Molecular characterization of Cryptosporidium isolates obtained from human and bovine infections in Japan

Cryptosporidium oocysts, morphologically identified as Cryptosporidium parvum, were isolated from 22 human and 14 bovine cases in Japan, and were genotyped by means of a PCR/RFLP analysis of the polythreonine gene. DNA profiles of human isolates gave three distinct genotypes, namely an anthroponotic genotype 1, zoonotic genotype 2 and a new genotype. Isolates from bovine samples gave zoonotic genotype 2. The unusual genotype of Cryptosporidium was isolated from the feces of three immunologically healthy adults, and was further characterized by the sequence analysis of the 18S rRNA gene. The third genotype was identified as Crypto sporidium meleagridis, demonstrating that C. meleagridis, which occurs worldwide, has the potential to infect humans regardless of their immunological condition.     

Molecular characterization of Cryptosporidium isolates obtained from humans in France

Cryptosporidium parvum is usually considered the agent of human cryptosporidiosis. However, only in the last few years, molecular biology-based methods have allowed the identification of Cryptosporidium species and genotypes, and only a few data are available from France. In the present work, we collected samples of whole feces from 57 patients from France (11 immunocompetent patients, 35 human immunodeficiency virus [HIV]-infected patients, 11 immunocompromised but non-HIV-infected patients) in whom Cryptosporidium oocysts were recognized by clinical laboratories. A fragment of the Cryptosporidium 18S rRNA gene encompassing the hypervariable region was amplified by PCR and sequenced. The results revealed that the majority of the patients were infected with cattle (29 of 57) or human (18 of 57) genotypes of Cryptosporidium parvum. However, a number of immunocompromised patients were infected with C. meleagridis (3 of 57), C. felis (6 of 57), or a new genotype of C. muris (1 of 57). This is the first report of the last three species of Cryptosporidium in humans in France. These results indicate that immunocompromised individuals are susceptible to a wide range of Cryptosporidium species and genotypes.     

Molecular subtyping and characterization of bovine and human Streptococcus agalactiae isolates

Streptococcus agalactiae causes severe invasive disease in humans and mastitis in cattle. Temporally matched bovine milk isolates and clinical human invasive isolates (52 each) collected in New York State over 18 months were characterized by molecular subtyping and phenotypic methods to probe the interspecies transmission potential of this species. EcoRI ribotyping differentiated 17 ribotypes, and DNA sequencing of the housekeeping gene sodA and the putative virulence gene hylB differentiated 7 and 17 allelic types, respectively. Human and bovine isolates were not randomly distributed between ribotypes or hylB and sodA clusters. The combined analysis of all subtyping data allowed the differentiation of 39 clonal groups; 26 groups contained only bovine isolates, and 2 groups contained both human and bovine isolates. The EcoRI ribotype diversity among bovine isolates (Simpson's numerical index of discrimination [mean +/- standard deviation], 0.90 +/- 0.05) being significantly higher than that among human isolates (0.42 +/- 0.15) further supports that these isolates represent distinct populations. Eight human isolates, but no bovine isolates, showed an IS1548 transposon insertion in hylB, which encodes a hyaluronidase. Based on data for 43 representative isolates, human isolates, on average, showed lower hyaluronidase activities than bovine isolates. Isolates with the IS1548 insertion in hylB showed no hyaluronidase activity. Human and bovine isolates did not differ in their abilities to invade HeLa human epithelial cells. Our data show that (i) EcoRI ribotyping, combined with hylB and sodA sequencing, provides a discriminatory subtype analysis of S. agalactiae; (ii) most human invasive and bovine S. agalactiae isolates represent distinct subtypes, suggesting limited interspecies transmission; and (iii) hyaluronidase activity is not required for all human infections.     

Molecular characterization of Cryptosporidium isolates obtained from human immunodeficiency virus-infected individuals living in Switzerland, Kenya, and the United States

A total of 22 Cryptosporidium isolates from human immunodeficiency virus-infected patients from Kenya, Switzerland, and the United States were examined at three genetic loci: the 18S ribosomal DNA, HSP-70, and acetyl coenzyme A synthetase genes. Four distinct Cryptosporidium genotypes were identified: (i) the Cryptosporidium parvum "human" genotype, (ii) the C. parvum "cattle" genotype, (iii) Cryptosporidium felis, and (iv) Cryptosporidium meleagridis. This is the first report of C. meleagridis in a human host. These results and those of others indicate that immunocompromised individuals are susceptible to a wide range of Cryptosporidium species and genotypes. Future studies are required to understand the full public health significance of Cryptosporidium genotypes and species in immunocompromised hosts.     

Molecular characterisation of Cryptosporidium isolates from humans in Slovenia

Twenty-nine faecal specimens from Slovenian patients in which Cryptosporidium oocysts had been identified were studied. A fragment of the Cryptosporidium 18S rRNA gene and a fragment of the Cryptosporidium COWP gene were amplified by PCR and sequenced. Cryptosporidium parvum was identified in 26 of the 29 specimens, Cryptosporidium hominis in two, and Cryptosporidium cervine genotype in one. The fact that C. parvum, which is associated traditionally with animals, was identified in the majority of human faecal specimens suggests that cryptosporidiosis may have primarily a zoonotic origin in Slovenia.     

Molecular analysis of the 18S rRNA gene of Cryptosporidium parasites from patients with or without human immunodeficiency virus infections living in Kenya,Malawi, Brazil,the United Kingdom,and Vietnam

An 840-bp fragment of the 18S rRNA gene was used to identify Cryptosporidium spp. recovered from human immunodeficiency virus (HIV)-infected and -uninfected patients from Kenya, Malawi, Brazil, the United Kingdom, and Vietnam. Initial identification was by Ziehl-Neelsen acid-fast staining. Confirmation was by nested PCR, targeting the most polymorphic region of the 18S rRNA gene. Genotyping was by restriction endonuclease digestion of the PCR product followed by nucleotide sequencing. Among 63 isolates analyzed, four genotypes of Cryptosporidium were identified; 75% of the isolates were of the C. parvum human genotype, while the potentially zoonotic species were of the C. parvum bovine genotype (21.7%), the C. meleagridis genotype (1.6% [one isolate]), and the C. muris genotype (1.6% [one case]). HIV-infected individuals were more likely to have zoonotic genotypes than the HIV-uninfected individuals. Among the C. parvum group, strains clustered distinctly into either human or bovine genotypes regardless of the geographical origin, age, or HIV status of the patients. The intragenotypic variation observed in the C. parvum human genotype was extensive compared to that within the C. parvum bovine genotype group. The variation within genotypes was conserved in all geographical regions regardless of the patients' HIV status. The extensive diversity within genotypes at the 18S rRNA gene locus may limit its application to phylogenetic analyses.     

Molecular characterization and phylogenetic relationships among microsporidian isolates infecting silkworm, Bombyx mori using small subunit rRNA (SSU-rRNA) gene sequence analysis

The life cycle, spore morphology, pathogenicity, tissue specificity, mode of transmission and small subunit rRNA (SSU-rRNA) gene sequence analysis of the five new microsporidian isolates viz., NIWB-11bp, NIWB-12n, NIWB-13md, NIWB-14b and NIWB-15mb identified from the silkworm, Bombyx mori have been studied along with type species, NIK-1s_mys. The life cycle of the microsporidians identified exhibited the sequential developmental cycles that are similar to the general developmental cycle of the genus, Nosema. The spores showed considerable variations in their shape, length and width. The pathogenicity observed was dose-dependent and differed from each of the microsporidian isolates; the NIWB-15mb was found to be more virulent than other isolates. All of the microsporidians were found to infect most of the tissues examined and showed gonadal infection and transovarial transmission in the infected silkworms. SSU-rRNA sequence based phylogenetic tree placed NIWB-14b, NIWB-12n and NIWB-11bp in a separate branch along with other Nosema species and Nosema bombycis; while NIWB-15mb and NIWB-13md together formed another cluster along with other Nosema species. NIK-1s_mys revealed a signature sequence similar to standard type species, N. bombycis, indicating that NIK-1s_mys is similar to N. bombycis. Based on phylogenetic relationships, branch length information based on genetic distance and nucleotide differences, we conclude that the microsporidian isolates identified are distinctly different from the other known species and belonging to the genus, Nosema. This SSU-rRNA gene sequence analysis method is found to be more useful approach in detecting different and closely related microsporidians of this economically important domestic insect.     

A case report of Linguatula serrata in human throat from Tehran,central Iran

A case of linguatulosis due to Linuatula serrata, a zoonotic pentastomid parasite in throat of a 28 years old woman from Tehran is described. After removal of the parasites the patient was discharged without any further complaining.     

Molecular characterization of Cryptosporidium isolates from high-excreting young dairy calves in dairy cattle herds in Western France

Ninety-two Cryptosporidium sp.-positive fecal samples of dairy diarrheic or non-diarrheic calves from 30 cattle herds in Normandy (France) were selected. Here, the aim was to investigate the species of Cryptosporidium excreted as well as the subtypes of Cryptosporidium parvum found in 7–17-day-old dairy calves. Excretion levels were comprised between 2?×?10⁴ and 4?×?10⁷ oocysts per gram of feces. Here, a nested 18S SSU rRNA PCR associated with sequencing was performed for identification of Cryptosporidium species and revealed the presence of C. parvum in most cases (80/82), except for two animals which were infected with Cryptosporidium bovis. Then, C. parvum samples were submitted to gp60 PCR. For 39 samples from 24 different herds, a multilocus analysis based on four mini-microsatellites loci (MM19, MM5, MSF, and MS9-Mallon) were conducted. These results were combined with sequence analysis of the gp60 to obtain multilocus types (MLTs). Here, C. parvum gp60 genotyping identified three subtypes in the IIa zoonotic allele family: IIaA15G2R1 (88 %), IIaA16G3R1 (10 %), and IIaA19G2R1 (2 %), and we identified 12 MLTs. The MS9-Mallon locus was reported as the most polymorphic (five alleles). The most common MLT was MLT 1 with 15 samples in 10 farms: (MS9-M: 298, MSF: 165, MM5: 264, MM19: 462, and gp60 subtype: IIaA15G2R1). When comparing diarrheic and non-diarrheic fecal samples, no difference was seen for distribution of Cryptosporidium species, C. parvum gp60 subtypes, and MLTs. Here, in a range of oocyst excretion of 10⁴–10⁷ opg, both in diarrheic and non-diarrheic calves, infection was mainly due to C. parvum and to the zoonotic subtype: IIaA15G2R1.     

Molecular characterization and phylogenetic study of velogenic Newcastle disease virus isolates in Iran

The pathogenicity and genetic characterizations of six Newcastle disease virus (NDV) isolates obtained from chicken farms in six different regions in Iran were carried out using conventional and molecular techniques. Based on the pathogenicity indices (MDT, ICPI, and IVPI), all of these isolates were found to be velogenic (highly virulent) strains. A sequence analysis of the full-length mRNA encoding the fusion glycoprotein precursor (F₀) of the NDV’s fusion proteins F₁ and F₂ in these six isolates showed the presence of point mutations in form of nucleic acid substitutions at positions 82^(C→T), 83^(T→C), 736^(A→G), and 1,633^(G→A). However, the nucleic acid residues at positions 330–347 of the precursor F₀ gene, corresponding to the cleavage site of the F₀ protein, were found to have remained conserved among the six NDV isolates. A phylogenetic comparison between the six Iranian isolates and the NDVs whose F₀ gene sequences were previously deposited in GenBank Database showed that all of the newly characterized Iranian NDV isolates belonged to genotype VII.     

Molecular identification of Hartmannella vermiformis and Vannella persistens from man-made recreational water environments, Tehran, Iran

A survey was conducted on man-made recreational water located in different regions of Tehran, Iran to detect the free-living amoebae present in ponds and fountains of parks and squares. Fifty water samples from 22 municipal districts of Tehran were screened for free-living amoebae and identified by morphological characters and polymerase chain reaction amplification. Amoebae detected were identified as Hartmannella vermiformis (12 %) and Vannella persistens (4 %), which are the first reports of these two amoebas in recreational water environments of Iran. Since, H. vermiformis, which is highly similar to strains serving as hosts for Legionella pneumophila, is a common component of the microbial community in fresh surface water. Although Vannella spp. is not proved to be pathogenic itself, they are capable of harboring pathogenic intracellular organisms. Due to some reports related to pathogenicity of these amoebas, the particular hazard related to these microorganisms should be taken into account in the encounter with drinking and washing in these waters. We recommend control strategies based on physical removal rather than on disinfection to be adopted where necessary.     

Molecular characterization of Cryptosporidium spp. from children in Kolkata, India

The intracellular parasite Cryptosporidium is responsible for severe diarrhea in immunocompromised persons in developing countries. Few studies on the characterization of the parasite in India are available. In this study, molecular characterization of the parasite from diarrheic children was carried out by PCR-restriction fragment length polymorphism analysis. At least three genotypes were identified. Out of 40 positive samples, 35 were positive for C. hominis, 4 were positive for C. parvum, and 1 was positive for C. felis. This study clearly suggests that cryptosporidiosis in this region is caused largely by anthroponotic transmission.     

Genotyping of Cryptosporidium isolates from human clinical cases in Poland

Cryptosporidium spp. infection is usually self-limited in immunocompetent hosts but can be severe and life threatening in children and in immunocompromised individuals including those with primary or acquired immunodeficiencies. One hundred and three faecal samples were collected from 35 hospitalised patients with different symptoms and tested for the presence of the parasite. Cryptosporidium oocysts were found in four of 35 patients (11.4%) using Ziehl–Neelsen staining of faecal smears and immunofluorescence assay, whereas 12 (34.3%) samples tested positive by nested polymerase chain reaction assay. Cryptosporidium DNA was detected in one bile sample but not in a liver tissue biopsy sample collected from a patient who suffered from sclerosing cholangitis. Sequence analysis of oocyst wall protein and beta-tubulin gene fragments revealed three different parasite species (Cryptosporidium hominis, Cryptosporidium meleagridis and Cryptosporidium parvum) in children with primary immunodeficiencies, whereas only C. parvum was found in immunocompetent individuals and in those with secondary immunodeficiencies. This study has revealed a high prevalence of Cryptosporidium infection in hospitalised patients in Poland and confirmed that molecular techniques enable a more sensitive detection of the parasite.     

Molecular analysis of human adenoviruses in hospitalized children <5 years old with acute gastroenteritis in Tehran,Iran

Human adenoviruses (HAdVs), especially AdV-40 and 41, are common causes of nonbacterial sporadic and outbreak gastroenteritis in children. The present study aimed to describe the frequency and genetic analysis of HAdVs in hospitalized children <5 years old with acute gastroenteritis. A total of 376 stool samples obtained from June 2015 to December 2017 were investigated for the presence of HAdVs by polymerase chain reaction. The HAdV DNA was detected in 16 (4.3%) out of 376 stool samples. Based on the hexon hypervariable region (HVR), B, C, and F HADV species including five types HAdV-1, 2, 3, 6, and 41 were identified, among which enteric AdV species F (EAdV-41) was the most dominant. Moreover, our findings showed the presence of genomic type cluster 1 (GTC1) pattern in Iranian type 41 strains, which was closely similar to the D1 prototype strain (Tak) and D28. In this regard, a recombination was found in AdV-41 strains presenting the hexon sequence that belonged to GTC1, while fiber sequence clustered with GTC2.     

Molecular epidemiological study of Vibrio cholerae isolates from infected patients in Teheran, Iran

A total of 110 clinical isolates of Vibrio cholerae O1 biotype El Tor serotype Ogawa isolated in a recent outbreak from different districts of Teheran, Iran, was subjected to 99 carbon source utilisation tests, ribotyping and toxinogenotyping. PCR showed that the genes encoding cholera toxin (ctxA), toxin co-regulated pilus (tcp), accessory cholera enterotoxin (ace) and zonula occludens toxin (zot) were present in 100%, 100%, 97.3% and 99.1% of the isolates, respectively. Restriction fragment length polymorphism (RFLP) study of the BglI-digested DNA probed with five oligonucleotides targeting the conserved regions of 16S and 23S rRNA genes revealed a similar ribotype pattern for 109 isolates. All but one isolate showed ribotype pattern B21a, containing seven bands with molecular sizes ranging from 11 to 3.9 kb. The toxin gene restriction pattern (toxinogenotype) showed that the isolates carried either three or two copies of the toxin genes (ace, zot, ctx) which were recognised as TB41a and TB69 patterns, respectively. Overall, the ribotyping data showed that, despite biochemical differences in 12 of the 99 carbon sources, most of the isolates studied belonged to a single clone.     

Molecular characterization,toxin detection and resistance testing of human clinical Clostridium difficile isolates from Lebanon

Clostridium (Clostridioides) difficile is the main cause for nosocomial diarrhoea in industrialised nations. Epidemiologic data on the pathogen’s occurrence in other world regions are still scarce. In this context we characterized with phenotypic and molecular genetic methods C. difficile isolates stemming from hospitalised patients with diarrhoea in Lebanon.From 129 stool samples of symptomatic patients at a tertiary care University hospital in Lebanon, a total of 107 C. difficile strains were cultivated and underwent ribotyping, toxin gene detection and antibiotic resistance testing.Ribotype 014 (RT014, 16.8%) predominated, followed by RT002 (9.3%), RT106 (8.4%) and RT070 (6.5%). Binary toxin gene-positive isolates (RT023, RT078 and RT126) were rarely detected and RT027 was absent. Interestingly, within one isolate only the toxin A gene (tcdA) was detected. Multiple-locus variable-number tandem repeat analysis (MLVA) revealed strong strain diversity in most RTs. The isolates were sensitive to metronidazole and vancomycin, and only a small proportion of strains displayed resistance against moxifloxacin, rifampicin, and clarithromycin (5.6%, 1.9%, and 2.8%), respectively.The data indicate that the genetic strain composition of Lebanese strains differs markedly from the situation seen in Europe and North America. Especially the epidemic RTs seen in the latter regions were almost absent in Lebanon. Interestingly, most strains showed almost no resistance to commonly used antibiotics that are suspected to play a major role in the development of C. difficile infection, despite frequent use of these antibiotics in Lebanon. Thus, the role of antimicrobial resistance as a major driving force for infection development remains uncertain in this area.     

Molecular cloning, nucleotide sequencing and characterization of the flagellin gene from isolates of urease-positive thermophilic Campylobacter

A primer pair which was expected to generate an amplicon of the estimated size (approximately 1700 base pair (bp)) of the flaA gene for Campylobacter jejuni amplified products of approximately 1450 bp for 33 of the 44 isolates of urease-positive thermophilic Campylobacter (UPTC). The primer pair, however, failed to amplify fragments for 11 isolates of UPTC, for all of the 12 isolates of urease-negative C. lari and for one isolate of C. coli. Nevertheless, it successfully amplified fragments of approximately 1700 bp for five isolates of C. jejuni and for nine isolates of C. coli. Thus, the fragments of the flaA gene of UPTC were shorter than those of C. jejuni and C. coli. After PCR amplification and nucleotide sequencing of the flaA genes from five UPTC NCTC isolates, the putative open reading frames (ORFs) were found to range from 1461 to 1479 bp. The amino acid and nucleotide sequence alignments demonstrated that the PCR clones contained the flaA gene; however, our data indicated that this locus was markedly shorter in the UPTC organisms examined, as they were approximately 85 amino acid residues shorter, mainly corresponding to approximate residue numbers 390-470 of the large variable region of C. jejuni 81116. Heterogeneity was indicated in the molecular mass of the flagellin purified from the isolates examined. Flagellin of UPTC was demonstrated to be genotypically and phenotypically smaller than those of C. jejuni.     

Molecular characterization of nasal methicillin resistant Staphylococcus aureus isolates from workers of an automaker company in southeast Iran

Colonization of methicillin resistant Staphylococccus aureus (MRSA) can occur more commonly in healthy people who live in close together or are in close physical contact with each other. Having knowledge about the molecular characteristics of these strains provides considerable discernment into the epidemiology of this important microorganism. A total of 806 nasal swabs were collected from healthy workers of an automaker company in the southeast of Iran and were analyzed to detect MRSA isolates. Multilocus sequence typing (MLST), spa typing, and detection of staphylococcal cassette chromosome mec (SCCmec) were performed. The presence of genes encoding Panton‐Valentine Leukocidin (PVL) and Arginine Catabolic Mobile Element (ACME) were also investigated. Carriage rate of S. aureus was 20%. Among 10 identified MRSA, no acme was found while high prevalence of pvl (60%) was of great concern. Seven different spa types including five new ones were identified. The most frequent sequence type was the novel one; ST 3373 (n = 3), followed by each of ST22, ST88, ST859 (n = 2) and ST1955 (n = 1). MRSA isolates were clustered into two main clonal complexes; CC22 (n = 6) and CC88 (n = 4). Low genetic diversity with the dominance of CC22, SCCmecIV was found. Distribution of previously found hospital‐associated MRSA was demonstrated among our isolates.     

Subgenotype analysis of Cryptosporidium parvum isolates from humans and animals in Japan using the 60-kDa glycoprotein gene sequences

Cryptosporidium parvum is a well-known intestinal parasite which is associated with severe acute diarrhea in humans and animals. This parasite is composed of morphologically identical but genetically different multiple genotypes. In humans, cryptosporidiosis is mainly caused by two C. parvum genotypes, human genotype (previously known as genotype 1 and recently proposed as new species C. hominis) and cattle genotype (previously known as genotype 2). However, recent molecular studies indicate the genetic heterogeneity among the isolates of C. parvum human or cattle genotype. Therefore, identification of the isolates at the subgenotype level is more useful for control of the Cryptosporidium infection or for understanding of the population structure of C. parvum genotypes. In the present study, we identified the subgenotypes of the C. parvum human or cattle genotype isolates from humans and animals in Japan using DNA sequencing analysis of the C. parvum 60-kDa glycoprotein gene (GP60) and showed the new subgenotype in a raccoon dog isolate. This study suggested that C. parvum cattle genotype might be composed of zoonotic and host-specific multiple subgenotypes.