Exploring the Impact of Primer-Template Mismatches on PCR Performance of DNA Polymerases Varying in Proofreading Activity.

Polymerase chain reaction (PCR) is a widely used technique in gene expression analysis, diagnostics, and various molecular biology applications. However, the accuracy and sensitivity of PCR can be compromised by primer-template mismatches, potentially leading to erroneous results. In this study, we strategically designed 111 primer-template combinations with varying numbers, types, and locations of mismatches to meticulously assess their impact on qPCR performance while two distinctly different types of DNA polymerases were used. Notably, when a single-nucleotide mismatch occurred at the 3' end of the primer, we observed significant decreases in the analytical sensitivity (0-4%) with Invitrogen™ Platinum™ Taq DNA Polymerase High Fidelity, while the analytical sensitivity remained unchanged with Takara Ex Taq Hot Start Version DNA Polymerase. Leveraging these findings, we designed a highly specific PCR to amplify Babesia while effectively avoiding the genetically close Theileria. Through elucidating the critical interplay between types of DNA polymerases and primer-template mismatches, this research provides valuable insights for improving PCR accuracy and performance. These findings have important implications for researchers aiming to achieve robust qPCR results in various molecular biology applications.

Experimental infection and co-infection with Chinese strains of Ehrlichia canis and Babesia vogeli in intact and splenectomized dogs: Insights on clinical, hematologic and treatment responses.

Animal infection models are crucial for studying various aspects of Ehrlichia canis infections. To understand the pathogenesis of the first Chinese isolate of E. canis and simulate the natural progression of canine ehrlichiosis, we developed a model with 18 Beagle dogs that consisted of E. canis initial infection (days 0-17), treatment with doxycycline or rifampicin (days 18-32), recovery (days 33-66), E. canis reinfection (days 67-91), and Babesia vogeli superinfection (days 92-116). We measured body weight and rectal temperature every other day, drew blood every 4 days for routine hematology and biochemistry tests, and for quantification of E. canis and B. vogeli by quantitative PCRs. In this study, the first isolate of E. canis from China was used to experimentally infect dogs, and the infected dogs exhibited clinical signs of acute severe ehrlichiosis, including high fever, loss of appetite, dehydration, and body weight loss, confirming the similar pathogenicity of E. canis in China as compared to isolates from other regions. Infection with E. canis and B. vogeli led to reduced body weight and fever in dogs. Doxycycline treatment led to absence of E. canis DNA in infected dogs, while rifampicin treatment lowered the blood E. canis copy number up to 1.5 folds. E. canis-free infected dogs after doxycycline treatment were successfully re-infected with E. canis, indicating dogs with antibodies are still at risk of re-infection. Super-infection with B. vogeli resulted in higher fever, more severe anemia, and a reduced number of platelets. Splenectomized dogs showed significantly higher E. canis numbers during recovery and re-infection than intact dogs. The histological changes were observed in brain, lung, kidney, liver and spleen of the infected dogs. The findings in this study provide insights into clinical and hematologic responses, as well as effective treatment options, for dogs infected with the first Chinese isolate of E. canis, and may contribute to our understanding of the diagnosis and prevention of tick-borne diseases in dogs, including canine monocytic ehrlichiosis.

First molecular detection of Plasmodium relictum in Anopheles sinensis and Armigeres subalbatus.

Background: Plasmodium relictum is one of the most important avian malaria species, which is mainly seen in wild birds, with infections reported in more than 70 different species and at high prevalence. Aim: The aim of this study was to determine the molecular prevalence of Plasmodium spp. in mosquitoes collected in China. Method: A Plasmodium -specific fluorescence resonance energy transfer (FRET) polymerase chain reaction (PCR) was established in this study to analyze five species of mosquitoes (1,620 Culex pipiens pallens, 806 Aedes albopictus, 377 Armigeres subalbatus, 168 Anopheles sinensis, and 80 Culex tritaeniorhynchus) collected in hand nets from homes in 25 provinces of China. Results: Only females originated from six provinces were determined to be positive (0.6%, 10/1,809). Plasmodium species were detected in three mosquito species, such as C.pipiens pallens (0.5%, 8/1,620), A.sinensis (0.6%, 1/168), and A.subalbatus (0.3%, 1/377). Of the three mosquito species positive for P. relictum, only C. pipiens pallens is known to feed on birds and is recognized as the natural vector of P. relictum. Conclusion: This is the first time that P. relictum has been detected in A. sinensis and A. subalbatus. P. relictum, the agent of avian malaria, was present in mosquitoes in China, including mosquito species not previously thought to be the vectors.

Molecular Detection of Rickettsia felis and Rickettsia bellii in Mosquitoes.

To add to the limited information on Rickettsia in mosquitoes in China, we carried out a PCR survey on convenience samples of 3051 mosquitoes collected with hand nets in and around domestic dwellings in 25 provinces. Five species of mosquitoes were identified: Culex pipiens pallens (n = 1620), Aedes albopictus (806), Armigeres subalbatus (377), Anopheles sinensis (168), and Culex tritaeniorhynchus (80). A Rickettsia nested-PCR targeting the variable domain of gltA showed Rickettsia felis in four mosquito species of 16 provinces Cx. pipiens pallens (1.8%, 29/1620); Ae. albopictus (1.2%, 10/806); An. sinensis (1.2%, 2/168); and Ar. subalbatus (2.1%, 8/377). Rickettsia bellii was also widespread, occurring in 12 provinces and 2 species: Cx. pipiens pallens (4.3%, 69/1620) and An. sinensis (0.6%, 1/168). R. felis and R. bellii were found in almost similar numbers in female [1.5% (27/1809) and 1.2% (21/1809), respectively] as in male mosquitoes [1.8% (22/1242) and 4.0% (49/1242), respectively]. Our results indicated that mosquitoes in China are widely infected with R. felis, the agent of human flea-borne spotted fever, and that R. bellii can also occur outside of the Americas and its usual tick hosts.

CRISPR/Cas9/sgRNA-mediated targeted gene modification confirms the cause-effect relationship between gyrA mutation and quinolone resistance in Escherichia coli.

Quinolones are broad-spectrum antibiotics that have been used for decades in treating bacterial infections in humans and animals, and subsequently bacterial resistance to these agents has increased. While studies indicated the relationship between gyrA mutations and bacterial resistance to quinolones, CRISPR/Cas9 was used in this study to investigate causal role of gyrA mutation in the quinolone resistance. In this study, 818 clinical Escherichia coli isolates were analyzed for gyrA mutations and their resistance to quinolones. The CRISPR/Cas9 system was used to generate gyrA mutations in quinolone-susceptible E. coli ATCC 25922, and quinolone-resistant clinical E. coli. The antimicrobial resistance prevalence rate in E. coli against nalidixic acid, ciprofloxacin and enrofloxacin was 77.1% (631/818), 51.1% (418/818) and 49.8% (407/818), respectively. The gyrA mutations were identified in nucleotide positions 248, 255, 259, 260, 261, 273 and 300, and mutations at positions 248 and 259 resulting in amino acid changes at positions 83 and 87 were associated with quinolone resistance. Double-site amino acid mutations increase resistance to quinolones. The gyrA mutations causing changes at amino acids 83 and 87 reversed the features of quinolone resistance in ATCC and clinical strains, verifying the causal role of gyrA mutation in the quinolone resistance of E. coli.

First description of the pathogenicity of Babesia vogeli in experimentally infected dogs.

Babesiosis is a tick-borne disease that occurs worldwide with the most recognized Babesia species that infect dogs being Babesia canis, B. vogeli, B. rossi and B. gibsoni. While B. vogeli is reported in dogs worldwide, clinical and laboratory data on infections is based on reports of naturally infected dogs. To provide reliable data on the clinical and laboratory abnormalities associated with acute and more chronic infections in healthy dogs free of other tick-borne diseases, we experimentally infected dogs with a Chinese strain of B. vogeli. All of the six infected Beagles, three of which were splenectomized, became infected with B. vogeli detected in blood smears taken the day following infection and the organism detected by FRET-qPCRs in most blood samples (77/86; 90%) collected about every 4 days until the end of the experiment on day 95. All the infected dogs showed fever, partial anorexia and malaise that was more severe in the splenectomized dogs that did not gain weight for three weeks in the period after initial infection. Regenerative anemia, thrombocytopenia and decreased white blood cell counts were seen in all dogs but were more severe in the splenectomized dogs, of which two had life threatening infections and had to be removed from the study for treatment. Following re-infection on day 66, none of the dogs showed clinical signs and copy numbers did not change significantly although all the dogs were negative by FRET-qPCR on at least some of the subsequent sampling days. Laboratory values in the non-splenectomized dogs were relatively unchanged while in the splenectomized dog there was a temporary small increase in the platelet and white blood cell counts and a temporary slight worsening of the anemia. In summary, our study shows dogs experimentally infected with a B. vogeli strain from China develop only mild clinical signs that are followed by asymptomatic infections that can last for least 95 days. In splenectomized dogs, however, severe life threatening signs may develop.

Molecular detection of colistin resistance genes (mcr-1 to mcr-5) in human vaginal swabs.

OBJECTIVE: Colistin resistance has emerged worldwide and has been threatening the efficacy of one of the last-resort antimicrobials used for treatment of multidrug resistant Gram-negative bacteria. While five colistin resistance genes (mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5) have been described, few data are available on the prevalence of mcr-genes other than mcr-1 in human samples. RESULTS: In this study, the presence of five currently described colistin resistance genes (mcr 1-5) in vaginal swabs of women undergoing infertility evaluation was reported. Most samples were found to be positive for the mcr-4 (12.7%), followed by two for the mcr-2 (1.5%), two for the mcr-3 (1.5%), one for the mcr-1 (0.7%), and one for the mcr-5 (0.7%). Phylogenetic comparison demonstrated identical (mcr-1, mcr-2, mcr-3, mcr-5) or similar (mcr-4) nucleotide sequences of human samples and those of animal origins from the same city, suggesting the potential transmission of mcr genes from animals to humans. This is the first detection of mcr-2, mcr-4 and mcr-5 genes in human samples, and warrants further research to determine the spread of the mcr genes and elucidate the full epidemiology of colistin resistance genes in humans.

Presence of Chlamydia trachomatis and Mycoplasma spp., but not Neisseria gonorrhoeae and Treponema pallidum, in women undergoing an infertility evaluation: high prevalence of tetracycline resistance gene tet(M).

Chlamydia trachomatis, Mycoplasma spp., Neisseria gonorrhoeae and Treponema pallidum are sexually transmitted pathogens that threaten reproductive health worldwide. In this study, vaginal swabs obtained from women (n = 133) that attended an infertility clinic in China were tested with qPCRs for C. trachomatis, Mycoplasma spp., N. gonorrhoeae, T. pallidum and tetracycline resistance genes. While none of vaginal swabs were positive for N. gonorrhoeae and T. pallidum, 18.8% (25/133) of the swabs were positive for Chlamydia spp. and 17.3% of the swabs (23/133) were positive for Mycoplasma species. All swabs tested were positive for tetracycline resistance gene tet(M) which is the most effective antibiotic for bacterial sexually transmitted infections. The qPCRs determined that the gene copy number per swab for tet(M) was 7.6 times as high as that of C. trachomatis 23S rRNA, and 14.7 times of Mycoplasma spp. 16S rRNA. In China, most hospitals do not detect C. trachomatis and Mycoplasma spp. in women with sexually transmitted infections and fertility problems. This study strongly suggests that C. trachomatis and Mycoplasma spp. should be routinely tested in women with sexually transmitted infections and infertility in China, and that antimicrobial resistance of these organisms should be monitored. Further studies are warranted to determine the prevalences in different regions and associated risk factors.

Antimicrobial resistance in clinical Escherichia coli isolates from poultry and livestock, China.

Poultry and livestock are the most important reservoirs for pathogenic Escherichia coli and use of antimicrobials in animal farming is considered the most important factor promoting the emergence, selection and dissemination of antimicrobial-resistant microorganisms. The aim of our study was to investigate antimicrobial resistance in E. coli isolated from food animals in Jiangsu, China. The disc diffusion method was used to determine susceptibility to 18 antimicrobial agents in 862 clinical isolates collected from chickens, ducks, pigs, and cows between 2004 and 2012. Overall, 94% of the isolates showed resistance to at least one drug with 83% being resistance to at least three different classes of antimicrobials. The isolates from the different species were most commonly resistant to tetracycline, nalidixic acid, sulfamethoxazole, trimethoprim/sulfamethoxazole and ampicillin, and showed increasing resistance to amikacin, aztreonam, ceftazidime, cefotaxime, chloramphenicol, ciprofloxacin. They were least resistant to amoxicillin/clavulanic acid (3.4%) and ertapenem (0.2%). MDR was most common in isolates from ducks (44/44, 100%), followed by chickens (568/644, 88.2%), pigs (93/113, 82.3%) and cows (13/61, 21.3%). Our finding that clinical E. coli isolates from poultry and livestock are commonly resistant to multiple antibiotics should alert public health and veterinary authorities to limit and rationalize antimicrobial use in China.

Chlamydia pecorum is the endemic intestinal species in cattle while C. gallinacea, C. psittaci and C. pneumoniae associate with sporadic systemic infection.

To investigate the prevalence and diversity of bovine Chlamydia spp. in cattle, whole blood from dairy and beef cattle in 11 provinces of China (n=2003) and vaginal swabs, whole blood samples, feces, milk samples from cows in a Yangzhou dairy farm (n=108) were examined using genus- and species-specific PCRs. In cattle from 11 provinces, 2.4% (48/2003) of whole-blood samples were positive for Chlamydia spp., and four Chlamydia species (C. pneumoniae, 41.7%, 20/48; C. psittaci, 22.9%, 11/48; C. gallinacea, 20.8%, 10/48; C. pecorum, 6.3%, 3/48) were identified. In a further study on a Yangzhou dairy farm, 64.8% (70/108) of the cows were positive for Chlamydia spp. C. pecorum was the intestinal endemic species (51/51, 100%), and C. gallinacea was the most frequent species in vaginal swabs (24/27, 88.9%), whole blood buffy coats (5/8, 62.5%) and milk (4/6, 66.7%). C. psittaci and C. pneumoniae were infrequently detected. DNA sequencing of the ompA gene demonstrated the presence of multiple in-herd C. pecorum serovars and single C. gallinacea and C. psittaci serovars which were identical with those of poultry from Yangzhou. This is the first report of C. gallinacea and C. pneumoniae in cattle. Further study is required to address the transmission of Chlamydia spp., in particular of C. gallinacea and C. pneumoniae from their natural hosts, and their potential pathogenic effect on health and production of cattle.

Molecular Detection of Anaplasma spp. and Ehrlichia spp. in Ruminants from Twelve Provinces of China.

Anaplasma spp. and Ehrlichia spp. are tick-transmitted bacteria that are of significant economic importance as they can infect large and small ruminants and also people. There is little information on anaplasmosis and ehrlichiosis in ruminants in China. 16S rRNA FRET-qPCRs were used to screen convenience whole blood samples from 2,240 domestic ruminants in 12 provinces of China for Anaplasma spp. and Ehrlichia spp. Positive samples were further analyzed with a standard PCR for the gltA. Anaplasma spp. DNA was detected in the sheep (11.7%; 13/111), goats (81.8%; 219/270), cattle (13.2%; 241/1,830), and water buffaloes (6.9%; 2/29). Ehrlichia spp. DNA was detected in sheep (1.8%; 2/111), goats (1.1%; 3/270), and cattle (3.6%; 65/1830) but not in water buffaloes (0/29). Sequencing of gltA PCR products showed that A. marginale, A. ovis, Ehrlichia canis, and Ehrlichia sp. (JX629807) were present in ruminants from China, while the 16S rRNA FRET-qPCR sequence data indicated that there might also be A. platys, A. phagocytophilum, Anaplasma sp. BL126-13 (KJ410243), and Anaplasma sp. JC3-6 (KM227012). Our study shows that domestic ruminants from China are not uncommonly infected with a variety of Anaplasma spp. and Ehrlichia spp.