Novel locked nucleic acid (LNA)-based probe for the rapid identification of Chlamydia suis using real-time PCR

Development of a Real-Time Reverse Transcription-PCR Assay for Global Differentiation of Yellow Fever Virus Vaccine-Related Adverse Events from Natural Infections

Yellow fever (YF) is a reemerging public health threat, with frequent outbreaks prompting large vaccination campaigns in regions of endemicity in Africa and South America. Specific detection of vaccine-related adverse events is resource-intensive, time-consuming, and difficult to achieve during an outbreak. To address this, we have developed a highly transferable rapid yellow fever virus (YFV) vaccine-specific real-time reverse transcription-PCR (RT-PCR) assay that distinguishes vaccine from wild-type lineages. The assay utilizes a specific hydrolysis probe that includes locked nucleic acids to enhance specific discrimination of the YFV17D vaccine strain genome. Promisingly, sensitivity and specificity analyses reveal this assay to be highly specific to vaccine strain(s) when tested on clinical samples and YFV cell culture isolates of global origin. Taken together, our data suggest the utility of this assay for use in laboratories of varied capacity for the identification and differentiation of vaccine-related adverse events from wild-type infections of both African and South American origin.

Antimicrobial Resistance in Chlamydiales, Rickettsia, Coxiella, and Other Intracellular Pathogens

This article will provide current insights into antimicrobial susceptibilities and resistance of an important group of bacterial pathogens that are not phylogenetically related but share lifestyle similarities in that they are generally considered to be obligate intracellular microbes. As such, there are shared challenges regarding methods for their detection and subsequent clinical management. Similarly, from the laboratory perspective, susceptibility testing is rarely undertaken, though molecular approaches might provide new insights. One should also bear in mind that the highly specialized microbial lifestyle restricts the opportunity for lateral gene transfer and, consequently, acquisition of resistance.

Occurrence of reproductive disorders in pig herds with and without Chlamydia suis infection - statistical analysis of breeding parameters

Chlamydiae are frequently encountered Gram-negative intracellular eubacteria that can cause clear manifestations or clinically asymptomatic disorders. C. suis and other chlamydia are primarily isolated in cases of reproductive disorders. This study was performed to estimate the impact of Chlamydia suis infection on reproduction in sows by analyzing reproduction rates and breeding parameters. The test was conducted on first generation (F1) pigs from Polish Landrace (PL) × Polish Large White (PLW). Sixty-four herds were investigated and 500 vaginal swabs were collected. Isolation of DNA was carried out directly from the swabs. All samples were analyzed for Chlamydia suis by real-time PCR with a locked nucleic acid (LNA)-containing probe. To analyze the impact of chlamydia infection on reproductive parameters, evaluation questionnaires were used. Reproductive problems were found in 77.3% of the farms tested. The receiver operating characteristic curve indicated that in the farms with 10 up to 120 sows, there were higher reproductive problems with chlamydia infection than in smaller and bigger pig farms. The most common problems were estrus repetition, which was reported by 57.81% of the surveyed farms, and the birth of dead piglets, which was reported by 31.25% of the investigated pig farms. Abortions, which were reported by 28.12% of the surveyed farms, were the least common reproductive disorders.

Development of a Chlamydia suis-specific antibody enzyme-linked immunosorbent assay based on the use of a B-cell epitope of the polymorphic membrane protein C

Chlamydia suis infections lead to economic loss in the pork industry. Chlamydia suis infections could be successfully treated with tetracyclines until the appearance of a tetracycline resistant phenotype, which was acquired via horizontal gene transfer of the tet(C) gene. Given the importance of C. suis as a swine pathogen and as a recently emerged tetracycline resistant pathogen with zoonotic potential, our aim was to develop a sensitive C. suis-specific antibody ELISA based on the polymorphic membrane proteins (Pmps). Chlamydia Pmps are important virulence factors and candidate antigens for serodiagnosis. We identified nine Pmps (PmpA to I) in C. suis strain MD56 using a recently developed Hidden-Markov model. PmpC was the most promising candidate for the development of a C. suis-specific antibody ELISA as the protein was absent in C. abortus, C. pecorum and C. psittaci which also infect pigs and as the protein contained C. suis-specific amino acid regions, absent in C. trachomatis PmpC. We identified an immunodominant B-cell epitope in C. suis PmpC using experimental porcine sera. The sensitivity and specificity of the PmpC ELISA was compared to the complement fixation test (CFT) and to a recombinant MOMP ELISA using experimental sera. The PmpC ELISA detected all positive control sera and was in contrast to CFT and the rMOMP ELISA 100% C. suis specific as positive control sera against other Chlamydia species did not react in the PmpC ELISA. The test was successfully validated using slaughterhouse sera and sera from clinically affected pigs. The PmpC ELISA could assist in diminishing the spread of C. suis infections in the pork industry.

Chlamydia prevalence in Polish pig herds

Chlamydiae are frequently encountered intracellular Gram-negative bacteria. In pigs, these bacteria in combination with other pathogens contribute to the induction of a multi-aetiological syndrome. One of the major characteristics of Chlamydia spp. is their ability to cause prolonged, often subclinical infections. While the economic consequences of Chlamydia spp. infections in pig farms are not fully established, we know that reproductive disorders and other syndromes correlated with Chlamydia infection can lead to financial loss as a result of a reduction in pork production. Additionally, Chlamydia spp. presents a potential zoonotic hazard, therefore determining the prevalence of Chlamydia in pig populations is critical. In the present study 97 pig herds from Poland were involved. To determine the prevalence of Chlamydia PCR and CFT tests were used. In total 797 vaginal samples, 797 conjunctival samples, and 235 serum samples were collected and tested. The study took place from 2011 to 2014. We found Chlamydia spp. present in 71·2% of all tested farms. The percentage of animals testing positive on any given farm varied from 20% to 100%.

Locked Nucleic Acid Probe-Based Real-Time PCR Assay for the Rapid Detection of Rifampin-Resistant Mycobacterium tuberculosis

Drug-resistant Mycobacterium tuberculosis can be rapidly diagnosed through nucleic acid amplification techniques by analyzing the variations in the associated gene sequences. In the present study, a locked nucleic acid (LNA) probe-based real-time PCR assay was developed to identify the mutations in the rpoB gene associated with rifampin (RFP) resistance in M. tuberculosis. Six LNA probes with the discrimination capability of one-base mismatch were designed to monitor the 23 most frequent rpoB mutations. The target mutations were identified using the probes in a “probe dropout” manner (quantification cycle = 0); thus, the proposed technique exhibited superiority in mutation detection. The LNA probe-based real-time PCR assay was developed in a two-tube format with three LNA probes and one internal amplification control probe in each tube. The assay showed excellent specificity to M. tuberculosis with or without RFP resistance by evaluating 12 strains of common non-tuberculosis mycobacteria. The limit of detection of M. tuberculosis was 10 genomic equivalents (GE)/reaction by further introducing a nested PCR method. In a blind validation of 154 clinical mycobacterium isolates, 142/142 (100%) were correctly detected through the assay. Of these isolates, 88/88 (100%) were determined as RFP susceptible and 52/54 (96.3%) were characterized as RFP resistant. Two unrecognized RFP-resistant strains were sequenced and were found to contain mutations outside the range of the 23 mutation targets. In conclusion, this study established a sensitive, accurate, and low-cost LNA probe-based assay suitable for a four-multiplexing real-time PCR instrument. The proposed method can be used to diagnose RFP-resistant tuberculosis in clinical laboratories.