Standardization of DNA extraction from sand flies: Application to genotyping by next generation sequencing

Genetic diversity and haplotype analysis of Leishmania tropica identified in sand fly vectors of the genera Phlebotomus and Sergentomyia using next-generation sequencing technology

Next-generation sequencing (NGS) was used to investigate the genetic diversity of Leishmania tropica in the sand fly vector, targeting the internal transcribed spacer 1 (ITS1) of the genus Leishmania. Bioinformatics analyses were conducted using Galaxy, MEGA version X, DnaSP ver. 6.12.03, and PopART 1.7 software for NGS analysis, phylogenetic tree, genetic diversity, and haplotype networking, respectively. A total of 307 engorged sand flies were trapped, with an overall Leishmania infection rate of 9.4 (29/307) and 6.8% by NGS and ITS1-PCR, respectively. Two Leishmania-infected sand fly genera were identified: Phlebotomus (10.2%, 26/254) and Sergentomyia (5.7% (3/53). The phylogenetic tree showed two clusters, cluster I included the four study sequences along with 25 GenBank-retrieved DNA sequences. Cluster II consisted of three sequences from Iran and Pakistan. The genetic diversity analysis for the 29 L. tropica sequences showed high haplotype (gene) diversity index (Hd) (0.62 ± 0.07) but low nucleotide diversity index (π) (0.04 ± 0.01). Tajima's D, a neutrality test, is more negative in cluster I (D = - 2.0) than in total population (D = - 1.83), but both are equally significant (P < 0.001), indicating that observed variation in cluster I and whole population is less frequent than expected. The median-joining haplotype network produced a total of 11 active haplotypes. In conclusion, L. tropica from sand flies in Palestine is monophyletic that assembled in one main phylogroup and one haplotype.

Optimized protocols for chromatin immunoprecipitation of exogenously expressed epitope-tagged proteins

Chromatin immunoprecipitation (ChIP) assay is widely used for investigating the interaction between DNA and DNA-binding proteins such as transcription factors, co-factors, or chromatin-associated proteins. However, a successful ChIP assay largely depends on the quality of a ChIP-grade primary antibody. In cases where specific antibodies are unavailable or with low binding affinity, here, we describe a tailored protocol to achieve robust and reproducible chromatin binding by expressing an exogenous epitope-tagged protein in cells, followed by ChIP assays using a tag-specific antibody. For complete details on the use and execution of this protocol, please refer to Fang et al. (2021)1 and Kidder et al. (2011).2.

Detection of non-tuberculosus mycobacteria (NTMs) in lung samples using 16S rRNA

BACKGROUND

Non-tuberculous mycobacteria (NTMs) cause diseases known as mycobacteriosis and are an important cause of morbidity and mortality. The diagnosis of pulmonary disease caused by NTM is hampered by its clinical similarity with tuberculosis (TB) and by the lack of an accurate and rapid laboratory diagnosis.

OBJECTIVES

Detect DNA from NTMs directly from lung samples using real-time polymerase chain reaction (qPCR) for amplification of 16S rRNA. Additionally, DNA sequencing (hsp65 and rpoB genes) was used to identify the species of MNTs.

METHODS

A total of 68 sputum samples (54 with suspected NTMs and 14 with TB) from patients treated at a referral hospital were used.

FINDINGS

Of these, 27/54 (50%) were qPCR positive for NTMs and 14/14 TB patients (controls) were qPCR negative with an almost perfect concordance (Kappa of 0.93) with the Mycobacterium spp. culture. Sequencing confirmed the presence of NTM in all positive samples. The most common species was Mycobacterium gordonae (33%), followed by Mycobacterium abscessus (26%), Mycobacterium fortuitum (22%), Mycobacterium avium (15%) and Mycobacterium peregrinum (4%).

MAIN CONCLUSIONS

The qPCR technique for detecting NTMs targeting 16S rRNA has the potential to detect NTMs and rapidly differentiate from Mycobacterium tuberculosis. However, it is necessary to identify the species to help in the differential diagnosis between disease and contamination, and to guide the choice of the therapeutic scheme.

Concurrent molecular characterization of sand flies and Leishmania parasites by amplicon-based next-generation sequencing

BACKGROUND

Phlebotomine sand flies are vectors of Leishmania parasites, which are the causative agents of leishmaniasis. Herein, we developed an amplicon-based next-generation sequencing (Amp-NGS) to characterize sand flies and Leishmania parasites simultaneously targeting partial fragments of 18S rDNA and ITS1 genes, respectively.

METHODS

Our assay was optimized using reference sand fly (n = 8) and Leishmania spp. (n = 9) samples and validated using wild-caught sand flies from Palestine. The assay was highly specific, and all DNA references were successfully identified to the species level.

RESULTS

Among the wild-caught sand flies (n = 187), Phlebotomus spp. represented 95% of the collected samples (177/187), including Ph. sergenti (147/187, 79%), Ph. papatasi (19/187, 10.2%), Ph. perfiliewi (3/187, 1.6%), Ph. tobbi (2/187, 1.2%) and Ph. syriacus (6/187, 3.2%). Sergentomyia spp. represented only 5% (10/187) of the collected samples and included S. dentata (n = 6), S. fallax (n = 2), S. schwetzi (n = 1) and S. ghesquiere (n = 1). The study observed strong positive correlation between sand fly identification results of the Amp-NGS and morphological identification method (r = 0.84, df = 185, P < 0.001). Some discrepancies between the two methods in the identification of closely related species (i.e. Ph. perfiliewi, Ph. tobbi and Ph. syriacus) were observed. Leishmania DNA was detected and identified as L. tropica in 14 samples (14/187, 7.5%).

CONCLUSIONS

Our assay was sensitive to detect (limit of detection was 0.0016 ng/reaction) and identify Leishmania DNA in sand flies, thus representing a new tool for studying sand flies and their associated Leishmania parasites in endemic areas.

DEFINITION OF THE MAIN VECTOR OF CUTANEOUS LEISHMANIASIS: ECOLOGY AND MAPPING IN ENDEMIC AREA OF NORTHEAST BRAZIL

Cutaneous leishmaniasis is endemic in Pernambuco. Aiming to determine the vector species of cutaneous leishmaniasis in an endemic area of the Northeast region of Brazil, this study aimed to use the spatial mapping of human cases of CL and correlate with ecological studies of the vectors in the municipality of Timbaúba, Pernambuco, Brazil. Individuals infected with CL were recruited through active search in their homes and clinically and serologically diagnosed during the period from 2018 to 2019. Sandflies were captured with CDC-type light traps in peridomiciliary environments and these were identified at the species level. Females were separated for DNA extraction and subsequent analysis by PCR. The points of collection of phlebotomes and the residences of individuals with lesions were marked with GPS. During the study period, 60 cases of CL were diagnosed. A higher concentration of CL cases was observed in proximity to Atlantic forest remnants confirmed by heat map. A total of 3,744 sandflies was captured and five distinct species were identified, with the predominance of Nyssomyia whitmani. From the females separated for the identification of Leishmania braziliensis DNA, a rate of 0.68% of infected sandflies was obtained. It was concluded that cutaneous leishmaniasis continues to be a rural feature of the area. And from this study, it is concluded that Ny. whitmani is the carrier species of CL in the municipality of Timbaúba, Pernambuco. This is due to abundance in catching, specialization of species and PCR positivity for Leishmania braziliensis.

Robust comparative performance of genomic DNA extraction methods from non-engorged phlebotomine sandflies

The present study is a comparative analysis of DNeasy Blood & Tissue Qiagen® kit (Qiagen®, Hilden, Alemanha), salting out, HotShot and phenol-chloroform protocols to extract DNA from sandflies. In addition, a comparative test using sandflies with and without eyes evaluated the potential inhibitory effect in the cPCR. An inhibition test was performed using an exogenous DNA added to the qPCR. The genomic DNA quality of each sample was evaluated by cPCR based on the cytochrome c oxidase subunit I (cox1) gene. The DNA extraction protocols showed the following percentage of amplification: HotShot (91.6% [55/60]), salting out (71.6% [43/60]), phenol-chloroform (95% [57/60]) and kit DNeasy Blood & Tissue Qiagen® (73.3% [44/60]). The phenol-chloroform method achieved a significantly higher frequency of cox1 gene amplification. The pigment present in the phlebotomine's eyes seems to inhibit cPCR reactions since the frequency of amplification of the cox1 gene increased in the sandflies without eyes (p < 0.0001). The HotShot method showed the highest inhibitory potential. These manual extraction techniques can be an inexpensive and effective alternative to study vector-pathogen interactions.

Analysis of DNA extraction methods for detection of Treponema pallidum: A comparison of three methods

Syphilis is a sexually transmitted disease caused by Treponema pallidum. DNA amplification methods have started to be used to facilitate diagnosis at different stages of the disease. The success of such methodologies depends on obtaining DNA from clinical samples in adequate quantity and quality for molecular reactions. There are many DNA extraction kits, but often the molecular analysis process is unfeasible due to its cost and access to imported products. Thus, this study aimed to analyze three methods of extracting DNA from Treponema pallidum from ulcers of patients investigated for syphilis. The three methods, an in house one (sonication) and two commercial ones (LGC, Brazil) and the PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific, USA) were compared to the sequencing of these samples, which were used as a reference. Each method was evaluated based on the detection of T. pallidum by PCR using the tpp47 gene as a target for amplification, DNA quantification and method execution time. When compared to the sequencing, the sensitivity and agreement of the PureLink, sonication and LGC methods to extracted DNA were 100% (K = 1.0), 96.5% (K = 0.96) and 72.4% (K = 0.694), respectively. Specificity was 100% with the three methods. The sonication method was the closest in concentration of DNA to the PureLink method with a similar degree of purity, besides having the lowest cost-benefit ratio. It can be an interesting option for laboratories that work with reduced costs, since it is much more financially viable.

Comparison of nitrogen removal efficiency and microbial characteristics of modified two-stage A/O, A2/O and SBR processes

The low temperature of sewage in north China results in low performance of biological treatment at municipal wastewater treatment plants (MWTPs), especially in biological nitrogen removal. A modified two-stage A/O process with an embedded biofilm was proposed to enhance nitrogen removal. The operation performance of a pilot test was compared with an A²/O and SBR process at existing MWTPs to investigate the resistance to low temperature. The microbial communities for the three processes were compared based on the metagenomics results of 16sDNA high-throughput sequencing from activated sludge. The modified A/O resulted in a higher average removal of COD (90.12%) than A²/O (85.23%) and SBR (83.03%), especially of small-molecule organic compounds (< 500 Da) and macromolecular refractory organics (> 5 k Da); the TN removal rate of A2/O, SBR and the modified A/O was also increased from 74.47%, 70.63% and 78.46%, respectively. High-throughput sequencing revealed increased microbial diversity and an abundance of denitrifying functional bacteria was observed in the modified A/O process at low temperatures. The abundance of nitrite oxidation bacteria (NOB) including Nitrosomonas and Nitrospira, the amount was 1.76% and 2.34% in modified A/O, respectively, whereas NOB only accounted for 1.82% in A²/O and 1.35% in SBR.

Opportunistic feeding behaviour and Leishmania infantum detection in Phlebotomus perniciosus females collected in the human leishmaniasis focus of Madrid, Spain (2012-2018)

Background

An outbreak of human leishmaniasis due to Leishmania infantum has been registered in an urban area of southwestern Madrid, Spain, since 2010. Entomological surveys carried out in the municipalities of Fuenlabrada, Leganés, Getafe and Humanes de Madrid showed that Phlebotomus perniciosus is the only potential vector. In this work, an intensive molecular surveillance was performed in P. perniciosus females captured in the region between 2012 and 2018.

Methodology/Principal findings

A total of 1805 P. perniciosus females were analyzed for Leishmania infection, and 1189 of them also for bloodmeal identification. Eleven different species of vertebrate were detected by amplification and subsequent sequencing of the 359 bp cytb fragment. The most prevalent blood source identified was hare (n = 553, 46.51%), followed by rabbit (n = 262, 21.95%). Less frequent were cat (n = 45, 3.80%), human (n = 34, 2.90%), pig (n = 14, 1.20%), horse (n = 11, 0.93%), sheep (n = 3, 0.25%), rhea (n = 3, 0.25%), partridge (n = 1, 0.09%) and chicken (n = 1, 0.09%). The distribution of the blood meal sources varied between the different locations. Regarding L. infantum detection, PCR amplification of a fragment of kDNA, cpb gene and ITS1 region showed 162 positive specimens (8.97%). The highest infection rate was found in the municipality of Leganés (15.17%).

Conclusions

The results of this molecular survey in P. perniciosus, the only leishmaniasis vector in the outbreak occurred in southwestern Madrid region, showed its opportunistic blood-feeding behaviour, high infection rates and the differences between the different points. This study was an essential part of the intensive surveillance plan in the area and the results obtained have supported the implementation of control measures in the outbreak.

Vector-borne diseases (VBD) comprise a pathogen-vector-reservoir relation, and control programs should take into account different factors involving this relationship. This study is focused on a leishmaniasis outbreak that has occurred in the southwestern Madrid region since 2010. An intensive molecular surveillance of the sand fly vector Phlebotomus perniciosus was carried out from 2012 to 2018 in 4 municipalities from the affected region: Fuenlabrada, Leganés, Getafe and Humanes de Madrid. The aim of this investigation was to discern how much the vector was infected and find out its blood-feeding habits in the different surveyed points. The results showed an important rate of infected sand flies and also that P. perniciosus presents an opportunistic blood-feeding behaviour, taking blood from many different hosts, depending on their availability and density. The results obtained in this surveillance helped the authorities to plan and implement more accurate and effective control measures in the area, reflecting the importance of applying molecular surveillance in VBD outbreaks.

Study of fauna, activity patterns and Leishmania infection rate of phlebotomine sand flies in Western Iran

Cutaneous leishmaniasis is a crucial vector-borne disease caused by various species of Leishmania and is transmitted by several species of sandflies. The present study was conducted to describe sand fly fauna on vectors of leishmaniasis and performing molecular identification of Leishmania isolates from them on the Iran-Iraq border. Entomological surveys were done from May to October 2016-2018 in 2 counties (Mehran and Dehloran) of Ilam province, west of Iran. Sandflies were collected by 40 Sticky Traps at each station. Samples were mounted for species identification using morphological characters of the head and abdominal terminalia. DNA was extracted from Phlebotomus papatasi females, and Leishmania isolates were identified through PCR on minicircle kDNA, followed by sequencing. A total of 5592 sandflies including 2 genera of Phlebotomus and Sergentomyia comprising 8 species of sand flies were detected. Leishmania major infection was detected in 3.33% of 300 tested female sandflies. Phlebotomus papatasi was predominant in outdoor and indoor resting places. Phlebotomus papatasi was determined as dominant vector of Leishmania major infection in Mehran and Dehloran counties, West of Iran. It seems the composition of sandfly species in the study area is almost similar to the other parts of Iran. A detailed description of the epidemiology and ecology of Phlebotomine sand flies needs to be established to accomplish effective vector control programs.

DNA extraction from individual Phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) specimens: Which is the method with better results?

Phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) are a group of small insects of great concern for Public Health. These dipterous are intensely studied worldwide due to their involvement in the transmission of several pathogens, mainly Leishmania spp. parasites. Nowadays, the molecular tools have been included in Phlebotomine sand flies studies and has shown to be powerful tools in bioecology studies of these dipterous. Thereby, when molecular approaches are employed, there is a great concern regarding the amount and quality of the DNA obtained for analysis. Here, seven methods of DNA extraction, between commercial kits and in house extraction protocols were evaluated. We considered measure of DNA concentration and purity ratios using a spectrophotometer to check the performance of each protocol. In addition, the quality evaluation of the DNA extracted was performed by endogenous gene PCR on samples. The results of the seven evaluated DNA extraction protocols and their implications are discussed.

Immunoglobulin gene rearrangement IGHV3-48 is a predictive marker of histological transformation into aggressive lymphoma in follicular lymphomas

Follicular lymphoma (FL) is a heterogeneous disease whose pathogenesis remains partially unknown. Around 20% of FL patients experience early progression or treatment-refractory disease and 2–3% of patients per year experience histological transformation (HT) into a more aggressive lymphoma (tFL). Here, we evaluate the immunoglobulin heavy chain variable (IGHV) gene usage and mutational status in 187 FL cases to assess its impact on clinical outcome and histological transformation. The IGHV gene repertoire was remarkably biased in FL. The IGHV4-34 (14%), IGHV3-23 (14%), IGHV3-48 (10%), IGHV3-30 (9%) and IGHV3-21 (7%) genes accounted for more than half of the whole cohort. IGHV3-48 was overrepresented in cases of tFL (19%) compared with non-transformed FL at 5 years (5%, P = 0.05). Patients with the IGHV3-48 gene were significantly more likely to have had HT after 10 years than those who used other genes (71% vs. 25%, P < 0.05), irrespective of the therapy they received. Moreover, IGHV3-30 was also overrepresented in cases of FL (9%) and tFL (13%) compared with diffuse large B-cell lymphoma in which it was nearly absent. In conclusion, our results indicate a role for antigen selection in the development of FL, while the use of IGHV3-48 could help predict histological transformation.

Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

BACKGROUND

Multidrug resistance is a growing global public health threat with far more serious consequences than generally anticipated. In this study, we investigated the antibiotic resistance and genomic traits of a clinical strain of Escherichia coli LCT-EC001.

RESULTS

LCT-EC001 was resistant to 16 kinds of widely used antibiotics, including fourth-generation cephalosporins and carbapenems. In total, up to 68 determinants associated with antibiotic resistance were identified, including 8 beta-lactamase genes (notably producing ESBLs and KPCs), 31 multidrug efflux system genes, 6 outer membrane transport system genes, 4 aminoglycoside-modifying enzyme genes, 10 two-component regulatory system genes, and 9 other enzyme or transcriptional regulator genes, covering nearly all known drug-resistance mechanisms in E. coli. More than half of the resistance genes were located close to mobile genetic elements, such as plasmids, transposons, genomics islands, and insertion sequences. Phylogenetic analysis revealed that this strain may have evolved from E. coli K-12 but is a completely new MLST type.

CONCLUSIONS

Antibiotic resistance was extremely severe in E. coli LCT-EC001, mainly due to mobile genetic elements that allowed the gain of a large quantity of resistance genes. The antibiotic resistance genes of E. coli LCT-EC001 can probably be transferred to other bacteria. To the best of our knowledge, this is the first report of a strain of E. coli which has such a large amount of antibiotic resistance genes. Apart from providing an E. coli reference genome with an extremely high multidrug-resistant background for future analyses, this work also offers a strategy for investigating the complement and characteristics of genes contributing to drug resistance at the whole-genome level.

Clinical Outcomes and Co-Occurring Mutations in Patients with RUNX1-Mutated Acute Myeloid Leukemia

(1) Runt-related transcription factor 1 (RUNX1) mutations in acute myeloid leukemia (AML) are often associated with worse prognosis. We assessed co-occurring mutations, response to therapy, and clinical outcomes in patients with and without mutant RUNX1 (mRUNX1); (2) We analyzed 328 AML patients, including 177 patients younger than 65 years who received intensive chemotherapy and 151 patients >65 years who received hypomethylating agents. RUNX1 and co-existing mutations were identified using next-generation sequencing; (3) RUNX1 mutations were identified in 5.1% of younger patients and 15.9% of older patients, and were significantly associated with increasing age (p = 0.01) as well as intermediate-risk cytogenetics including normal karyotype (p = 0.02) in the elderly cohort, and with lower lactate dehydrogenase (LDH; p = 0.02) and higher platelet count (p = 0.012) overall. Identified co-occurring mutations were primarily ASXL1 mutations in older patients and RAS mutations in younger patients; FLT3-ITD and IDH1/2 co-mutations were also frequent. Younger mRUNX1 AML patients treated with intensive chemotherapy experienced inferior treatment outcomes. In older patients with AML treated with hypomethylating agent (HMA) therapy, response and survival was independent of RUNX1 status. Older mRUNX1 patients with prior myelodysplastic syndrome or myeloproliferative neoplasms (MDS/MPN) had particularly dismal outcome. Future studies should focus on the prognostic implications of RUNX1 mutations relative to other co-occurring mutations, and the potential role of hypomethylating agents for this molecularly-defined group.