in transmission in 11 (22%) of 51 transmission incidents occurring in England from 1997 through 2002. The spread of the variant was primarily associated with injection drug use. CONCLUSIONS: The finding of a single, genetically identical variant (over the 600 bp sequenced) occupying a large niche among the circulating viruses was unexpected. This finding has major implications for the use of DNA sequencing analysis in the investigation of chains of transmission. The study also highlights the need for better protection of at-risk groups through vaccination against HBV, a strategy that currently achieves poor coverage.

Norovirus outbreak in a cruise ship sailing around the British Isles: investigation and multi-agency management of an international outbreak.

OBJECTIVE: Managing an outbreak of gastroenteritis (GI) on board a cruise ship while minimising disruption to passengers' on board and shore visit activities is difficult. For this reason it is important to understand the complex patterns of transmission in a closed community. We describe the epidemiological investigation of an outbreak of norovirus during an international cruise. METHODS: A retrospective cohort study was conducted using information from lists routinely maintained by the travel company, including the passenger manifest, and organised coach tour lists. Information on air-conditioning (AC) systems was used to assess the possible sources of exposures. FINDINGS: Of the 1194 passengers 191 (16%) and 5 crew (<1%) became ill with GI symptoms. The attack rate was higher amongst passengers whose cabin was on the main deck (RR 3.41, 95% CI 1.47-7.94) that houses both passengers' cabins and leisure facilities including shops. Passengers who went on one of the organised coach tours where there were symptomatic passengers were at an increased risk of infection (RR 2.14, CI 1.51-3.03). Analysis of the 56 AC sections on the ship and did not detect an association with infection. CONCLUSIONS: Patterns of transmission of norovirus on a cruise ship are complex. Our study suggests infections are more likely among those passengers staying in areas of the ship that are highly transited or used for communal activities and more difficult to clean. Emphasis on the importance of early reporting of symptoms can help minimise transmission. Internationally agreed guidelines on the management of outbreaks on cruise ships are needed.

Causes of encephalitis and differences in their clinical presentations in England: a multicentre, population-based prospective study.

BACKGROUND: Encephalitis has many causes, but for most patients the cause is unknown. We aimed to establish the cause and identify the clinical differences between causes in patients with encephalitis in England. METHODS: Patients of all ages and with symptoms suggestive of encephalitis were actively recruited for 2 years (staged start between October, 2005, and November, 2006) from 24 hospitals by clinical staff. Systematic laboratory testing included PCR and antibody assays for all commonly recognised causes of infectious encephalitis, investigation for less commonly recognised causes in immunocompromised patients, and testing for travel-related causes if indicated. We also tested for non-infectious causes for acute encephalitis including autoimmunity. A multidisciplinary expert team reviewed clinical presentation and hospital tests and directed further investigations. Patients were followed up for 6 months after discharge from hospital. FINDINGS: We identified 203 patients with encephalitis. Median age was 30 years (range 0-87). 86 patients (42%, 95% CI 35-49) had infectious causes, including 38 (19%, 14-25) herpes simplex virus, ten (5%, 2-9) varicella zoster virus, and ten (5%, 2-9) Mycobacterium tuberculosis; 75 (37%, 30-44) had unknown causes. 42 patients (21%, 15-27) had acute immune-mediated encephalitis. 24 patients (12%, 8-17) died, with higher case fatality for infections from M tuberculosis (three patients; 30%, 7-65) and varicella zoster virus (two patients; 20%, 2-56). The 16 patients with antibody-associated encephalitis had the worst outcome of all groups-nine (56%, 30-80) either died or had severe disabilities. Patients who died were more likely to be immunocompromised than were those who survived (OR = 3·44). INTERPRETATION: Early diagnosis of encephalitis is crucial to ensure that the right treatment is given on time. Extensive testing substantially reduced the proportion with unknown cause, but the proportion of cases with unknown cause was higher than that for any specific identified cause. FUNDING: The Policy Research Programme, Department of Health, UK.

Unique BK virus non-coding control region (NCCR) variants in hematopoietic stem cell transplant recipients with and without hemorrhagic cystitis.

Hematopoietic stem cell transplant recipients frequently develop BK virus (BKV)-associated hemorrhagic cystitis, which coincides with BK viruria. However, the precise role of BKV in the etiology of hemorrhagic cystitis in hematopoietic stem cell transplant recipients remains unclear, since approximately 50% of all such adult transplant recipients excrete BKV, yet do not develop this clinical condition. In the present study, BKV were analyzed to determine if mutations in the non-coding control region (NCCR), and specific BKV sub-types defined by sequence analysis of major capsid protein VP1, were associated with development of hemorrhagic cystitis in hematopoietic stem cell transplant recipients. The regions encoding VP1 and NCCRs of BKV in urine samples collected from 15 hematopoietic stem cell transplant recipients with hemorrhagic cystitis and 20 without this illness were amplified and sequenced. Sequence variations in the NCCRs of BKV were identified in urine samples from those with and without hemorrhagic cystitis. Furthermore, five unique sequence variations within transcription factor binding sites in the canonical NCCR, O-P-Q-R-S, were identified, representing new BKV variants from a population of cloned quasi-species obtained from patients with and without hemorrhagic cystitis. Thirty-five BKV VP1 sequences were analyzed by phylogenetic analysis but no specific BKV sub-type was associated with hemorrhagic cystitis. Five previously unrecognized naturally occurring variants of the BKV are described which involve amplifications, deletions, and rearrangements of the archetypal BKV NCCRs in individuals with and without hemorrhagic cystitis. Architectural rearrangements in the NCCRs of BKV did not appear to be a prerequisite for development of hemorrhagic cystitis in hematopoietic stem cell transplant recipients.

Unusual manifestations of primary cytomegalovirus infection in patients without HIV infection and without organ transplants.

Primary cytomegalovirus (CMV) infection with marked constitutional symptoms is rare in immunocompetent individuals and in those with iatrogenic immunosuppression, except transplant recipients. Four patients admitted to hospital with clinical illnesses associated with primary CMV infection were identified over a 12-month period. Their medical records were reviewed with regard to clinical and laboratory data, and outcome. Primary CMV infection was defined by the concomitant presence of CMV IgM and low avidity CMV IgG antibody. Of two patients with no known underlying illness, one presented with thrombocytopenic purpura and the other with vasculitis. Two patients receiving immunosuppressants for underlying ulcerative colitis presented with CMV-induced pancytopenia and CMV colitis. Atypical lymphocytosis was a feature on blood film examination in three of the four cases. One patient with disseminated CMV infection died of progressive multiorgan failure despite antiviral treatment. CMV disease following primary CMV infection should be considered in otherwise immunocompetent individuals with atypical lymphocytosis on blood film analysis, and particularly in patients on immunosuppressants such as those with ulcerative colitis, since early diagnosis and treatment with antiviral drugs may improve outcome.