Multiplex PCR and reverse line blot hybridization assay (mPCR/RLB)

Ticks on wild boar in the metropolitan area of Barcelona (Spain) are infected with spotted fever group rickettsiae

Tick-borne pathogens (TBPs) constitute an emerging public health concern favoured by multidimensional global changes. Amongst these, increase and spread of wild boar (Sus scrofa) populations are of special concern since this species can act as a reservoir of zoonotic pathogens and promote tick abundance. Thus, we aimed to make a first assessment of the risk by TBPs resulting from wild boar and ticks in the vicinity of a highly populated area. Between 2014 and 2016, we collected spleen samples and 2256 ticks from 261 wild boars (out of 438 inspected) in the metropolitan area of Barcelona (MAB; northeast Spain). We morphologically identified four tick species: Hyalomma lusitanicum (infestation prevalence: 33.6%), Dermacentor marginatus (26.9%), Rhipicephalus sanguineus sensu lato (18.9%) and R. bursa (0.2%). Ticks were pooled according to species and individual host. A total of 180 tick pools and 167 spleen samples were screened by real-time PCR and/or reverse line blot hybridization assay for Ehrlichia sp., Anaplasma sp., Babesia sp., Rickettsia sp., Borrelia burgdorferi sensu lato and Coxiella burnetii. Seventy-two out of the 180 tick pools were positive to Rickettsia spp. (minimum prevalence of 8.7%), including Rickettsia massiliae, R. slovaca and R. raoultii. We did not detect Rickettsia spp. in wild boar spleens nor other TBPs in ticks or wild boars. Since the ticks identified can bite humans, and the recorded spotted fever group (SFG) rickettsiae are zoonotic pathogens, there is a risk of SFG rickettsiae transmission for MAB inhabitants. Our results suggest a broader distribution of H. lusitanicum, competent vector for the Crimean-Congo haemorrhagic fever virus than previously known. Wild boar is not a Rickettsia spp. reservoir according to the spleen negative results. However, its abundance could favour tick life cycle and abundance, and its proximity to humans could promote the infection risk by Rickettsia spp.

Results of the first external quality assessment scheme (EQA) for isolation and analysis of circulating tumour DNA (ctDNA)

BACKGROUND

Circulating tumour DNA (ctDNA) is considered to have a high potential for future management of malignancies. This pilot external quality assessment (EQA) scheme aimed to address issues of analytical quality in this new area of laboratory diagnostics.

METHODS

The EQA scheme consisted of three 2-mL EDTA-plasma samples spiked with fragmented genomic DNA with a mutant allele frequency ranging from 0% to 10% dedicated to the analysis of nine known sequence variations in KRAS codon 12/13 and of BRAF V600E. Laboratories reported: (1) time elapsed for processing, (2) storage temperatures, (3) methods for extraction and quantification, (4) genotyping methodologies and (5) results.

RESULTS

Specimens were sent to 42 laboratories from 10 European countries; 72.3% reported to isolate cell-free DNA (cfDNA) manually, 62.5% used the entire plasma volume for cfDNA isolation and 38.5% used >10% of cfDNA extracted for downstream genotyping. Of the methods used for quantification, PicoGreen demonstrated the lowest coefficient of variation (33.7%). For genotyping, 11 different methods were reported with the highest error rate observed for Sanger sequencing and the lowest for highly sensitive approaches like digital PCR. In total, 197 genotypes were determined with an overall error rate of 6.09%.

CONCLUSIONS

This pilot EQA scheme illustrates the current variability in multiple phases of cfDNA processing and analysis of ctDNA resulting in an overall error rate of 6.09%. The areas with the greatest variance and clinical impact included specimen volume, cfDNA quantification method, and preference of genotyping platform. Regarding quality assurance, there is an urgent need for harmonisation of procedures and workflows.

Comparison of a Real-Time Multiplex PCR and Sequetyping Assay for Pneumococcal Serotyping

BACKGROUND

Pneumococcal serotype identification is essential to monitor pneumococcal vaccine effectiveness and serotype replacement. Serotyping by conventional serological methods are costly, labour-intensive, and require significant technical expertise. We compared two different molecular methods to serotype pneumococci isolated from the nasopharynx of South African infants participating in a birth cohort study, the Drakenstein Child Health Study, in an area with high 13-valent pneumococcal conjugate vaccine (PCV13) coverage.

METHODS

A real-time multiplex PCR (rmPCR) assay detecting 21 different serotypes/-groups and a sequetyping assay, based on the sequence of the wzh gene within the pneumococcal capsular locus, were compared. Forty pneumococcal control isolates, with serotypes determined by the Quellung reaction, were tested. In addition, 135 pneumococcal isolates obtained from the nasopharynx of healthy children were tested by both serotyping assays and confirmed by Quellung testing. Discordant results were further investigated by whole genome sequencing of four isolates.

RESULTS

Of the 40 control isolates tested, 25 had a serotype covered by the rmPCR assay. These were all correctly serotyped/-grouped. Sequetyping PCR failed in 7/40 (18%) isolates. For the remaining isolates, sequetyping assigned the correct serotype/-group to 29/33 (88%) control isolates. Of the 132/135 (98%) nasopharyngeal pneumococcal isolates that could be typed, 69/132 (52%) and 112/132 (85%) were assigned the correct serotype/-group by rmPCR and sequetyping respectively. The serotypes of 63/132 (48%) isolates were not included in the rmPCR panel. All except three isolates (serotype 25A and 38) were theoretically amplified and differentiated into the correct serotype/-group with some strains giving ambigous results (serotype 13/20, 17F/33C, and 11A/D/1818F). Of the pneumococcal serotypes detected in this study, 69/91 (76%) were not included in the current PCV13. The most frequently identified serotypes were 11A, 13, 15B/15C, 16F and 10A.

CONCLUSION

The rmPCR assay performed well for the 21 serotypes/-groups included in the assay. However, in our study setting, a large proportion of serotypes were not detected by rmPCR. The sequetyping assay performed well, but did misassign specific serotypes. It may be useful for regions where vaccine serotypes are less common, however confirmatory testing is advisable.

Tick-borne haemoparasites in African buffalo (Syncerus caffer) from two wildlife areas in Northern Botswana

BACKGROUND

The African buffalo (Syncerus caffer) is a host for many pathogens known to cause economically important diseases and is often considered an important reservoir for livestock diseases. Theileriosis, heartwater, babesiosis and anaplasmosis are considered the most important tick-borne diseases of livestock in sub-Saharan Africa, resulting in extensive economic losses to livestock farmers in endemic areas. Information on the distribution of tick-borne diseases and ticks is scarce in Northern Botswana. Nevertheless, this data is necessary for targeting surveillance and control measures in livestock production at national level.

METHODS

In order to address this gap, we analyzed 120 blood samples from buffalo herds for the presence of common tick-borne haemoparasites causing disease in livestock, collected in two of the main wildlife areas of Northern Botswana: the Chobe National Park (CNP, n=64) and the Okavango Delta (OD, n=56).

RESULTS

Analysis of the reverse line blot (RLB) hybridization assay results revealed the presence of Theileria, Babesia, Anaplasma and Ehrlichia species, either as single or mixed infections. Among the Theileria spp. present, T. parva (60%) and T. mutans (37%) were the most prevalent. Other species of interest were Anaplasma marginale subsp. centrale (30%), A. marginale (20%), Babesia occultans (23%) and Ehrlichia ruminantium (6%). The indirect fluorescent antibody test (IFAT) indicated 74% of samples to be positive for the presence of T. parva antibodies. Quantitative real-time PCR (qPCR) detected the highest level of animals infected with T. parva (81% of the samples). The level of agreement between the tests for detection of T. parva positive animals was higher between qPCR and IFAT (kappa=0.56), than between qPCR and RLB (kappa=0.26) or the latter and IFAT (kappa=0.15).

CONCLUSIONS

This is the first report of tick-borne haemoparasites in African buffalo from northern Botswana, where animals from the CNP showed higher levels of infection than those from OD. Considering the absence of fences separating wildlife and livestock in the CNP and the higher levels of some parasite species in buffalo from that area, surveillance of tick-borne diseases in livestock at the interface in the CNP should be prioritized.

Serotyping of Streptococcus pneumoniae based on capsular genes polymorphisms

Streptococcus pneumoniae serotype epidemiology is essential since serotype replacement is a concern when introducing new polysaccharide-conjugate vaccines. A novel PCR-based automated microarray assay was developed to assist in the tracking of the serotypes. Autolysin, pneumolysin and eight genes located in the capsular operon were amplified using multiplex PCR. This step was followed by a tagged fluorescent primer extension step targeting serotype-specific polymorphisms. The tagged primers were then hybridized to a microarray. Results were exported to an expert system to identify capsular serotypes. The assay was validated on 166 cultured S. pneumoniae samples from 63 different serotypes as determined by the Quellung method. We show that typing only 12 polymorphisms located in the capsular operon allows the identification at the serotype level of 22 serotypes and the assignation of 24 other serotypes to a subgroup of serotypes. Overall, 126 samples (75.9%) were correctly serotyped, 14 were assigned to a member of the same serogroup, 8 rare serotypes were erroneously serotyped, and 18 gave negative serotyping results. Most of the discrepancies involved rare serotypes or serotypes that are difficult to discriminate using a DNA-based approach, for example 6A and 6B. The assay was also tested on clinical specimens including 43 cerebrospinal fluid samples from patients with meningitis and 59 nasopharyngeal aspirates from bacterial pneumonia patients. Overall, 89% of specimens positive for pneumolysin were serotyped, demonstrating that this method does not require culture to serotype clinical specimens. The assay showed no cross-reactivity for 24 relevant bacterial species found in these types of samples. The limit of detection for serotyping and S. pneumoniae detection was 100 genome equivalent per reaction. This automated assay is amenable to clinical testing and does not require any culturing of the samples. The assay will be useful for the evaluation of serotype prevalence changes after new conjugate vaccines introduction.

Software for selecting the most informative sets of genomic loci for multi-target microbial typing

Background

High-throughput sequencing can identify numerous potential genomic targets for microbial strain typing, but identification of the most informative combinations requires the use of computational screening tools. This paper describes novel software – Automated Selection of Typing Target Subsets (AuSeTTS) - that allows intelligent selection of optimal targets for pathogen strain typing. The objective of this software is to maximise both discriminatory power, using Simpson’s index of diversity (D), and concordance with existing typing methods, using the adjusted Wallace coefficient (AW). The program interrogates molecular typing results for panels of isolates, based on large target sets, and iteratively examines each target, one-by-one, to determine the most informative subset.

Results

AuSeTTS was evaluated using three target sets: 51 binary targets (13 toxin genes, 16 phage-related loci and 22 SCCmec elements), used for multilocus typing of 153 methicillin-resistant Staphylococcus aureus (MRSA) isolates; 17 MLVA loci in 502 Streptococcus pneumoniae isolates from the MLVA database (http://www.mlva.eu) and 12 MLST loci for 98 Cryptococcus spp. isolates.

The maximum D for MRSA, 0.984, was achieved with a subset of 20 targets and a D value of 0.954 with 7 targets. Twelve targets predicted MLST with a maximum AW of 0.9994. All 17 S. pneumoniae MLVA targets were required to achieve maximum D of 0.997, but 4 targets reached D of 0.990. Twelve targets predicted pneumococcal serotype with a maximum AW of 0.899 and 9 predicted MLST with maximum AW of 0.963. Eight of the 12 MLST loci were sufficient to achieve the maximum D of 0.963 for Cryptococcus spp.

Conclusions

Computerised analysis with AuSeTTS allows rapid selection of the most discriminatory targets for incorporation into typing schemes. Output of the program is presented in both tabular and graphical formats and the software is available for free download from http://www.cidmpublichealth.org/pages/ausetts.html.

Prospective genotyping of hospital-acquired methicillin-resistant Staphylococcus aureus isolates by use of a novel, highly discriminatory binary typing system

In settings of high methicillin-resistant Staphylococcus aureus (MRSA) prevalence, detection of nosocomial transmission events can be difficult without strain typing. Prospective typing of all MRSA isolates could potentially identify transmission in a timely fashion, making infection control responses to outbreaks more effective. We describe the development and evaluation of a novel 19-target binary typing system for MRSA using the multiplex-PCR/reverse line blot hybridization platform. Pulse-field gel electrophoresis (PFGE), spa typing, and phage-derived open reading frame (PDORF) typing were performed for comparison. The system was utilized to identify transmission events in three general surgical wards over a 12-month period. Initial MRSA isolates from 273 patients were differentiated into 55 unique binary types. One or more potential contacts colonized with the same MRSA strain were identified in 69 of 87 cases (79%) in which definite or possible nosocomial MRSA acquisition had occurred. The discriminatory power of the typing system was similar to that of PFGE (Simpson's index of diversity [D] = 0.994, versus 0.987) and higher than that of spa typing (D = 0.926). Strain typing reduced the total number of potential MRSA-colonized source contacts from 859 to 212 and revealed temporal clustering of transmission events. Prospective MRSA typing using this novel binary typing method can rapidly identify nosocomial transmission events, even in high-prevalence settings, which allows timely infection control interventions. The system is rapid, inexpensive, discriminatory, and suitable for routine, high-throughput use in the hospital microbiology laboratory.

Quantitative estimation of the stability of methicillin-resistant Staphylococcus aureus strain-typing systems by use of Kaplan-Meier survival analysis

Knowledge concerning stability is important in the development and assessment of microbial molecular typing systems and is critical for the interpretation of their results. Typing system stability is usually measured as the fraction of isolates that change type after several in vivo passages, but this does not necessarily reflect in vivo stability. The aim of this study was to utilize survival analysis to provide an informative quantitative measure of in vivo stability and to compare the stabilities of various techniques employed in typing methicillin-resistant Staphylococcus aureus (MRSA). We identified 100 MRSA pairs (isolated from the same patient ≥ 1 month apart) and typed them using multilocus sequence typing (MLST), phage-derived open reading frame (PDORF) typing, toxin gene profiling (TGP), staphylococcal cassette chromosome mec (SCCmec) subtyping, pulsed-field gel electrophoresis (PFGE), and spa sequence typing. Discordant isolate pairs, belonging to different MLST clonal complexes, were excluded, leaving 81 pairs for analysis. The stabilities of these methods were examined using Kaplan-Meier survival analysis, and discriminatory power was measured by Simpson's index of diversity. The probability percentages that the type remained unchanged at 6 months for spa sequence typing, TGP, multilocus variable number of tandem repeats analysis (MLVA), SCCmec subtyping, PDORF typing, and PFGE were 95, 95, 88, 82, 71, and 58, respectively, while the Simpson's indices of diversity were 0.48, 0.47, 0.70, 0.72, 0.89, and 0.88, respectively. Survival analysis using sequential clinical isolates adds an important quantitative dimension to the measurement of stability of a microbial typing system. Of the methods compared here, PDORF typing provides high discriminatory power, comparable with that of PFGE, and a level of stability suitable for MRSA surveillance and outbreak investigations.