Regional Public Health Laboratory Research Articles

A response playbook for early detection and population surveillance of new SARS-CoV-2 variants in a regional public health laboratory.

Timely genomic surveillance is required to inform public health responses to new SARS-CoV-2 variants. However, the processes involved in local genomic surveillance introduce inherent time constraints. The Regional Innovative Public Health Laboratory in Chicago developed and employed a genomic surveillance response playbook for the early detection and surveillance of emerging SARS-CoV-2 variants. The playbook outlines modifications to sampling strategies, laboratory workflows, and communication processes based on the emerging variant's predicted viral characteristics, observed public health impact in other jurisdictions and local community risk level. The playbook outlines procedures for implementing and reporting enhanced and accelerated genomic surveillance, including supplementing whole genome sequencing (WGS) with variant screening by quantitative PCR (qPCR). The ability of the playbook to improve the response to an emerging variant was tested for SARS-CoV-2 Omicron BA.1. Increased submission of clinical remnant samples from local hospital laboratories enabled detection of a new variant at an average of 1.4% prevalence with 95% confidence rather than 3.5% at baseline. Genotyping qPCR concurred with WGS lineage assignments in 99.9% of 1541 samples with results by both methods, and was more sensitive, providing lineage results in 90.4% of 1833 samples rather than 85.1% for WGS, while significantly reducing the time to lineage result. The genomic surveillance response playbook provides a structured, stepwise, and data-driven approach to responding to emerging SARS-CoV-2 variants. These pre-defined processes can serve as a template for other genomic surveillance programs to streamline workflows and expedite the detection and public health response to emerging variants. Based on the processes piloted during the Omicron BA.1 response, this method has been applied to subsequent Omicron subvariants and can be readily applied to future SARS-CoV-2 emerging variants and other public health surveillance activities.

Similar Sensitivity of SARS-CoV-2 Detection in Oropharyngeal/Nasopharyngeal and Saliva Samples on the Hologic Panther Platform.

Oropharyngeal (OP) and nasopharyngeal (NP) sampling has historically been considered the reference specimen type used for respiratory virus detection. Saliva could be a less invasive alternative for SARS-CoV-2 detection, but limited evidence is available. The technical and clinical performance of saliva was compared to OP/NP on the Hologic Panther platform with two Aptima assays, the End-Point Transcription-Mediated Amplification assay (EP-TMA) and Real-Time Transcription-Mediated Amplification assay (RT-TMA). The samples were collected at the Public Health Service Testing Site XL location in Schiphol Amsterdam Airport. At the site, the Regional Public Health Laboratory Kennemerland (RPHLK) has a fully equipped laboratory facility. A total of 374 samples (187 OP/NP swabs and 187 saliva samples) were collected from 187 unique patients. The Real-Time Transcription-Mediated Amplification assay (RT-TMA) resulted in comparable sensitivities for the detection of SARS-CoV-2 in both the OP/NP swabs (88.3%; 113/128) and saliva samples (87.5%; 112/128). The End-Point Transcription-Mediated Amplification assay (EP-TMA) analyses showed a similar sensitivity (86.7%; 111/128) in the OP/NP swabs but a lower sensitivity in the saliva samples (80.5%; 103/128). Within the discordant analyses, we found no associations in the symptoms, earlier SARS-CoV-2 infections and eating, smoking, drinking and tooth brushing habits within one hour before testing. The Hologic Panther platform Real-Time Transcription-Mediated Amplification assay (RT-TMA) yields a sensitivity for the detection of SARS-CoV-2 in saliva that is comparable to the OP/NP swabs derived from participants presenting themselves at a public health testing facility with minimal or mild symptoms.

Institutionalization of the Philippine Health Laboratory System (PHLS)

In 1966, Section 3 of Republic Act (R.A.) 4688, entitled “An Act Regulating the Operation and Maintenance of Clinical Laboratories and Requiring the Registration of the Same with the Department of Health, Providing Penalty for the Violation Thereof, and for Other Purposes,” provided for the establishment of the Bureau of Research and Laboratories (BRL) under the Department of Health (DOH). The BRL served as the central laboratory that governed the operation of regional public health laboratories. The BRL’s function was delegated to different offices in 2000 by Executive Order 102 s. 1999 entitled “Redirecting the Functions and Operations of the Department of Health,” which was premised in part with Section 78 of the General Provisions of R.A. 8522 (“General Appropriations Act of 1998”) authorizing the President to direct changes in organization and key positions of any department, bureau, or agency. Towards this direction, the function of the BRL was distributed to different agencies, and the Philippines designated six (6) national reference laboratories that catered to communicable and non-communicable diseases. Five (5) subnational reference laboratories for emerging and re-emerging infectious diseases were established in response to the 2009 Influenza AH1N1 pandemic. The DOH issued Administrative Order No 2012-0021 to establish a national and regional network of laboratories.

PulseNet International Survey on the Implementation of Whole Genome Sequencing in Low and Middle-Income Countries for Foodborne Disease Surveillance.

PulseNet International (PNI) is a global network of 88 countries who work together through their regional and national public health laboratories to track foodborne disease around the world. The vision of PNI is to implement globally standardized surveillance using whole genome sequencing (WGS) for real-time identification and subtyping of foodborne pathogens to strengthen preparedness and response and lower the burden of disease. Several countries in North America and Europe have experienced significant benefits in disease mitigation after implementing WGS. To broaden the routine use of WGS around the world, challenges and barriers must be overcome. We conducted this study to determine the challenges and barriers countries are encountering in their attempts to implement WGS and to identify how PNI can provide support to improve and become a better integrated system overall. A survey was designed with a set of qualitative questions to capture the status, challenges, barriers, and successes of countries in the implementation of WGS and was administered to laboratories in Africa, Asia-Pacific, Latin America and the Caribbean, and Middle East. One-third of respondents do not use WGS, and only 8% reported using WGS for routine, real-time surveillance. The main barriers for implementation of WGS were lack of funding, gaps in expertise, and training, especially for data analysis and interpretation. Features of an ideal system to facilitate implementation and global surveillance were identified as an all-in-one software that is free, accessible, standardized and validated. This survey highlights the minimal use of WGS for foodborne disease surveillance outside the United States, Canada, and Europe to date. Although funding remains a major barrier to WGS-based surveillance, critical gaps in expertise and availability of tools must be overcome. Opportunities to seek sustainable funding, provide training, and identify solutions for a globally standardized surveillance platform will accelerate implementation of WGS worldwide.

Türkiyenin Doğusunda Çeşitli Klinik Örneklerden İzole Edilen Mycobacterium tuberculosis Suşlarinin Major Anti-Tüberküloz İlaçlara Duyarlılıklarının Araştırılması

Objective: In the study, 419 Mycobacterium tuberculosis complex strains (MTC), which were isolated from samples sent to the Regional Tuberculosis Laboratory in our city between 2015 and 2019 with suspected tuberculosis from Erzurum and surrounding cities were investigated. Methods: Our research is a retrospective cross-sectional study and clinical samples sent to the Regional Public Health Laboratory with suspicion of Tuberculosis within a five-year period from January 2015 to December 2019 were first evaluated by using Ehrlich-Ziehl-Neelsen staining technique. The samples were then simultaneously inoculated into the automated culture system (BACTEC MGIT 960) with Löwenstein-Jensen medium. Sensitivity research was conducted for isoniazide, rifampicin, streptomycin and ethambutol antibiotics with BACTEC MGIT 960 system to samples defined by MTC identification test (TBc ID) from reproduction positive tubes. Results: In our study, 337 (80.4%) of the 419 MTC strains investigated in our study were susceptible to all major anti-TB drugs, while 82 (19.6%) were found to be resistant to at least one major anti-TB drug. The distribution of resistance ratios was isoniazid (11.9%), streptomycin (11.7%), rifampicin (4.1%), ethambutol (3.6%). Multi-drug resistant (MDR)–TB ratio (isoniazid+ rifampicin) was found to be (3.6%). Conclusions: In our study, in the strains in which resistance to anti-TB drugs was investigated, the highest drug resistance was determined for isoniazid. The lowest drug resistance was determined for ethambutol.

Getting back on track: control of covid-19 outbreaks in the community.

Peter Roderick , Alison Macfarlane, and Allyson M Pollock argue there’s still time to change tack on the UK’s ad hoc system for covid-19 tracking, testing, and contact tracing Historically, England’s system of communicable disease control has relied on close cooperation between local health services and authorities. General practitioners, NHS and public health laboratories, and local public health officers play key roles, backed by legal notification requirements. That local system has gradually been eroded over several decades. (box 1) But instead of prioritising and rebuilding this system at the start of this epidemic, the government has created a separate system which steers patients away from GPs, avoids local authorities, and relies on commercial companies and laboratories to track, test, and contact trace. The ad hoc parallel system in England has three components: Box 1 ### Erosion of local communicable disease control in England At its height, local communicable disease control was supported by more than 60 national, regional, and local public health laboratories. The service was strengthened from 1977-2002 by the creation of the Communicable Disease Surveillance Centre in Colindale. Erosion began after NHS reorganisation in 1974 and continued when the Public Health Laboratory Service Board was abolished in 2003 and its local laboratories transferred to NHS trusts, at the same time as communicable disease control was centralised in the Health Protection Agency. In 2012, the Health and Social Care Act abolished locally based bodies in England and carved public health functions out of the NHS. Public Health England was set up as an executive agency to fulfil the government’s duty to protect the public from disease, with only nine laboratories and eight regional centres. Local authorities were charged with improving public health. Each local authority was required, acting jointly with the secretary of state, to appoint a director of public health, with responsibility for exercising the authority’s public health functions. … RETURN TO TEXT

HIV serology false positivity among expatriates from Africa: a screening dilemma.

HIV prevalence in Oman is low (<5 %); however, 45 % of the population are expatriates, including a portion originating from countries with high HIV prevalence (>5 %). HIV screening is performed at regional public health laboratories as part of a medical fitness programme for residency applicants. We conducted a retrospective evaluation of indeterminate serology results from 11 females of African origin, aged 21–43 years. Serology testing for HIV was conducted according to the national Oman algorithm: fourth-generation immunoassays (Bio-Rad GS HIV Combo Ag/Ab EIA, Siemens Enzygnost HIV Integral 4, Abbott ARCHITECT HIV Ag/Ab Combo, Roche Elecsys HIV Combi PT, bioMérieux VIDAS HIV DUO QUICK), confirmatory assays (Geenius HIV 1/2 Confirmatory, INNO-LIA HIV I/II Score) and PCR testing. Confirmatory testing to resolve indeterminate results was conducted with available samples for five patients using a combination of immunoassays, confirmatory assays, PCR/PERT and pro-viral DNA levels, at three external laboratories; Roche Diagnostics (Germany), Swiss National Laboratory (Switzerland) and Barts Health NHS Trust (UK). Nineteen serum, 15 plasma and two whole-blood samples were analysed. Nine of ten patients analysed on Bio-Rad and Siemens immunoassays were highly reactive; seven were highly reactive on the Abbott assay. Eight of nine patients tested with the Roche assay were negative. Three of four patients tested on the bioMérieux assay were negative. Five patients underwent confirmatory testing at external laboratories; all were negative by HIV-RNA or pro-viral DNA testing. In conclusion, HIV-RNA and pro-viral DNA testing is recommended for HIV screening of individuals from high-prevalence regions coming to low-prevalence regions.

The temporal RNA virome patterns of a lesser dawn bat (Eonycteris spelaea) colony revealed by deep sequencing.

The virosphere is largely unexplored and the majority of viruses are yet to be represented in public sequence databases. Bats are rich reservoirs of viruses, including several zoonoses. In this study, high throughput sequencing (HTS) of viral RNA extracted from swabs of four body sites per bat per timepoint is used to characterize the virome through a longitudinal study of a captive colony of fruit nectar bats, species Eonycteris spelaea in Singapore. Through unbiased shotgun and target enrichment sequencing, we identify both known and previously unknown viruses of zoonotic relevance and define the population persistence and temporal patterns of viruses from families that have the capacity to jump the species barrier. To our knowledge, this is the first study that combines probe-based viral enrichment with HTS to create a viral profile from multiple swab sites on individual bats and their cohort. This work demonstrates temporal patterns of the lesser dawn bat virome, including several novel viruses. Given the known risk for bat-human zoonoses, a more complete understanding of the viral dynamics in South-eastern Asian bats has significant implications for disease prevention and control. The findings of this study will be of interest to U.S. Department of Defense personnel stationed in the Asia-Pacific region and regional public health laboratories engaged in emerging infectious disease surveillance efforts.

Correlation Between Etest and Reference Broth Microdilution for Antimicrobial Susceptibility Testing of Burkholderia pseudomallei.

A three-center study was performed to see if Etest gradient diffusion minimum inhibitory concentration (MIC) methodology correlated with reference broth microdilution (BMD) for antimicrobial susceptibility testing of Burkholderia pseudomallei against six antimicrobial agents known to be usually effective against B. pseudomallei. This study was performed to assist in the decision-making process for possible deployment of the Etest method for antimicrobial susceptibility testing of B. pseudomallei into several regional public health laboratories in the United States. Three laboratories each tested a challenge set of 30 genotypically diverse isolates collected from 15 different countries. MICs were performed by both Etest gradient diffusion and reference BMD for amoxicillin/clavulanate, ceftazidime, doxycycline, imipenem, tetracycline, and trimethoprim/sulfamethoxazole. Etest results for amoxicillin/clavulanate, ceftazidime, doxycycline, and imipenem correlated well with reference BMD by both category interpretation (≥97%) and essential agreement of MIC (≥93%). Tetracycline and trimethoprim/sulfamethoxazole Etests yielded poor correlation with BMD by category interpretation (80%) and essential agreement (70%), respectively. In conclusion, Etest gradient diffusion represents a valid option for antimicrobial susceptibility testing of B. pseudomallei against amoxicillin/clavulanate, ceftazidime, doxycycline, and imipenem. Tetracycline and trimethoprim/sulfamethoxazole Etest results showed some concerning lack of correlation with the corresponding reference BMD results.

Increasing the volume of blood received in adult paired blood culture bottles at a regional public health laboratory: results of a quality improvement project to optimise the diagnosis of bacteraemia

BackgroundOptimising the diagnosis of bacteraemia has clinical, infection control and antimicrobial stewardship benefits. It's well documented that volume of blood received in blood culture bottles affects test sensitivity. The ability of blood cultures to detect bacteraemia is proportional to the volume of blood cultured. We undertook a period of baseline measurement and established that mean blood culture fill volume was inadequate. AimThe primary aim was to increase the percentage of adequately filled blood cultures (≥5ml) by 20% and increase the percentage of optimally filled bottles (8–10ml) by 10% in six months (by 1st August 2018). Our secondary aim was to increase the mean volume in blood culture bottles to 8ml (by 1st August 2018). We measured the clinical impact of this on test sensitivity by comparing blood culture positivity rate between adequately and inadequately filled bottles. MethodsFollowing a period of baseline measurement we implemented three phases of plan/do/study/act (PDSA) intervention cycles (including a small test pilot cycle). Interventions were focused around user education/engagement, real time user feedback and laboratory reporting. User questionnaires were administered to investigate knowledge and practice; further informing the interventions. Results & ConclusionBetween 1st March - 1st August 2018 the mean volume of blood inoculated into culture bottles rose from 5ml (95% CI 4.1–6.0ml) to 7.5ml (95% CI 6.4–8.5ml). The percentage of adequately-filled (≥5ml) blood culture bottles increased from 47% to 61% (absolute increase of 14%) and the percentage of optimally-filled (≥8ml) bottles increased from 16% to 29% (absolute increase of 13%). Although our project didn't fully meet its aims, we observed a significant and sustained improvement in filling of blood culture bottles.

Trends of invasive pneumococcal disease and its serotypes in the Autonomous Community of Madrid

IntroductionStreptococcus pneumoniae is an important cause of morbidity. Vaccination is the most effective measure to prevent it. The aim of this study is to analyse the evolution of invasive pneumococcal disease (IPD). Material and methodsObservational study of IPD cases notified to the Epidemiological Surveillance Network of the Autonomous Community of Madrid between 2008 and 2015. The IPD case was defined as the disease caused by S. pneumoniae, with isolation and DNA or antigen detection, in samples from normally sterile sites. The isolated strains were sent to the Regional Public Health Laboratory for identification of the serotype. Serotypes were classified according to their inclusion in the 7-valent conjugate vaccine (PCV7), in the 13-valent vaccine, but not in the 7-valent vaccine (PCV13-additional) and not included in the 13-valent vaccine (non-PCV). The incidence rate ratios (IRRs) were calculated comparing the 2011–2012 and 2013–2015 periods with the 2008–2010 period. Results4,307 cases were reported. 86.6% were serotyped. The IRR of IPD was 0.67 and 0.67 for all serotypes; 0.43 and 0.45 for PCV7 serotypes; 0.46 and 0.25 for PCV13-additional serotypes, and 1.01 and 1.32 for non-PCV13 serotypes in the 2011–2012 and 2013–2015 periods. The incidence of serotypes 8, 9N, 10A, 23B, 24F and serogroup 33 increased significantly in the 2013–2015 period. Serotypes 15B and 24F accounted for 24% of non-PCV13 cases in children under 5 years, serotypes 8 and 9N for 51% in the population aged 5–59 years and serotypes 8 and 22F for 25% in the population aged over 59 years. ConclusionsThe incidence of serotypes not included in conjugate vaccines has increased, especially in children under 5 years, but the total incidence of IPD has decreased. It is important to continue with the epidemiological and microbiological surveillance programmes to assess the effect of vaccination on the incidence of IPD.

Streamlining Foodborne Disease Surveillance with Open-Source Data Management Software

Objective: The “ledsmanageR”, a data management platform built in R, aims to improve the timeliness and accuracy of national foodborne surveillance data submitted to the Laboratory-based Enteric Disease Surveillance (LEDS) system by automating the data processing, validating, and reporting workflow.Introduction: The National Surveillance Team in the Enteric Diseases Epidemiology Branch of the Centers for Disease Control and Prevention (CDC) collects electronic data from all state and regional public health laboratories on human infections caused by Campylobacter, Salmonella, Shiga toxin-producing E. coli, and Shigella in LEDS. These data inform annual estimates of the burden of illness, assessments of patterns in bacterial subtypes, and can be used to describe trends in incidence. Robust digital infrastructure is required to process, validate, and summarize data on approximately 60,000 infections annually while optimizing use of financial and personnel resources.Methods: We leveraged the robust and extensible programming facilities of the R programming language and the active community of R users to develop a data integration, processing, and reporting pipeline for LEDS via an internal software package we named “ledsmanageR”. We designed all data retrieval, cleaning, and provisioning algorithms using tools from RStudio software packages1–3 and tracked changes to source code and data using CDC’s internal Gitlab server. We automated data validation requests to reporting partners by generating customizable emails directly from the R console4. We streamlined the data reconciliation process using OpenRefine5, a point-and-click tool for cleaning big data. We automated generation of annual reports, a process that was previously manual, using parameterized RMarkdown documents. Staff epidemiologists performed design and implementation internally, requiring no external consulting.Results: Developing our free and open-source software platform for national foodborne surveillance data management has saved the Enteric Diseases Epidemiology Branch thousands of dollars because we no longer depend on proprietary software requiring annual licensing fees. This transition occurred without any disruption in surveillance operations. Partial automation of email-based data validation and annual report generation processes reduced employee time requirement from one full-time position to one part-time position. The modular nature of ledsmanageR permitted LEDS to collect an expanded set of data elements with no changes to the core data processing and reporting workflow.Conclusions: We developed and implemented a flexible tool that helps maintain the integrity of surveillance data and reduces the need for manual data cleaning, which can be laborious and error-prone. The user-friendly design features of ledsmanageR demonstrate that data management can be optimized using programming skills that are increasingly common among epidemiologists. Our work on improving the accuracy and efficiency of enteric disease surveillance has served as a proof of concept for plans to streamline data processing for other surveillance systems.

Evolución de la enfermedad neumocócica invasora y sus serotipos en la Comunidad de Madrid

IntroductionStreptococcus pneumoniae is an important cause of morbidity. Vaccination is the most effective measure to prevent it. The aim of this study is to analyse the evolution of invasive pneumococcal disease (IPD). Material and methodsObservational study of IPD cases notified to the Epidemiological Surveillance Network of the Autonomous Community of Madrid between 2008 and 2015. The IPD case was defined as the disease caused by Streptococcus pneumoniae, with isolation and DNA or antigen detection, in samples from normally sterile sites. The isolated strains were sent to the Regional Public Health Laboratory for identification of the serotype. Serotypes were classified according to their inclusion in the 7-valent conjugate vaccine (PCV7), in the 13-valent vaccine, but not in the 7-valent vaccine (PCV13-additional) and not included in the 13-valent vaccine (non-PCV). The Incidence Rate Ratios (IRRs) were calculated comparing the 2011-2012 and 2013-2015 periods with the 2008-2010 period. Results4,307 cases were reported. 86.6% were serotyped. The IRR of IPD was 0.67 and 0.67 for all serotypes; 0.43 and 0.45 for PCV7 serotypes; 0.46 and 0.25 for PCV13-additional serotypes, and 1.01 and 1.32 for non-PCV13 serotypes in the 2011-2012 and 2013-2015 periods. The incidence of serotypes 8, 9N, 10A, 23B, 24F and serogroup 33 increased significantly in the 2013-2015 period. Serotypes 15B and 24F accounted for 24% of non-PCV13 cases in children under 5years, serotypes 8 and 9N for 51% in the population aged 5 to 59years and serotypes 8 and 22F for 25% in the population aged over 59years. ConclusionsThe incidence of serotypes not included in conjugate vaccines has increased, especially in children under 5years, but the total incidence of IPD has decreased. It is important to continue with the epidemiological and microbiological surveillance programmes to assess the effect of vaccination on the incidence of IPD.

Legionellosis: A Walk-Through to Identification of the Source of Infection

Although a number of human Legionnaires' disease in tourists are recorded annually in Europe, there are few cases where a direct link can be made between the infected person and the source of infection (hotel or other accommodation). We present a scheme followed in order to track down and identify the source of infection in a tourist suffering from L. pneumophila sg 5 infection, who was accommodated in seven different hotels during his holidays in the island of Crete, and we comment on various difficulties and draw-backs of the process. Water samples were collected from the seven hotels where the patient had resided and analyzed at the regional public health laboratory using cultivation and molecular tests. Of 103 water samples analyzed, 19 (18.4%) were positive for Legionella non-pneumophila and 8 (7.8%) were positive for L. pneumophila. A successful L. pneumophila sg 5 match was found between the clinical and environmental sample, which led us to the final identification of the liable hotel. Timely notification of the case, within the the European Legionnaires' Disease Surveillance Network (ELDSNet) of the partners involved, is crucial during a course of travel associated with Legionella case investigation. Moreover, the urinary antigen test alone cannot provide sufficient information for the source identification. However, acquiring clinical as well as environmental isolates for serogroup and SBT identification is highly important for the successful matching.

Prevalence, risk factors and molecular epidemiology of highly resistant gram negative rods in hospitalized patients in the Dutch region Kennemerland

BackgroundThis paper describes (1) the Highly Resistant Gram Negative Rod (HR-GNR) prevalence rate, (2) their genotypes, acquired resistance genes and (3) associated risk factors of HR-GNR colonization among the hospitalized population in the Dutch region Kennemerland.MethodsBetween 1 October 2013 and 31 March 2014, cross-sectional prevalence measurements were performed in three regional hospitals as part of each hospitals infection control program. Rectal swabs were analyzed at the Regional Public Health Laboratory Kennemerland by direct culturing. Genotypes and acquired resistance genes of positive isolates were determined using Whole Genome Sequencing with the MiSeq instrument (Illumina). Association between several independent variables and HR-GNR positivity was examined using logistic regression models.ResultsOut of 427 patients, 24 HR-GNR positive isolates were recovered from 22 patients, resulting in a regional HR-GNR colonization prevalence (95 % CI) of 5.2 % (3.6–7.9). Of these 22 positive patients, 15 were Extended Spectrum Beta-Lactamase (ESBL) positive (3.5 % (2.1–5.7)), 7 patients were positive for a Fluoroquinolones and Aminoglycosides (Q&A) resistant Enterobacteriaceae (1.6 % (0.8–3.3)) and from one patient (0.2 % (0–1.3)) a Stenotrophomonas maltophilia resistant towards co-trimoxazole was isolated. No carbapenemase producing Enterobacteriaceae (CPE), multi-resistant Acinetobacter species or multi-resistant Pseudomonas aeruginosa were isolated. The ESBL genes found were blaCTX-M-1 (n = 4, 25.0 %), blaCTX-M-15 (n = 3, 18.8 %), blaCTX-M-27 (n = 2, 12.5 %), blaCTX-M-14b (n = 2, 12.5 %), blaCTX-M-9 (n = 2, 12.5 %), blaCTX-M-14 (n = 1, 6.3 %), blaCTX-M-3 (n = 1, 6.3 %), blaSHV-11 (n = 1, 6.3 %) and blaSHV-12 (n = 1, 6.3 %). Being known HR-GNR positive in the past was the only significant associated risk factor for HR-GNR positivity, odds ratio (95 % CI): 7.32 (1.82–29.35), p-value = 0.005.ConclusionsSimilar ESBL prevalence rates and genotypes (3.5 %) were found in comparison to other Dutch studies. When previously HR-GNR positive patients are readmitted, they should be screened for HR-GNR colonization since colonization with GR-GNRs could be prolonged. We recommend for future studies to include all defined HR-GNRs in addition to ESBLs in prevalence studies, in order to obtain a more comprehensive overview of colonization with HR-GNRs.

Dennis Mackay Jones

After house jobs, Dennis Mackay Jones embarked on a career in pathology, specialising in medical microbiology. He joined the Public Health Laboratory Service (PHLS) and trained in the Manchester laboratory...

Endolysins: redefining antibacterial therapy.

Bjorn Lars Herpers speaks to Natasha Leeson, Commissioning Editor: Bjorn Lars Herpers was born on 16 February 1974 in Schaesberg. In 1992 he graduated summa cum laude at Gymnasium Rolduc in Kerkrade (The Netherlands) and started to study medical biology at the University of Utrecht. After 3 years, he started to study medicine as well. He graduated cum laude in medical biology in 1999 and obtained his medical degree in 2001. After 1 year of residency in internal medicine at Gooi-Noord Hospital under supervision of DW Erkelens and P Niermeier, he switched to a residency in medical microbiology at the University Medical Center Utrecht and the St Antonius Hospital Nieuwegein under supervision of J Verhoef and B M de Jongh. During his residency, he started to work on his thesis on genetic polymorphisms in MBL and L-ficolin, two complement-activating pattern recognition receptors. In 2009 he became a medical microbiologist and joined the staff at the Regional Public Health Laboratory Kennemerland in Haarlem. Since 2012, he has been involved in clinical research on endolysin therapy in collaboration with Micreos in Bilthoven.

Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response

The rapid advancement of genome technologies holds great promise for improving the quality and speed of clinical and public health laboratory investigations and for decreasing their cost. The latest generation of genome DNA sequencers can provide highly detailed and robust information on disease-causing microbes, and in the near future these technologies will be suitable for routine use in national, regional, and global public health laboratories. With additional improvements in instrumentation, these next- or third-generation sequencers are likely to replace conventional culture-based and molecular typing methods to provide point-of-care clinical diagnosis and other essential information for quicker and better treatment of patients. Provided there is free-sharing of information by all clinical and public health laboratories, these genomic tools could spawn a global system of linked databases of pathogen genomes that would ensure more efficient detection, prevention, and control of endemic, emerging, and other infectious disease outbreaks worldwide.

Enfermedad invasora neumocócica en pediatría: ¿qué puede esperarse de la nueva vacuna conjugada neumocócica 13-valente?

IntroductionThe objective was to analyse the trends of invasive pneumococcal serotypes and antimicrobial resistance patterns in children in the Madrid Autonomous Region (CAM), paying special attention to the first results obtained after the introduction in June 2010 of a 13-valent pneumococcal conjugate vaccine (PCV13). MethodsDuring 2007–2011, 100 cases (96 patients) of invasive pneumococcal disease (IPD) were identified. Susceptibilities to penicillin and cefotaxime were determined by microdilution. The strains were sent to the Madrid Regional Public Health Laboratory for serotyping. ResultsA total of 100 isolates of pneumococcus were made at the Hospital Infantil Niño Jesús, Madrid, 88 in blood and 12 in cerebrospinal fluid. Fifty percent of patients were aged <2 years. Eighteen serotypes were found. Serotype 19A was found in 29% of cases: 55% of IPD in children aged <2 years was due to 19A. Ten percent of isolates were penicillin non-susceptible (PNS) and 4% cefotaxime non-susceptible. Seven out of ten PNS strains were 19A. Serotypes 1, 5, 7F, 6A and 19A decreased after introduction of PVC13. Between 2007 and 2009, there was a progressive increase in IPD due to serotype 19A, with a predominance of penicillin-susceptible strains. This increase decreased slowly in 2010 and 2011 and in 2011 IPD was due in equal parts to susceptible and PNS 19A strains. ConclusionsPCV13 reduced the incidence of IPD due to vaccine serotypes, especially 19A. The reduction was linked to a reduction in penicillin non-susceptibility. Our findings suggest that the impact of PCV13 on pneumococcal colonization could be exercised on a predominantly susceptible population, probably due to the insufficient time after implementation of PCV7 in Madrid.

A Decentralized Molecular Diagnostic Testing Plan for Pandemic Influenza in the Ontario Public Health Laboratory System

The Ontario Public Health Laboratories system (OPHL) is in the midst of a six-year plan to implement molecular tools for pandemic influenza diagnostics in one central and three regional public health laboratories. This plan has been formulated as a consequence of: 1) experiences gained through severe acute respiratory syndrome (SARS), and comments of the members of the Expert Panel on SARS and Infectious Disease Control (i.e., the Walker report); 2) a review of pandemic preparedness literature; 3) historical and epidemiologic discussions about previous pandemics; and 4) suggestions made by various pandemic working committees. The OPHL plan includes: 1) an aggressive restructuring of the overall molecular microbiology testing capacity of the OPHL; 2) the ability to shift influenza testing of samples between designated OPHL laboratories; and 3) the development of screening tools for pandemic influenza diagnostic tests. The authors believe that investing in increased molecular testing capacity for regional laboratories outside the greater Toronto area will be beneficial to the OPHL system whether or not an influenza pandemic occurs. Well-trained technologists and microbiologists, and the introduction of new technologies, will facilitate the development of a wide variety of molecular tests for other infectious diseases at public health laboratories geographically distant from Toronto, thus enhancing overall laboratory testing capacity in the province of Ontario.