Health Service Executive Dublin Mid-Leinster. Public Health Laboratory Cherry Orchard Hospital Ballyfermot Dublin 10

Transcription

1 Health Service Executive Dublin Mid-Leinster Public Health Laboratory Cherry Orchard Hospital Ballyfermot Dublin 10 Tel: Fax: Annual Report For the year ended 31 st Dec

2 Contents Introduction Page 3 Accreditation Page 4 LIMS Page 4 Total Laboratory workload Page 5 Clinical Laboratory workload Page 5 Food Laboratory workload Page 6 Unsatisfactory Foods Page 7 Water Laboratory workload Page 7 Unsatisfactory Waters Page 9 VTEC Page 10 Staff Page 15 Education /Research Page 15 Publications Page 16 Presentations Page 17 Future Developments Page 17 2

3 INTRODUCTION The Public Health Laboratory, located in, and is administered by HSE Dublin Mid-Leinster in the grounds of Cherry Orchard Hospital. Its aim is to provide the most effective and efficient service possible to support the diagnosis, prevention and control of infectious communicable diseases and food borne illnesses. The laboratory provides a range of microbiological services: 1. A National Verocytotoxin E. coli diagnostic clinical service accessed by Consultant Microbiologist and Laboratory Directors; 2. A Regional Public Health Microbiology service accessed by the Environmental Health Service and Public Health Doctors; 3. A local routine clinical microbiology diagnostic service for hospital inpatients and utilised by General Practitioners in the surrounding region. The Public Health Laboratory, which is accredited ( to ISO 17025) and is an EU Official designated Food testing laboratory (S.I. 85 of 1998 and S.I. 117 of 2010) has developed robust operational protocols implemented by a highly skilled technical and medical staff experienced in surveillance and the investigation of outbreaks of communicable disease. Close working liaisons are established with the Environmental Health Service, Public Health Medical Service, Food Safety Authority of Ireland, Safe Food, and Health Protection Surveillance Centre, all of which are major stake holders in the public health of this region. Scope of the laboratory Since 1998 the PHL-HSE-DML has been providing a VTEC diagnostic service based on phenotypic methods. This service was extended in 2002 to a National service incorporating molecular typing facilities. Current VTEC diagnostic facilities at PHL, HSE, DML include: 3

4 Sample analysis for E. coli O157 and non-o157 utilising enrichment and IMS methodology E. coli serotyping for O157 and non-o157 Verotoxin analysis by PCR PCR analysis for VT1 and VT2, eae genes from O157 and non- O157 isolates. O26, O145, O121 and O111 PCR PFGE, this has been utilised in outbreak investigations. The PHL is a member of PulseNet Europe The PHL is a member of Enter-Net. Participation in this enteric surveillance network means that the PHL is at the forefront of recognising food and water-borne VTEC infection and will enable investigations to be mounted to identify contaminated sources and thus protect consumers in an EU context. The routine clinical diagnostic service provides a microbiological service for hospital inpatients and can be utilised by General Practitioners in the surrounding region. This service includes analysis of Faecal, urine, swabs, blood and sputum samples. Accreditation The food and water microbiology service is accredited since 1998 by the National Accreditation Board to the current ISO Standard and is an official designated food microbiology laboratory (under S.I 85 of 1998 and S.I. 117 of 2010). For full scope of accreditation see appendix A. LIMS In February 2006 the PHL went live in Foods and with its Laboratory Information Management System, LabWare LIMS. The use of LIMS in the PHL was accredited by INAB in LIMS went live in 2008 for the Clinical laboratory encompassing VTEC and TB. 4

5 Laboratory Workload Table 1: Total Laboratory Workload in 2009 Samples Tests Food Water Clinical VTEC Total Table 2: Breakdown of Clinical Laboratory Workload in 2009 Clinical Sample Type Number of Samples Number of Tests Urine Swabs Stool Blood Culture TB Sputum VTEC: VTEC Stools Isolate Confirmation PCR PFGE Total

6 Foods Table 3: Source of food samples received in 2009 Food Category Number of % change from 2008 samples Routine Hospital Control Outbreak Food Poisoning Follow Up Repeats Surveys Total Table 4: parameters of food tests performed in 2009 Food Samples 4101 Tests Number Aerobic Colony Count 3166 Enumeration of Escherichia coli 3218 Enumeration of coagulase positive Staphylococcus 3258 Enumeration of Bacillus species including presumptive Bacillus cereus 1999 Enumeration of Clostridium perfringens 1769 Detection of Salmonella species 3084 including S.enteritidis and S.typhimurium by culture and vidas Detection and Enumeration of 3582 L.monocytogenes and Other Listeria species Detection of Campylobacter species 901 including C.jejuni and C.coli by culture and vidas Enumeration of Enterobacteriaceae 1270 Detection of Escherichia coli O157 by Immuno Magnetic Separation (IMS) 76 Total number of tests

7 Table 5: RTE food compliance results in 2009 Paramater No. Tested Satisfactory Unsatisfactory(%)* A.C.C (12.4) E. coli (<1) Coag Pos Staph (<1) B. cereus (<1) C. perfringens (<1) Listeria Detection (<1) Listeria Enumeration (<1) Enterobacteriaceae (6.8) E. coli O (0) Salmonella (0) Campylobacter (<1) Total (2.3) * RTE guidelines FSAI guidance note E. coli O146 was isolated according to non accredited methods Waters Table 6: Water sample categories received in 2009 Water Category Number Tested % Change on 2008 Potable: Public Supply Private Supply Bottled 1 88 Ice 7 0 Hydrotherapy pool Spa/Swimming pool Endoscopy Seawater Other IQC/EQA River

8 Not Stated Total % Table 6: Water test parameters performed in 2009 Water samples 3062 Tests Number Enumeration and confirmation of 82 Coliform Bacteria Enumeration of E coli 86 Enumeration and confirmation of 785 Enterococci Enumeration and confirmation of 375 Clostridium perfringens Enumeration of Total Plate Counts 78 Enumeration and confirmation of Ps aeruginosa Detection and enumeration of Coliform 1658 Bacteria and E. coli by IDEXX Quantitray Detection of E coli 0157 Using IMS 243 Detection of Salmonella spp. by VIDAS 204 and/or by culture Total Viable Count for 1119 Environmental/Endoscopy water Detection of Mycobacterium spp. 144 Detection and Enumeration of Legionella 165 species by membrane filtration Total number of tests

9 Table 7: Non-compliant water results in 2009 Parameter Water category No. Unsatisfactory (%) Coliforms Potable 90 (11) Ice 3 (43) Seawater 38 (9) Hydrotherapy 3 (<1) E. coli Seawater 28 (7) Potable 54 (7) Enterococci Potable 48 (6) C. perfringens Potable 27 (3) Total plate count Potable 3 (<1) 36 o C 48 hrs P. aeruginosa Endoscopy 4 (<1) Hydrotherapy 3 (<1) E. coli O157 Potable 8^ (1) Total Viable Count Endoscopy 172 (21)* Prefilter 17 Postfilter 155 Potable 7 (<1) Micobacterium spp Endoscopy 4 (<1) Total 492 (16) *Official regulations state allowable limit as 0 cfu/ml, in this case 100% of samples were unsatisfactory. However in practice <10 cfu/ml is considered acceptable, thus 12.3% of samples were nono-compliant ^ One E. coli O26 was also isolated from a potable water 9

10 VTEC The Public Health Laboratory-HSE-Dublin Mid Leinster would like to thank all our colleagues for sending samples and isolates for VTEC detection and confirmation in As a result, for the 7 th year we have a complete national laboratory database of clinical VTEC infection in the Republic of Ireland was another busy year for the VTEC lab, with 3550 samples screened for VTEC, an increase of 48% on isolates were VTEC positive, this is an increase of 7.5% on 2008 and is a rate of approx 5.6/ (highest incidence in Europe based on 2008 data). The majority of VTEC isolates were VTEC O157 (n=165) 68%, however as in previous years the proportion of non-o157 VTEC is increasing (n=75) 32%. The most notable change in clinical VTEC is the diversity of non-o157 VTEC. In 2009 the non-o157 VTEC were composed of 60% O26 (n= 45) and most notably 40% other Serogroups (n=30).this highlights the challenges faced by diagnostic laboratories in identifying the growing number of non-o157 VTEC and also the importance of utilising DNA methodology in VTEC detection. In 2009 the PHL continued typing VTEC via Pulsed field Gel Electrophoresis (PFGE) according to public health priority and the profiles entered into the database. This database allows comparison of inter and intra outbreak isolates and hence aid VTEC outbreak investigations. In 2009 teleconferences were held periodically with HPSC to review laboratory and epidemiological VTEC data. VTEC typing data was sent to HPSC on a monthly basis during busy periods and a quarterly basis in quieter periods, this data together with the enhanced VTEC epidemiological data collected by HPSC was forwarded to ECDC by HPSC. After a review of Public Health significance and a cost analysis, we have decided that for 2010 we will not be accessing a routine phage typing service in HPA- UK. However we will provide an enhanced PFGE typing service. PFGE will be carried out on all isolates in a timely manner and a report produced for each outbreak. PFGE is a lot more discriminatory than Phage typing; as such, we do not envisage any gap in surveillance knowledge. Attached are tables and graphs that show the 2009 data in greater detail. If you have any queries relating to this data or our VTEC services please do not hesitate to contact us. We look forward to continued service provision in 2010 and are happy to continue receiving high risk primary samples for VTEC analysis, however, we do request that urgent samples are preceded by a phone call and accompanied by a completed PHL-VTEC request form. Attached is a copy of our VTEC request form, we would greatly appreciate if all samples and isolates for VTEC screening, 10

11 confirmation and typing could be accompanied by this form. Also attached is an outbreak information form, we would be grateful if Public Health personnel could complete this and e mail it to the PHL prior to sending outbreak samples. Table 1: PHL-HSE-DML VTEC workload Year No. Samples Analysed* * Stool and isolates Serotype No. (%) VT1 pos (%) VT2 pos (%) VT1+ VT2 (%) O (68.5) 0(0) 147(89) 18(11) O26 45(18.75)) 19(42) 23(51) 3(7) O103 3(1.25) 3(100) 0(0) 0(0) O145 3(1.25) 0(0) 3(100) 0(0) O105ac 3(1.25) 0(0) 3(100) 0(0) O78 1(.5) 0(0) 1(100) 0(0) O21 2(.75) 0(0) 2(100) 0(0) O3 1(.5) 1(100) 0(0) 0(0) O55 1(.5) 1(100) 0(0) 0(0) O5 1(.5) 1(100) 0(0) 0(0) O unidentifiable 15(6.25) 3(20) 8(53)* 4(27)* Total 240(100) 28(12) 187(78) 25(10) Table 2: Serogrou ps and toxin types of VTEC in ROI in 2009 * 3 samples were VTEC PCR positive only and culture negative (2=VT2 positive and 1=VT1+VT2positive) 11

12 Incidence/ Total O157 non-o Year 2004 Year 2005 Year 2006 Year 2007 Year 2008 Year 2009 Fig 1: VTEC incidence/100000, RoI Serogroups 100% 90% 80% 70% % of VTEC isolates 60% 50% 40% Other O26 O157 30% 20% 10% 0% year 2004 year 2005 year 2006 year 2007 year 2008 year 2009 Year Fig2: VTEC Serogroups RoI 12

13 Table 3: Phage types of VTEC O157 in ROI in 2009 Phage Type No. % PT PT 21/ PT PT PT PT Others 7 4 RDNC 9 6 To follow Total Note: Phage typing was performed at HPA Colindale Major Phage Types % of O Phage Type 32 Phage Type 8 Phage Type21/28 Phage Type 14 Phage Type year 2004 year 2005 year 2006 year 2007 year 2008 year 2009 Year Fig 3: Major E. coli O157 Phage Types

14 PFGE To Date approx 70% of all 2009 VTEC isolates have been typed using PFGE, The remaining 30% are being typed retrospectively and will be completed by February Below is an example of a PFGE report sent out in Pulse-Field Gel Electrophoresis of outbreak E2009-Sept-03 Dice (Opt:0.50%) (Tol 1.0%-1.0%) (H>0.0% S>0.0%) [0.0%-100.0%] PFGE PFGE E. coli. E. coli. E. coli to follow to follow O103 E2009-sept. 09-S1897 E2009-sept. 09-S1879 E2009-sept. 09-S1830 Dublin Dublin Dublin VT1 VT1 VT1 PFGE Interpretation; S1897 and S1879 have a one band difference and are therefore considered closely related. S1830 has a different PFGE pattern to both S1897 and S1879 and is therefore unrelated to either. ECDC has taken over responsibility for PulseNet Europe and it is hoped that this PFGE network will resume operation in 2010, when this happens Irish VTEC PFGE profiles will be submitted to PulseNet Europe for strain type assignment and international comparison. 14

15 PHL Staff Position WTE Consultant Microbiologist 1 Chief Medical Scientist 1 Senior Medial Scientist 6 Basic Grade Medical scientist 12 Laboratory Aide 2 Surveillance scientist ½ Molecular Biologist ½ Clerical 3 Education/Research External projects/research The PHL participated in the following research projects and surveillance networks in 2009 Pathogenic E. coli Network (PEN) Partner PulseNet Europe European Antimicrobial Resistance Surveillance System (EARSS) European Centre for Disease Control (ECDC) Food and waterborne disease network. Republic of Ireland Verocytotoxigenic E. coli Network Food Institutional Research Measure (FIRM); Public health significance of emergent Campylobacter and Arcobacter spp. in the Irish Food chain. 15

16 Four members of Staff carried out research projects to successfully complete the MSc in biomedical science from the University of Ulster. Project titles were as follows: The prevalence of nasal carriage of MRSA among hospital staff in a non acute hospital setting Virulence PCR analysis and PFGE profiling of campylobacter isolates from humans Rapid detection of verocytotoxigenic E. coli in potable water supplies Evaluation o novel real-time multiplex PCR in the detection of VTEC in human clinical stool samples Publications Epidemiology of Verotoxigenic E. coli In Ireland, 2008, Epi-Insight, Volume 10 issue 9, September 2009 Lenahan M, O'Brien SB, Byrne C, Ryan M, Kennedy CA, McNamara EB, Fanning S, Sheridan JJ, Sweeney T. Molecular characterization of Irish E. coli O157:H7 isolates of human, bovine, ovine and porcine origin. J Appl Microbiol Oct;107(4): Epub 2009 Apr 18. McGill K, Kelly L, Madden RH, Moran L, Carroll C, O'Leary A, Moore JE, McNamara E, O'Mahony M, Fanning S, Whyte P.Comparison of disc diffusion and epsilometer (E-test) testing techniques to determine antimicrobial susceptibility of Campylobacter isolates of food and human clinical origin. J Microbiol Methods Nov;79(2): Epub 2009 Sep 28. M B O Sullivan 1, P Garvey 2, M O Riordan 1, H Coughlan 1, P McKeown 2, A Brennan 1, E McNamara 3. INCREASE IN VTEC CASES IN THE SOUTH OF IRELAND: LINK TO PRIVATE WELLS? Eurosurveillance, Volume 13, Issue 39, 25 September

17 Presentations Pathogenic E. coli Network Development Of The National VTEC Laboratory Service To Meet The Challenges Of Evolving VTEC Infections In Ireland Irish VTEC Network VTEC 2008:Incidence and Issues Table 9: courses/conferences attended in 2008 COURSE/CONFERENCE ORGANISERS No of attendees Food Seminar Oxoid 3 The national trust for Ireland An Taisce 1 Beach seminar Internal audit workshop Safefood 1 Sense and susceptibility AMLS 2 Clinical Safety Seminar VWR 1 The evolution of food safety FSAI MSc in Biomedical Science University of 4 awarded Ulster Food and water microbiology Health Protection 1 quality conference Agency PEN conference Pathogenic E. coli 6 network Food and waterborne disease ECDC 1 network Irish VTEC Network Teagasc/Safefood 1 Msc Biomedical Science (year 2) University of 1 Ulster Coleraine ECCMID 1 ICAAC 1 Future Developments The PHL will continue the clinical accreditation project in 2010 A PHL website will be setup in