A pilot comparison of fixatives for hookworm real-time polymerase chain reaction
- Bradbury, Richard, Inagaki, Kengo, Singh, Gurbaksh, Agana, Urita, Patterson, Kayla, Malloch, Lacy, Rodriguez, Eduardo, Qvarnstrom, Yvonne, Hobbs, Charlotte
- Authors: Bradbury, Richard , Inagaki, Kengo , Singh, Gurbaksh , Agana, Urita , Patterson, Kayla , Malloch, Lacy , Rodriguez, Eduardo , Qvarnstrom, Yvonne , Hobbs, Charlotte
- Date: 2023
- Type: Text , Journal article
- Relation: American Journal of Tropical Medicine and Hygiene Vol. 108, no. 2 (2023), p. 335-339
- Full Text:
- Reviewed:
- Description: Polymerase chain reaction (PCR) is increasingly used in the diagnosis of soil-transmitted helminth infections. Despite this, few studies have evaluated the impact of different fecal fixatives on the outcome of fecal helminth qPCR analysis, and none have evaluated the effect of commercial parasitology fixatives commonly used in diagnostic laboratories. We fixed dog feces containing Ancylostoma spp. hookworm eggs in zinc polyvinyl alcohol (Zn-PVA) and Total-Fix, and with 70% ethanol (EtOH) as a control. DNA was extracted at timepoints 11, 33, 64, and 94 days and subjected to Ancylostoma spp. quantitative PCR (qPCR). A linear regression model was created to assess the effect of preservative types on the temporal change of qPCR quantification cycle number (Cq) values, accounting for variances among individual animals. Fixation in 70% EtOH least affected Cq values over 94 days. Total-Fix preservation yielded a higher Cq overall, but there was no significant difference compared with 70% EtOH fixation. Fixation in Zn-PVA resulted in significantly (P < 0.001) higher Cq values than 70% EtOH after only 33 days and loss of amplification at 64 days. Consistent with other helminth fixation studies, 70% EtOH performed well in preserving hookworm DNA over 94 days. Total-Fix provided a comparable alternative for qPCR analysis for hookworm. Fixation in Zn-PVA resulted in loss of detectable hookworm DNA at 64 days, as determined by qPCR. Copyright © 2023 The American Society of Tropical Medicine and Hygiene.
- Authors: Bradbury, Richard , Inagaki, Kengo , Singh, Gurbaksh , Agana, Urita , Patterson, Kayla , Malloch, Lacy , Rodriguez, Eduardo , Qvarnstrom, Yvonne , Hobbs, Charlotte
- Date: 2023
- Type: Text , Journal article
- Relation: American Journal of Tropical Medicine and Hygiene Vol. 108, no. 2 (2023), p. 335-339
- Full Text:
- Reviewed:
- Description: Polymerase chain reaction (PCR) is increasingly used in the diagnosis of soil-transmitted helminth infections. Despite this, few studies have evaluated the impact of different fecal fixatives on the outcome of fecal helminth qPCR analysis, and none have evaluated the effect of commercial parasitology fixatives commonly used in diagnostic laboratories. We fixed dog feces containing Ancylostoma spp. hookworm eggs in zinc polyvinyl alcohol (Zn-PVA) and Total-Fix, and with 70% ethanol (EtOH) as a control. DNA was extracted at timepoints 11, 33, 64, and 94 days and subjected to Ancylostoma spp. quantitative PCR (qPCR). A linear regression model was created to assess the effect of preservative types on the temporal change of qPCR quantification cycle number (Cq) values, accounting for variances among individual animals. Fixation in 70% EtOH least affected Cq values over 94 days. Total-Fix preservation yielded a higher Cq overall, but there was no significant difference compared with 70% EtOH fixation. Fixation in Zn-PVA resulted in significantly (P < 0.001) higher Cq values than 70% EtOH after only 33 days and loss of amplification at 64 days. Consistent with other helminth fixation studies, 70% EtOH performed well in preserving hookworm DNA over 94 days. Total-Fix provided a comparable alternative for qPCR analysis for hookworm. Fixation in Zn-PVA resulted in loss of detectable hookworm DNA at 64 days, as determined by qPCR. Copyright © 2023 The American Society of Tropical Medicine and Hygiene.
An atypical case of autochthonous cutaneous leishmaniasis associated with naturally infected phlebotomine sand flies in Texas, United States
- Kipp, Evan, de Almeida, Marcos, Marcet, Paula, Bradbury, Richard, Benedict, Theresa, Lin, Wuling, Dotson, Ellen, Hergert, Melinda
- Authors: Kipp, Evan , de Almeida, Marcos , Marcet, Paula , Bradbury, Richard , Benedict, Theresa , Lin, Wuling , Dotson, Ellen , Hergert, Melinda
- Date: 2020
- Type: Text , Journal article
- Relation: American Journal of Tropical Medicine and Hygiene Vol. 103, no. 4 (2020), p. 1496-1501
- Full Text:
- Reviewed:
- Description: In the United States, phlebotomine sand flies carrying Leishmania (Leishmania) mexicana are endemic along the southern border. However, relatively little is known about the enzootic and zoonotic transmission of L. (L.) mexicana within the United States, and autochthonous cases of the consequent disease are rarely reported. We investigated an atypical case of cutaneous leishmaniasis (CL) caused by L. (L.) mexicana in a patient from central Texas which did not respond to a typical antileishmanial chemotherapy. We also investigated sand fly vectors around the patient's residence. PCR followed by DNA sequencing was used for determination of Leishmania spp., sand fly species, and host blood meal source. The L. (L.) mexicana genotype from the patient was identical to one found in a positive sand fly. Moreover, this genotype presented the same single-nucleotide polymorphisms as other historical CL cases acquired in Texas over the last 10 years, but distinct from those originating in Mexico and Central America. Three sand fly species were identified among the samples analyzed (n = 194), the majority of which were Lutzomyia (Dampfomyia) anthophora (n = 190), of which four specimens tested positive for Leishmania and two blood-fed specimens showed the presence of a human blood meal. This study highlights the complexity of clinical management of CL in a setting where the disease is infrequently encountered. The detection of human blood in Lu. (D.) anthophora is the first documentation of anthropophagy in this species. This is the first report of wild-caught, naturally infected sand flies found in association with an autochthonous case of human leishmaniasis and the specific strain of Leishmania (Leishmania) mexicana in the United States. Copyright © 2020 by The American Society of Tropical Medicine and Hygiene
- Authors: Kipp, Evan , de Almeida, Marcos , Marcet, Paula , Bradbury, Richard , Benedict, Theresa , Lin, Wuling , Dotson, Ellen , Hergert, Melinda
- Date: 2020
- Type: Text , Journal article
- Relation: American Journal of Tropical Medicine and Hygiene Vol. 103, no. 4 (2020), p. 1496-1501
- Full Text:
- Reviewed:
- Description: In the United States, phlebotomine sand flies carrying Leishmania (Leishmania) mexicana are endemic along the southern border. However, relatively little is known about the enzootic and zoonotic transmission of L. (L.) mexicana within the United States, and autochthonous cases of the consequent disease are rarely reported. We investigated an atypical case of cutaneous leishmaniasis (CL) caused by L. (L.) mexicana in a patient from central Texas which did not respond to a typical antileishmanial chemotherapy. We also investigated sand fly vectors around the patient's residence. PCR followed by DNA sequencing was used for determination of Leishmania spp., sand fly species, and host blood meal source. The L. (L.) mexicana genotype from the patient was identical to one found in a positive sand fly. Moreover, this genotype presented the same single-nucleotide polymorphisms as other historical CL cases acquired in Texas over the last 10 years, but distinct from those originating in Mexico and Central America. Three sand fly species were identified among the samples analyzed (n = 194), the majority of which were Lutzomyia (Dampfomyia) anthophora (n = 190), of which four specimens tested positive for Leishmania and two blood-fed specimens showed the presence of a human blood meal. This study highlights the complexity of clinical management of CL in a setting where the disease is infrequently encountered. The detection of human blood in Lu. (D.) anthophora is the first documentation of anthropophagy in this species. This is the first report of wild-caught, naturally infected sand flies found in association with an autochthonous case of human leishmaniasis and the specific strain of Leishmania (Leishmania) mexicana in the United States. Copyright © 2020 by The American Society of Tropical Medicine and Hygiene
Application of a universal parasite diagnostic test to biological specimens collected from animals
- Lane, Meredith, Kashani, Mitra, Barratt, Joel, Qvarnstrom, Yvonne, Yabsley, Michael, Garrett, Kayla, Bradbury, Richard
- Authors: Lane, Meredith , Kashani, Mitra , Barratt, Joel , Qvarnstrom, Yvonne , Yabsley, Michael , Garrett, Kayla , Bradbury, Richard
- Date: 2023
- Type: Text , Journal article
- Relation: International Journal for Parasitology: Parasites and Wildlife Vol. 20, no. (2023), p. 20-30
- Full Text:
- Reviewed:
- Description: A previously described universal parasite diagnostic (nUPDx) based on PCR amplification of the 18S rDNA and deep-amplicon sequencing, can detect human blood parasites with a sensitivity comparable to real-time PCR. To date, the efficacy of this assay has only been assessed on human blood. This study assessed the utility of nUPDx for the detection of parasitic infections in animals using blood, tissues, and other biological sample types from mammals, birds, and reptiles, known to be infected with helminth, apicomplexan, or pentastomid parasites (confirmed by microscopy or PCR), as well as negative samples. nUPDx confirmed apicomplexan and/or nematode infections in 24 of 32 parasite-positive mammals, while also identifying several undetected coinfections. nUPDx detected infections in 6 of 13 positive bird and 1 of 2 positive reptile samples. When applied to 10 whole parasite specimens (worms and arthropods), nUPDx identified all to the genus or family level, and detected one incorrect identification made by morphology. Babesia sp. infections were detected in 5 of the 13 samples that were negative by other diagnostic approaches. While nUPDx did not detect PCR/microscopy-confirmed trichomonads or amoebae in cloacal swabs/tissue from 8 birds and 2 reptiles due to primer template mismatches, 4 previously undetected apicomplexans were detected in these samples. Future efforts to improve the utility of the assay should focus on validation against a larger panel of tissue types and animal species. Overall, nUPDx shows promise for use in both veterinary diagnostics and wildlife surveillance, especially because species-specific PCRs can miss unknown or unexpected pathogens. © 2022
- Authors: Lane, Meredith , Kashani, Mitra , Barratt, Joel , Qvarnstrom, Yvonne , Yabsley, Michael , Garrett, Kayla , Bradbury, Richard
- Date: 2023
- Type: Text , Journal article
- Relation: International Journal for Parasitology: Parasites and Wildlife Vol. 20, no. (2023), p. 20-30
- Full Text:
- Reviewed:
- Description: A previously described universal parasite diagnostic (nUPDx) based on PCR amplification of the 18S rDNA and deep-amplicon sequencing, can detect human blood parasites with a sensitivity comparable to real-time PCR. To date, the efficacy of this assay has only been assessed on human blood. This study assessed the utility of nUPDx for the detection of parasitic infections in animals using blood, tissues, and other biological sample types from mammals, birds, and reptiles, known to be infected with helminth, apicomplexan, or pentastomid parasites (confirmed by microscopy or PCR), as well as negative samples. nUPDx confirmed apicomplexan and/or nematode infections in 24 of 32 parasite-positive mammals, while also identifying several undetected coinfections. nUPDx detected infections in 6 of 13 positive bird and 1 of 2 positive reptile samples. When applied to 10 whole parasite specimens (worms and arthropods), nUPDx identified all to the genus or family level, and detected one incorrect identification made by morphology. Babesia sp. infections were detected in 5 of the 13 samples that were negative by other diagnostic approaches. While nUPDx did not detect PCR/microscopy-confirmed trichomonads or amoebae in cloacal swabs/tissue from 8 birds and 2 reptiles due to primer template mismatches, 4 previously undetected apicomplexans were detected in these samples. Future efforts to improve the utility of the assay should focus on validation against a larger panel of tissue types and animal species. Overall, nUPDx shows promise for use in both veterinary diagnostics and wildlife surveillance, especially because species-specific PCRs can miss unknown or unexpected pathogens. © 2022
Cross-sectional study of soil-transmitted helminthiases in black belt region of Alabama, USA
- Poole, Claudette, Barker, Troy, Bradbury, Richard, Capone, Drew, Chatham, Amy, Handali, Sukwan, Rodriguez, Eduardo, Qvarnstrom, Yvonne, Brown, Joe
- Authors: Poole, Claudette , Barker, Troy , Bradbury, Richard , Capone, Drew , Chatham, Amy , Handali, Sukwan , Rodriguez, Eduardo , Qvarnstrom, Yvonne , Brown, Joe
- Date: 2023
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 29, no. 12 (2023), p. 2461-2470
- Full Text:
- Reviewed:
- Description: We conducted a cross-sectional study to determine the prevalence of soil-transmitted helminthiases (STH) in areas of rural Alabama, USA, that have sanitation deficits. We enrolled 777 children; 704 submitted stool specimens and 227 a dried blood spot sample. We microscopically examined stool specimens from all 704 children by using Mini-FLOTAC for helminth eggs. We tested a subset by using molecular techniques: real-time PCR analysis for 5 STH species, TaqMan Array Cards for enteric helminths, and digital PCR for Necator americanus hookworm. We analyzed dried blood spots for Strongyloides stercoralis and Toxocara spp. roundworms by using serologic testing. Despite 12% of our cohort reporting living in homes that directly discharge untreated domestic wastewater, stool testing for STH was negative; however, 5% of dried blood spots were positive for Toxocara spp. roundworms. Survey data suggests substantial numbers of children in this region may be exposed to raw sewage, which is itself a major public health concern. © 2023 Centers for Disease Control and Prevention (CDC). All rights reserved.
- Authors: Poole, Claudette , Barker, Troy , Bradbury, Richard , Capone, Drew , Chatham, Amy , Handali, Sukwan , Rodriguez, Eduardo , Qvarnstrom, Yvonne , Brown, Joe
- Date: 2023
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 29, no. 12 (2023), p. 2461-2470
- Full Text:
- Reviewed:
- Description: We conducted a cross-sectional study to determine the prevalence of soil-transmitted helminthiases (STH) in areas of rural Alabama, USA, that have sanitation deficits. We enrolled 777 children; 704 submitted stool specimens and 227 a dried blood spot sample. We microscopically examined stool specimens from all 704 children by using Mini-FLOTAC for helminth eggs. We tested a subset by using molecular techniques: real-time PCR analysis for 5 STH species, TaqMan Array Cards for enteric helminths, and digital PCR for Necator americanus hookworm. We analyzed dried blood spots for Strongyloides stercoralis and Toxocara spp. roundworms by using serologic testing. Despite 12% of our cohort reporting living in homes that directly discharge untreated domestic wastewater, stool testing for STH was negative; however, 5% of dried blood spots were positive for Toxocara spp. roundworms. Survey data suggests substantial numbers of children in this region may be exposed to raw sewage, which is itself a major public health concern. © 2023 Centers for Disease Control and Prevention (CDC). All rights reserved.
Evaluation of the performance of Ortho T. cruzi ELISA test system for the detection of antibodies to Trypanosoma cruzi
- Rivera, Hilda, McAuliffe, Isabel, Aderohunmu, TaLesa, Wiegand, Ryan, Montgomery, Susan, Bradbury, Richard, Handali, Sukwan
- Authors: Rivera, Hilda , McAuliffe, Isabel , Aderohunmu, TaLesa , Wiegand, Ryan , Montgomery, Susan , Bradbury, Richard , Handali, Sukwan
- Date: 2022
- Type: Text , Journal article
- Relation: Journal of Clinical Microbiology Vol. 60, no. 8 (2022), p.
- Full Text:
- Reviewed:
- Description: The serologic diagnosis of chronic Chagas disease, caused by infection with the parasite Trypanosoma cruzi, is challenging and lacks a gold-standard assay. To overcome the problem, CDC uses an algorithm that uses two tests on different platforms and applies a third test as a tiebreaker. The Ortho T. cruzi ELISA Test System from Ortho Diagnostics was cleared by FDA for clinical diagnosis usage. We evaluated this test against the CDC algorithm for chronic Chagas disease. We tested several sets of serum specimens: 104 specimens tested positive for T. cruzi specific antibody and 283 (including 30 specimens positive for antibody to Leishmania spp.) tested negative based on the current CDC chronic T. cruzi infection diagnostic testing algorithm. Concordance of the Ortho T. cruzi ELISA Test System with the CDC algorithm result was 90% (95% CI 87 to 93%) overall and 92% (95% CI 89 to 95%) when excluding Leishmania spp. antibody positive specimens. The cross-reactivity of the Ortho T. cruzi ELISA Test System was 37% to Leishmania spp. serologically positive specimens, 1% to specimens from patients diagnosed with other parasitic infections, and 0% against specimens from a US noninfected population. In conclusion, the Ortho T. cruzi ELISA Test System compares well against the CDC diagnostic algorithm for chronic Chagas disease. The availability of this FDA-cleared assay will improve the chronic Chagas disease diagnosis. © 2022 American Society for Microbiology. All rights reserved.
- Authors: Rivera, Hilda , McAuliffe, Isabel , Aderohunmu, TaLesa , Wiegand, Ryan , Montgomery, Susan , Bradbury, Richard , Handali, Sukwan
- Date: 2022
- Type: Text , Journal article
- Relation: Journal of Clinical Microbiology Vol. 60, no. 8 (2022), p.
- Full Text:
- Reviewed:
- Description: The serologic diagnosis of chronic Chagas disease, caused by infection with the parasite Trypanosoma cruzi, is challenging and lacks a gold-standard assay. To overcome the problem, CDC uses an algorithm that uses two tests on different platforms and applies a third test as a tiebreaker. The Ortho T. cruzi ELISA Test System from Ortho Diagnostics was cleared by FDA for clinical diagnosis usage. We evaluated this test against the CDC algorithm for chronic Chagas disease. We tested several sets of serum specimens: 104 specimens tested positive for T. cruzi specific antibody and 283 (including 30 specimens positive for antibody to Leishmania spp.) tested negative based on the current CDC chronic T. cruzi infection diagnostic testing algorithm. Concordance of the Ortho T. cruzi ELISA Test System with the CDC algorithm result was 90% (95% CI 87 to 93%) overall and 92% (95% CI 89 to 95%) when excluding Leishmania spp. antibody positive specimens. The cross-reactivity of the Ortho T. cruzi ELISA Test System was 37% to Leishmania spp. serologically positive specimens, 1% to specimens from patients diagnosed with other parasitic infections, and 0% against specimens from a US noninfected population. In conclusion, the Ortho T. cruzi ELISA Test System compares well against the CDC diagnostic algorithm for chronic Chagas disease. The availability of this FDA-cleared assay will improve the chronic Chagas disease diagnosis. © 2022 American Society for Microbiology. All rights reserved.
First international external quality assessment scheme of nucleic acid amplification tests for the detection of schistosoma and soil-transmitted helminths, including strongyloides : A pilot study
- Cools, Piet, van Lieshout, Lisette, Koelewijn, Rob, Addiss, David, Ajjampur, Sitara, Ayana, Mio, Bradbury, Richard, Cantera, Jason, Dana, Daniel, Fischer, Kerstin, Imtiaz, Rubina, Kabagenyi, Joyce, Lok, James, McCarthy, James, Mejia, Rojelio, Mekonnen, Zeleke, Njenga, Sammy, Othman, Nurulhasanah, Shao, Hongguang, Traub, Rebecca, Van Esbroeck, Marjan, Vercruysse, Jozef, Vlaminck, Johnny, Williams, Steven, Verweij, Jaco, van Hellemond, Jaap, Levecke, Bruno
- Authors: Cools, Piet , van Lieshout, Lisette , Koelewijn, Rob , Addiss, David , Ajjampur, Sitara , Ayana, Mio , Bradbury, Richard , Cantera, Jason , Dana, Daniel , Fischer, Kerstin , Imtiaz, Rubina , Kabagenyi, Joyce , Lok, James , McCarthy, James , Mejia, Rojelio , Mekonnen, Zeleke , Njenga, Sammy , Othman, Nurulhasanah , Shao, Hongguang , Traub, Rebecca , Van Esbroeck, Marjan , Vercruysse, Jozef , Vlaminck, Johnny , Williams, Steven , Verweij, Jaco , van Hellemond, Jaap , Levecke, Bruno
- Date: 2020
- Type: Text , Journal article
- Relation: PLoS Neglected Tropical Diseases Vol. 14, no. 6 (2020), p. 1-19
- Full Text:
- Reviewed:
- Description: Background Nucleic acid amplification tests (NAATs) are increasingly being used as diagnostic tools for soil-transmitted helminths (STHs; Ascaris lumbricoides, Trichuris trichiura, Necator ameri-canus, Ancylostoma duodenale and A. ceylanicum), Strongyloides stercoralis and Schisto-soma in human stool. Currently, there is a large diversity of NAATs being applied, but an external quality assessment scheme (EQAS) for these diagnostics is lacking. An EQAS involves a blinded process where test results reported by a laboratory are compared to those reported by reference or expert laboratories, allowing for an objective assessment of the diagnostic performance of a laboratory. In the current study, we piloted an international EQAS for these helminths (i) to investigate the feasibility of designing and delivering an EQAS; (ii) to assess the diagnostic performance of laboratories; and (iii) to gain insights into the different NAAT protocols used. Methods and principal findings A panel of twelve stool samples and eight DNA samples was validated by six expert laboratories for the presence of six helminths (Ascaris, Trichuris, N. americanus, Ancylostoma, Strongyloides and Schistosoma). Subsequently this panel was sent to 15 globally dispersed laboratories. We found a high degree of diversity among the different DNA extraction and NAAT protocols. Although most laboratories performed well, we could clearly identify the laboratories that were poorly performing. Conclusions/Significance We showed the technical feasibility of an international EQAS for the NAAT of STHs, Stron-gyloides and Schistosoma. In addition, we documented that there are clear benefits for par-ticipating laboratories, as they can confirm and/or improve the diagnostic performance of their NAATs. Further research should aim to identify factors that explain poor performance of NAATs. © 2020 Cools et al.
- Authors: Cools, Piet , van Lieshout, Lisette , Koelewijn, Rob , Addiss, David , Ajjampur, Sitara , Ayana, Mio , Bradbury, Richard , Cantera, Jason , Dana, Daniel , Fischer, Kerstin , Imtiaz, Rubina , Kabagenyi, Joyce , Lok, James , McCarthy, James , Mejia, Rojelio , Mekonnen, Zeleke , Njenga, Sammy , Othman, Nurulhasanah , Shao, Hongguang , Traub, Rebecca , Van Esbroeck, Marjan , Vercruysse, Jozef , Vlaminck, Johnny , Williams, Steven , Verweij, Jaco , van Hellemond, Jaap , Levecke, Bruno
- Date: 2020
- Type: Text , Journal article
- Relation: PLoS Neglected Tropical Diseases Vol. 14, no. 6 (2020), p. 1-19
- Full Text:
- Reviewed:
- Description: Background Nucleic acid amplification tests (NAATs) are increasingly being used as diagnostic tools for soil-transmitted helminths (STHs; Ascaris lumbricoides, Trichuris trichiura, Necator ameri-canus, Ancylostoma duodenale and A. ceylanicum), Strongyloides stercoralis and Schisto-soma in human stool. Currently, there is a large diversity of NAATs being applied, but an external quality assessment scheme (EQAS) for these diagnostics is lacking. An EQAS involves a blinded process where test results reported by a laboratory are compared to those reported by reference or expert laboratories, allowing for an objective assessment of the diagnostic performance of a laboratory. In the current study, we piloted an international EQAS for these helminths (i) to investigate the feasibility of designing and delivering an EQAS; (ii) to assess the diagnostic performance of laboratories; and (iii) to gain insights into the different NAAT protocols used. Methods and principal findings A panel of twelve stool samples and eight DNA samples was validated by six expert laboratories for the presence of six helminths (Ascaris, Trichuris, N. americanus, Ancylostoma, Strongyloides and Schistosoma). Subsequently this panel was sent to 15 globally dispersed laboratories. We found a high degree of diversity among the different DNA extraction and NAAT protocols. Although most laboratories performed well, we could clearly identify the laboratories that were poorly performing. Conclusions/Significance We showed the technical feasibility of an international EQAS for the NAAT of STHs, Stron-gyloides and Schistosoma. In addition, we documented that there are clear benefits for par-ticipating laboratories, as they can confirm and/or improve the diagnostic performance of their NAATs. Further research should aim to identify factors that explain poor performance of NAATs. © 2020 Cools et al.
Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia
- Darboe, Saffiatou, Bradbury, Richard, Phelan, Jody, Kanteh, Abdoulie, Muhammad, Abdul-Khalie, Worwui, Archibald, Yang, Shangxin, Nwakanma, Davis, Perez-Sepulveda, Blanca, Kariuki, Samuel, Kwambana-Adams, Brenda, Antonio, Martin
- Authors: Darboe, Saffiatou , Bradbury, Richard , Phelan, Jody , Kanteh, Abdoulie , Muhammad, Abdul-Khalie , Worwui, Archibald , Yang, Shangxin , Nwakanma, Davis , Perez-Sepulveda, Blanca , Kariuki, Samuel , Kwambana-Adams, Brenda , Antonio, Martin
- Date: 2022
- Type: Text , Journal article
- Relation: Microbial Genomics Vol. 8, no. 3 (2022), p.
- Full Text:
- Reviewed:
- Description: Non-typhoidal Salmonella associated with multidrug resistance cause invasive disease in sub-Saharan Africa. Specific lineages of serovars Typhimurium and Enteritidis have been implicated. Here we characterized the genomic diversity of 100 clinical non-typhoidal Salmonella collected from 93 patients in 2001 from the eastern, and in 2006–2018 from the western regions of The Gambia respectively. A total of 93 isolates (64 invasive, 23 gastroenteritis and six other sites) representing a single infection episode were phenotypically tested for antimicrobial susceptibility using the Kirby–Bauer disc diffusion technique. Whole genome sequencing of 100 isolates was performed using Illumina, and the reads were assembled and analysed using SPAdes. The Salmonella in Silico Typing Resource (SISTR) was used for serotyping. SNP differences among the 93 isolates were determined using Roary, and phylogenetic analysis was performed in the context of 495 African strains from the European Nucleotide Archive. Salmonella serovars Typhimurium (26/64; 30.6%) and Enteritidis (13/64; 20.3%) were associated with invasive disease, whilst other serovars were mainly responsible for gastroenteritis (17/23; 73.9%). The presence of three major serovar Enteritidis clades was confirmed, including the invasive West African clade, which made up more than half (11/16; 68.8%) of the genomes. Multidrug resistance was confined among the serovar Enteritidis West African clade. The presence of this epidemic virulent clade has potential for spread of resistance and thus important implications for systematic patient management. Surveillance and epidemiological investigations to inform control are warranted. © 2022 The Authors.
- Authors: Darboe, Saffiatou , Bradbury, Richard , Phelan, Jody , Kanteh, Abdoulie , Muhammad, Abdul-Khalie , Worwui, Archibald , Yang, Shangxin , Nwakanma, Davis , Perez-Sepulveda, Blanca , Kariuki, Samuel , Kwambana-Adams, Brenda , Antonio, Martin
- Date: 2022
- Type: Text , Journal article
- Relation: Microbial Genomics Vol. 8, no. 3 (2022), p.
- Full Text:
- Reviewed:
- Description: Non-typhoidal Salmonella associated with multidrug resistance cause invasive disease in sub-Saharan Africa. Specific lineages of serovars Typhimurium and Enteritidis have been implicated. Here we characterized the genomic diversity of 100 clinical non-typhoidal Salmonella collected from 93 patients in 2001 from the eastern, and in 2006–2018 from the western regions of The Gambia respectively. A total of 93 isolates (64 invasive, 23 gastroenteritis and six other sites) representing a single infection episode were phenotypically tested for antimicrobial susceptibility using the Kirby–Bauer disc diffusion technique. Whole genome sequencing of 100 isolates was performed using Illumina, and the reads were assembled and analysed using SPAdes. The Salmonella in Silico Typing Resource (SISTR) was used for serotyping. SNP differences among the 93 isolates were determined using Roary, and phylogenetic analysis was performed in the context of 495 African strains from the European Nucleotide Archive. Salmonella serovars Typhimurium (26/64; 30.6%) and Enteritidis (13/64; 20.3%) were associated with invasive disease, whilst other serovars were mainly responsible for gastroenteritis (17/23; 73.9%). The presence of three major serovar Enteritidis clades was confirmed, including the invasive West African clade, which made up more than half (11/16; 68.8%) of the genomes. Multidrug resistance was confined among the serovar Enteritidis West African clade. The presence of this epidemic virulent clade has potential for spread of resistance and thus important implications for systematic patient management. Surveillance and epidemiological investigations to inform control are warranted. © 2022 The Authors.
Human strongyloidiasis : complexities and pathways forward
- Buonfrate, Dora, Bradbury, Richard, Watts, Matthew, Bisoffi, Zeno
- Authors: Buonfrate, Dora , Bradbury, Richard , Watts, Matthew , Bisoffi, Zeno
- Date: 2023
- Type: Text , Journal article , Review
- Relation: Clinical Microbiology Reviews Vol. 36, no. 4 (2023), p.
- Full Text:
- Reviewed:
- Description: Strongyloidiasis is a World Health Organization neglected tropical disease usually caused by Strongyloides stercoralis, a parasitic worm with a complex life cycle. Globally, 300-600 million people are infected through contact with fecally contaminated soil. An autoinfective component of the life cycle can lead to chronic infection that may be asymptomatic or cause long-term symptoms, including malnourishment in children. Low larval output can limit the sensitivity of detection in stool, with serology being effectivebut less sensitive in immunocompromise. Host immunosuppression can trigger catastrophic, fatal hyperinfection/dissemination, where large numbers of larvae pierce the bowel wall and disseminate throughout the organs. Stable disease is effectivelytreated by single-dose ivermectin, with disease in immunocompromised patients treated with multiple doses. Strategies for management include raising awareness, clarifying zoonotic potential, the development and use of effectivediagnostic tests for epidemiological studies and individual diagnosis, and the implementation of treatment programs with research into therapeutic alternatives and medication safety. © 2023 American Society for Microbiology. All rights reserved.
- Authors: Buonfrate, Dora , Bradbury, Richard , Watts, Matthew , Bisoffi, Zeno
- Date: 2023
- Type: Text , Journal article , Review
- Relation: Clinical Microbiology Reviews Vol. 36, no. 4 (2023), p.
- Full Text:
- Reviewed:
- Description: Strongyloidiasis is a World Health Organization neglected tropical disease usually caused by Strongyloides stercoralis, a parasitic worm with a complex life cycle. Globally, 300-600 million people are infected through contact with fecally contaminated soil. An autoinfective component of the life cycle can lead to chronic infection that may be asymptomatic or cause long-term symptoms, including malnourishment in children. Low larval output can limit the sensitivity of detection in stool, with serology being effectivebut less sensitive in immunocompromise. Host immunosuppression can trigger catastrophic, fatal hyperinfection/dissemination, where large numbers of larvae pierce the bowel wall and disseminate throughout the organs. Stable disease is effectivelytreated by single-dose ivermectin, with disease in immunocompromised patients treated with multiple doses. Strategies for management include raising awareness, clarifying zoonotic potential, the development and use of effectivediagnostic tests for epidemiological studies and individual diagnosis, and the implementation of treatment programs with research into therapeutic alternatives and medication safety. © 2023 American Society for Microbiology. All rights reserved.
Imported Haycocknema perplexum Infection, United States
- Pritt, Bobbi, Mathison, Blaine, Bradbury, Richard, Liewluck, Teerin, Nicolau, Stefan, O’Horo, John, Grunst, David, Pinto, Marcus, Swanson, Amy, Virk, Abinash
- Authors: Pritt, Bobbi , Mathison, Blaine , Bradbury, Richard , Liewluck, Teerin , Nicolau, Stefan , O’Horo, John , Grunst, David , Pinto, Marcus , Swanson, Amy , Virk, Abinash
- Date: 2022
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 28, no. 11 (2022), p. 2281-2284
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- Description: We report an imported case of myositis caused by a rare parasite, Haycocknema perplexum, in Australia in a 37-year-old man who had progressive facial, axial, and limb weakness, dysphagia, dysphonia, increased levels of creatine kinase and hepatic aminotransferases, and peripheral eosinophilia for 8 years. He was given extended, high-dose albendazole. © 2022 Centers for Disease Control and Prevention (CDC). All rights reserved.
- Authors: Pritt, Bobbi , Mathison, Blaine , Bradbury, Richard , Liewluck, Teerin , Nicolau, Stefan , O’Horo, John , Grunst, David , Pinto, Marcus , Swanson, Amy , Virk, Abinash
- Date: 2022
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 28, no. 11 (2022), p. 2281-2284
- Full Text:
- Reviewed:
- Description: We report an imported case of myositis caused by a rare parasite, Haycocknema perplexum, in Australia in a 37-year-old man who had progressive facial, axial, and limb weakness, dysphagia, dysphonia, increased levels of creatine kinase and hepatic aminotransferases, and peripheral eosinophilia for 8 years. He was given extended, high-dose albendazole. © 2022 Centers for Disease Control and Prevention (CDC). All rights reserved.
Inactivating effects of common laboratory disinfectants, fixatives, and temperatures on the eggs of soil transmitted helminths
- Kines, Kristine, Fox, Mark, Ndubuisi, MacKevin, Verocai, Guilherme, Cama, Vitaliano, Bradbury, Richard
- Authors: Kines, Kristine , Fox, Mark , Ndubuisi, MacKevin , Verocai, Guilherme , Cama, Vitaliano , Bradbury, Richard
- Date: 2021
- Type: Text , Journal article
- Relation: Microbiology Spectrum Vol. 9, no. 3 (2021), p.
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- Description: Soil-transmitted helminths (STH) are important and widespread intestinal pathogens of humans and animals. It is presently unknown which inactivating procedures may be universally effective for safe transport, preservation, and disinfection of STH-contaminated specimens, and this lack of knowledge may expose laboratory staff to higher risk of laboratory-acquired infections (LAI’s). There are limited data on the efficacy of commonly used disinfectants and fecal fixatives for inactivating the eggs of STH. This work tested five disinfectants for surface cleanup, four storage temperature conditions, and six transport/storage fixatives, to inactivate eggs of three species of STH of animal origin (Ascaris suum “roundworm,” Trichuris vulpis “whipworm” and Ancylostoma caninum “hookworm”) as surrogates for human STH. Among disinfectants, exposure to 10% povidone-iodine for $5 min inactivated 100% of the three species tested, while 5 min exposure to 95% ethanol inactivated T. vulpis and A. caninum eggs. All of the fixatives tested had inactivation effects on A. caninum hookworm eggs within 24 h of exposure, except potassium dichromate, which required 48 h. 95% ethanol for $48 h inactivated eggs from all three STH species. Freezing at #220°C for $24 h inactivated eggs of T. vulpis and A. caninum, but only freezing at 280°C for $24 h inactivated .99% eggs, including A. suum. This work provides an evidence base for health and safety guidelines and mitigation strategies for the handling, storage, and disposal of stool samples containing STH eggs in laboratory, health care, childcare, or veterinary settings. IMPORTANCE This study systematically evaluates common laboratory disinfectants and storage conditions for their effectiveness in inactivating the infective stages of soil-transmitted helminths (STH). Animal-infecting proxy species were chosen to represent three major groups of STH that infect humans: roundworms, whipworms, and hookworms. Previously published work in this area typically focuses on a particular inactivation method, either for a single STH species, or on a subset of closely related species. Because prediagnostic fecal specimens must be regarded as potentially infectious with a mix of species, such information may be of limited utility in a working laboratory. We provide a straightforward summary of storage and disinfection methods that can achieve complete inactivation across a range of STH species, which represents a significant advance for clinical, veterinary and research laboratory biosafety. Copyright © 2021 Kines et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
- Authors: Kines, Kristine , Fox, Mark , Ndubuisi, MacKevin , Verocai, Guilherme , Cama, Vitaliano , Bradbury, Richard
- Date: 2021
- Type: Text , Journal article
- Relation: Microbiology Spectrum Vol. 9, no. 3 (2021), p.
- Full Text:
- Reviewed:
- Description: Soil-transmitted helminths (STH) are important and widespread intestinal pathogens of humans and animals. It is presently unknown which inactivating procedures may be universally effective for safe transport, preservation, and disinfection of STH-contaminated specimens, and this lack of knowledge may expose laboratory staff to higher risk of laboratory-acquired infections (LAI’s). There are limited data on the efficacy of commonly used disinfectants and fecal fixatives for inactivating the eggs of STH. This work tested five disinfectants for surface cleanup, four storage temperature conditions, and six transport/storage fixatives, to inactivate eggs of three species of STH of animal origin (Ascaris suum “roundworm,” Trichuris vulpis “whipworm” and Ancylostoma caninum “hookworm”) as surrogates for human STH. Among disinfectants, exposure to 10% povidone-iodine for $5 min inactivated 100% of the three species tested, while 5 min exposure to 95% ethanol inactivated T. vulpis and A. caninum eggs. All of the fixatives tested had inactivation effects on A. caninum hookworm eggs within 24 h of exposure, except potassium dichromate, which required 48 h. 95% ethanol for $48 h inactivated eggs from all three STH species. Freezing at #220°C for $24 h inactivated eggs of T. vulpis and A. caninum, but only freezing at 280°C for $24 h inactivated .99% eggs, including A. suum. This work provides an evidence base for health and safety guidelines and mitigation strategies for the handling, storage, and disposal of stool samples containing STH eggs in laboratory, health care, childcare, or veterinary settings. IMPORTANCE This study systematically evaluates common laboratory disinfectants and storage conditions for their effectiveness in inactivating the infective stages of soil-transmitted helminths (STH). Animal-infecting proxy species were chosen to represent three major groups of STH that infect humans: roundworms, whipworms, and hookworms. Previously published work in this area typically focuses on a particular inactivation method, either for a single STH species, or on a subset of closely related species. Because prediagnostic fecal specimens must be regarded as potentially infectious with a mix of species, such information may be of limited utility in a working laboratory. We provide a straightforward summary of storage and disinfection methods that can achieve complete inactivation across a range of STH species, which represents a significant advance for clinical, veterinary and research laboratory biosafety. Copyright © 2021 Kines et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children
- Nabwera, Helen, Espinoza, Josh, Worwui, Archibald, Betts, Modupeh, Bradbury, Richard
- Authors: Nabwera, Helen , Espinoza, Josh , Worwui, Archibald , Betts, Modupeh , Bradbury, Richard
- Date: 2021
- Type: Text , Journal article
- Relation: EBioMedicine Vol. 73, no. (2021), p.
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- Description: Background: The specific roles that gut microbiota, known pathogens, and host energy-regulating hormones play in the pathogenesis of non-edematous severe acute malnutrition (marasmus SAM) and moderate acute malnutrition (MAM) during outpatient nutritional rehabilitation are yet to be explored. Methods: We applied an ensemble of sample-specific (intra- and inter-modality) association networks to gain deeper insights into the pathogenesis of acute malnutrition and its severity among children under 5 years of age in rural Gambia, where marasmus SAM is most prevalent. Findings: Children with marasmus SAM have distinct microbiome characteristics and biologically-relevant multimodal biomarkers not observed among children with moderate acute malnutrition. Marasmus SAM was characterized by lower microbial richness and biomass, significant enrichments in Enterobacteriaceae, altered interactions between specific Enterobacteriaceae and key energy regulating hormones and their receptors. Interpretation: Our findings suggest that marasmus SAM is characterized by the collapse of a complex system with nested interactions and key associations between the gut microbiome, enteric pathogens, and energy regulating hormones. Further exploration of these systems will help inform innovative preventive and therapeutic interventions. Funding: The work was supported by the UK Medical Research Council (MRC; MC-A760-5QX00) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement; Bill and Melinda Gates Foundation (OPP 1066932) and the National Institute of Medical Research (NIMR), UK. This network analysis was supported by NIH U54GH009824 [CLD] and NSF OCE-1558453 [CLD]. © 2021 The Author(s). **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Richard Bradbury" is provided in this record**
- Authors: Nabwera, Helen , Espinoza, Josh , Worwui, Archibald , Betts, Modupeh , Bradbury, Richard
- Date: 2021
- Type: Text , Journal article
- Relation: EBioMedicine Vol. 73, no. (2021), p.
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- Description: Background: The specific roles that gut microbiota, known pathogens, and host energy-regulating hormones play in the pathogenesis of non-edematous severe acute malnutrition (marasmus SAM) and moderate acute malnutrition (MAM) during outpatient nutritional rehabilitation are yet to be explored. Methods: We applied an ensemble of sample-specific (intra- and inter-modality) association networks to gain deeper insights into the pathogenesis of acute malnutrition and its severity among children under 5 years of age in rural Gambia, where marasmus SAM is most prevalent. Findings: Children with marasmus SAM have distinct microbiome characteristics and biologically-relevant multimodal biomarkers not observed among children with moderate acute malnutrition. Marasmus SAM was characterized by lower microbial richness and biomass, significant enrichments in Enterobacteriaceae, altered interactions between specific Enterobacteriaceae and key energy regulating hormones and their receptors. Interpretation: Our findings suggest that marasmus SAM is characterized by the collapse of a complex system with nested interactions and key associations between the gut microbiome, enteric pathogens, and energy regulating hormones. Further exploration of these systems will help inform innovative preventive and therapeutic interventions. Funding: The work was supported by the UK Medical Research Council (MRC; MC-A760-5QX00) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement; Bill and Melinda Gates Foundation (OPP 1066932) and the National Institute of Medical Research (NIMR), UK. This network analysis was supported by NIH U54GH009824 [CLD] and NSF OCE-1558453 [CLD]. © 2021 The Author(s). **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Richard Bradbury" is provided in this record**
Medical parasitology taxonomy update, January 2018 to May 2020
- Mathison, Blaine, Bradbury, Richard, Pritt, Bobbi
- Authors: Mathison, Blaine , Bradbury, Richard , Pritt, Bobbi
- Date: 2021
- Type: Text , Journal article , Review
- Relation: Journal of Clinical Microbiology Vol. 59, no. 2 (2021), p.
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- Description: The taxonomy of parasites of medical and public health importance is rapidly evolving. This minireview provides an update of taxonomic revisions and additions in the field of medical parasitology from January 2018 to May 2020. Several established human parasites have been reassigned to different genera over the past 2 years, while a number of novel parasites of humans have been identified. A comprehensive summary of these changes is provided here, and Taenia suihominis is proposed as a replacement name for Taenia asiaticus Eom et al., which is a homonym of Taenia asiatica von Linstow. © 2021 American Society for Microbiology. All rights reserved. Erratum: Medical parasitology taxonomy update, January 2018 to May 2020 (Journal of Clinical Microbiology (2021) 59:2 (e01308-20) DOI: https://doi.org/10.1128/JCM.01308-20
- Authors: Mathison, Blaine , Bradbury, Richard , Pritt, Bobbi
- Date: 2021
- Type: Text , Journal article , Review
- Relation: Journal of Clinical Microbiology Vol. 59, no. 2 (2021), p.
- Full Text:
- Reviewed:
- Description: The taxonomy of parasites of medical and public health importance is rapidly evolving. This minireview provides an update of taxonomic revisions and additions in the field of medical parasitology from January 2018 to May 2020. Several established human parasites have been reassigned to different genera over the past 2 years, while a number of novel parasites of humans have been identified. A comprehensive summary of these changes is provided here, and Taenia suihominis is proposed as a replacement name for Taenia asiaticus Eom et al., which is a homonym of Taenia asiatica von Linstow. © 2021 American Society for Microbiology. All rights reserved. Erratum: Medical parasitology taxonomy update, January 2018 to May 2020 (Journal of Clinical Microbiology (2021) 59:2 (e01308-20) DOI: https://doi.org/10.1128/JCM.01308-20
Mosquito surveillance of West Nile and Usutu viruses in four territorial units of Slovakia and description of a confirmed autochthonous human case of West Nile fever, 2018 to 2019
- Čabanová, Viktória, Tichá, Elena, Bradbury, Richard, Zubriková, Dana, Valentová, Daniela, Chovancová, Gabriela, Grešáková,, Víchová, Bronislava, Šikutová, Silvie, Csank, Tomas, Hurníková, Zuzana, Miterpáková, Martina, Rudolf, Ivo
- Authors: Čabanová, Viktória , Tichá, Elena , Bradbury, Richard , Zubriková, Dana , Valentová, Daniela , Chovancová, Gabriela , Grešáková, , Víchová, Bronislava , Šikutová, Silvie , Csank, Tomas , Hurníková, Zuzana , Miterpáková, Martina , Rudolf, Ivo
- Date: 2021
- Type: Text , Journal article
- Relation: Eurosurveillance Vol. 26, no. 19 (2021), p.
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- Description: Background: Despite the known circulation of West Nile virus (WNV) and Usutu virus (USUV) in Slovakia, no formal entomological surveillance programme has been established there thus far. Aim: To conduct contemporaneous surveillance of WNV and USUV in different areas of Slovakia and to assess the geographical spread of these viruses through mosquito vectors. The first autochthonous human WNV infection in the country is also described. Methods: Mosquitoes were trapped in four Slovak territorial units in 2018 and 2019. Species were characterised morphologically and mosquito pools screened for WNV and USUV by real-time reverse-transcription PCRs. In pools with any of the two viruses detected, presence of pipiens complex group mosquitoes was verified using molecular approaches. Results: Altogether, 421 pools containing in total 4,508 mosquitoes were screened. Three pools tested positive for WNV and 16 for USUV. USUV was more prevalent than WNV, with a broader spectrum of vectors and was detected over a longer period (June-October vs August for WNV). The main vectors of both viruses were Culex pipiens sensu lato. Importantly, WNV and USUV were identified in a highly urbanised area of Bratislava city, Slovakias' capital city. Moreover, in early September 2019, a patient, who had been bitten by mosquitoes in southwestern Slovakia and who had not travelled abroad, was laboratory-confirmed with WNV infection. Conclusion: The entomological survey results and case report increase current understanding of the WNV and USUV situation in Slovakia. They underline the importance of vector surveillance to assess public health risks posed by these viruses. © 2021 European Centre for Disease Prevention and Control (ECDC). All rights reserved.
- Authors: Čabanová, Viktória , Tichá, Elena , Bradbury, Richard , Zubriková, Dana , Valentová, Daniela , Chovancová, Gabriela , Grešáková, , Víchová, Bronislava , Šikutová, Silvie , Csank, Tomas , Hurníková, Zuzana , Miterpáková, Martina , Rudolf, Ivo
- Date: 2021
- Type: Text , Journal article
- Relation: Eurosurveillance Vol. 26, no. 19 (2021), p.
- Full Text:
- Reviewed:
- Description: Background: Despite the known circulation of West Nile virus (WNV) and Usutu virus (USUV) in Slovakia, no formal entomological surveillance programme has been established there thus far. Aim: To conduct contemporaneous surveillance of WNV and USUV in different areas of Slovakia and to assess the geographical spread of these viruses through mosquito vectors. The first autochthonous human WNV infection in the country is also described. Methods: Mosquitoes were trapped in four Slovak territorial units in 2018 and 2019. Species were characterised morphologically and mosquito pools screened for WNV and USUV by real-time reverse-transcription PCRs. In pools with any of the two viruses detected, presence of pipiens complex group mosquitoes was verified using molecular approaches. Results: Altogether, 421 pools containing in total 4,508 mosquitoes were screened. Three pools tested positive for WNV and 16 for USUV. USUV was more prevalent than WNV, with a broader spectrum of vectors and was detected over a longer period (June-October vs August for WNV). The main vectors of both viruses were Culex pipiens sensu lato. Importantly, WNV and USUV were identified in a highly urbanised area of Bratislava city, Slovakias' capital city. Moreover, in early September 2019, a patient, who had been bitten by mosquitoes in southwestern Slovakia and who had not travelled abroad, was laboratory-confirmed with WNV infection. Conclusion: The entomological survey results and case report increase current understanding of the WNV and USUV situation in Slovakia. They underline the importance of vector surveillance to assess public health risks posed by these viruses. © 2021 European Centre for Disease Prevention and Control (ECDC). All rights reserved.
Parasitic disease surveillance, Mississippi, USA
- Bradbury, Richard, Lane, Meredioth, Arguello, Irene, Handali, Sukwan, Cooley, Gretchen
- Authors: Bradbury, Richard , Lane, Meredioth , Arguello, Irene , Handali, Sukwan , Cooley, Gretchen
- Date: 2021
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 27, no. 8 (2021), p. 2201-2204
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- Description: Surveillance for soil-transmitted helminths, strongyloidiasis, cryptosporidiosis, and giardiasis was conducted in Mississippi, USA. PCR performed on 224 fecal samples for all soil-transmitted helminths and on 370 samples for only Necator americanus and Strongyloides stercoralis identified 1 S. stercoralis infection. Seroprevalences were 8.8% for Toxocara, 27.4% for Cryptosporidium, 5.7% for Giardia, and 0.2% for Strongyloides parasites. © 2021 Centers for Disease Control and Prevention (CDC). All rights reserved. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Richard Bradbury" is provided in this record**
- Authors: Bradbury, Richard , Lane, Meredioth , Arguello, Irene , Handali, Sukwan , Cooley, Gretchen
- Date: 2021
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 27, no. 8 (2021), p. 2201-2204
- Full Text:
- Reviewed:
- Description: Surveillance for soil-transmitted helminths, strongyloidiasis, cryptosporidiosis, and giardiasis was conducted in Mississippi, USA. PCR performed on 224 fecal samples for all soil-transmitted helminths and on 370 samples for only Necator americanus and Strongyloides stercoralis identified 1 S. stercoralis infection. Seroprevalences were 8.8% for Toxocara, 27.4% for Cryptosporidium, 5.7% for Giardia, and 0.2% for Strongyloides parasites. © 2021 Centers for Disease Control and Prevention (CDC). All rights reserved. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Richard Bradbury" is provided in this record**
Parasitic infection surveillance in Mississippi delta children
- Bradbury, Richard, Arguello, Irene, Lane, Meredith, Cooley, Gretchen, Handali, Sukwan
- Authors: Bradbury, Richard , Arguello, Irene , Lane, Meredith , Cooley, Gretchen , Handali, Sukwan
- Date: 2020
- Type: Text , Journal article
- Relation: American Journal of Tropical Medicine and Hygiene Vol. 103, no. 3 (2020), p. 1150-1153
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- Description: Some recent studies suggest ongoing transmission of parasitic diseases in the American South; however, surveys in Mississippi children are lacking. We enrolled 166 children (median age 8 years, range 4–13 years) from the Mississippi Delta region and carried out multi-parallel real-time polymerase chain reaction (PCR) for Necator americanus, Ascaris lumbricoides, and Strongyloides stercoralis on their stool samples. Dried blood spots were obtained for multiplex serology antibody detection. Of 166 children, all reported having flushable toilets, 11% had soil exposure, and 34% had a pet dog or cat. None had prior diagnosis or treatment of parasitic disease. Multi-parallel real-time PCRs were negative on the 89 stool DNA extracts available for testing. Dried blood spot testing of all 166 children determined the seroprevalence of IgG antibodies to Toxocara spp. (3.6%), Cryptosporidium (2.4%), S. stercoralis, Fasciola hepatica, and Giardia duodenalis (all 0%). In conclusion, parasitic infections and exposure were scarce in this population. Larger studies of at-risk populations are needed. © 2020 by The American Society of Tropical Medicine and Hygiene. ***Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Richard Bradbury ” is provided in this record***
- Description: This work was funded by the Centers for Disease Control and Prevention (RSB), the Blakeslee Fund for Genetics Research at Smith College (N. P. and S. A. W.), and the University of Mississippi Medical Center (Office of the Vice Chancellor for Research, the University of Mississippi Medical Center). R. B. reports a patent WO2019060840 “Removing Interfering Host NucleicAcids for Molecular Parasite Detection” with royalties paid to Centers for Disease Control and Prevention. This trial was observational and is exempt from registration at clinicaltrials.gov Disclaimer: The findings and conclusions of this work are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention/the Agency for Toxic Substances and Disease Registry. This work was presented at the American Society of Tropical Medicine and Hygiene Conference: Poster 522, October 28–November 1, New Orleans, LA
- Authors: Bradbury, Richard , Arguello, Irene , Lane, Meredith , Cooley, Gretchen , Handali, Sukwan
- Date: 2020
- Type: Text , Journal article
- Relation: American Journal of Tropical Medicine and Hygiene Vol. 103, no. 3 (2020), p. 1150-1153
- Full Text:
- Reviewed:
- Description: Some recent studies suggest ongoing transmission of parasitic diseases in the American South; however, surveys in Mississippi children are lacking. We enrolled 166 children (median age 8 years, range 4–13 years) from the Mississippi Delta region and carried out multi-parallel real-time polymerase chain reaction (PCR) for Necator americanus, Ascaris lumbricoides, and Strongyloides stercoralis on their stool samples. Dried blood spots were obtained for multiplex serology antibody detection. Of 166 children, all reported having flushable toilets, 11% had soil exposure, and 34% had a pet dog or cat. None had prior diagnosis or treatment of parasitic disease. Multi-parallel real-time PCRs were negative on the 89 stool DNA extracts available for testing. Dried blood spot testing of all 166 children determined the seroprevalence of IgG antibodies to Toxocara spp. (3.6%), Cryptosporidium (2.4%), S. stercoralis, Fasciola hepatica, and Giardia duodenalis (all 0%). In conclusion, parasitic infections and exposure were scarce in this population. Larger studies of at-risk populations are needed. © 2020 by The American Society of Tropical Medicine and Hygiene. ***Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Richard Bradbury ” is provided in this record***
- Description: This work was funded by the Centers for Disease Control and Prevention (RSB), the Blakeslee Fund for Genetics Research at Smith College (N. P. and S. A. W.), and the University of Mississippi Medical Center (Office of the Vice Chancellor for Research, the University of Mississippi Medical Center). R. B. reports a patent WO2019060840 “Removing Interfering Host NucleicAcids for Molecular Parasite Detection” with royalties paid to Centers for Disease Control and Prevention. This trial was observational and is exempt from registration at clinicaltrials.gov Disclaimer: The findings and conclusions of this work are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention/the Agency for Toxic Substances and Disease Registry. This work was presented at the American Society of Tropical Medicine and Hygiene Conference: Poster 522, October 28–November 1, New Orleans, LA
Pathogen genomics in public health
- Armstrong, Gregory, MacCannell, Duncan, Taylor, Jill, Carleton, Heather, Neuhaus, Elizabeth, Bradbury, Richard, Posey, James, Gwinn, Marta
- Authors: Armstrong, Gregory , MacCannell, Duncan , Taylor, Jill , Carleton, Heather , Neuhaus, Elizabeth , Bradbury, Richard , Posey, James , Gwinn, Marta
- Date: 2019
- Type: Text , Journal article
- Relation: New England Journal of Medicine Vol. 381, no. 26 (2019), p. 2569-2580
- Full Text:
- Reviewed:
- Authors: Armstrong, Gregory , MacCannell, Duncan , Taylor, Jill , Carleton, Heather , Neuhaus, Elizabeth , Bradbury, Richard , Posey, James , Gwinn, Marta
- Date: 2019
- Type: Text , Journal article
- Relation: New England Journal of Medicine Vol. 381, no. 26 (2019), p. 2569-2580
- Full Text:
- Reviewed:
Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing
- Flaherty, Briana, Barratt, Joel, Lane, Meredith, Talundzic, Eldin, Bradbury, Richard
- Authors: Flaherty, Briana , Barratt, Joel , Lane, Meredith , Talundzic, Eldin , Bradbury, Richard
- Date: 2021
- Type: Text , Journal article
- Relation: Microbiome Vol. 9, no. 1 (2021), p.
- Full Text:
- Reviewed:
- Description: Background: Targeted amplicon deep sequencing (TADS) has enabled characterization of diverse bacterial communities, yet the application of TADS to communities of parasites has been relatively slow to advance. The greatest obstacle to this has been the genetic diversity of parasitic agents, which include helminths, protozoa, arthropods, and some acanthocephalans. Meanwhile, universal amplification of conserved loci from all parasites without amplifying host DNA has proven challenging. Pan-eukaryotic PCRs preferentially amplify the more abundant host DNA, obscuring parasite-derived reads following TADS. Flaherty et al. (2018) described a pan-parasitic TADS method involving amplification of eukaryotic 18S rDNA regions possessing restriction sites only in vertebrates. Using this method, host DNA in total DNA extracts could be selectively digested prior to PCR using restriction enzymes, thereby increasing the number of parasite-derived reads obtained following NGS. This approach showed promise though was only as sensitive as conventional PCR. Results: Here, we expand on this work by designing a second set of pan-eukaryotic primers flanking the priming sites already described, enabling nested PCR amplification of the established 18S rDNA target. This nested approach facilitated introduction of a second restriction digestion between the first and second PCR, reducing the proportional mass of amplifiable host-derived DNA while increasing the number of PCR amplification cycles. We applied this method to blood specimens containing Babesia, Plasmodium, various kinetoplastids, and filarial nematodes and confirmed its limit of detection (LOD) to be approximately 10-fold lower than previously described, falling within the range of most qPCR methods. Conclusions: The assay detects and differentiates the major malaria parasites of humans, along with several other clinically important blood parasites. This represents an important step towards a TADS-based universal parasite diagnostic (UPDx) test with a sufficient LOD for routine applications. [MediaObject not available: see fulltext.]. © 2021, The Author(s).
- Authors: Flaherty, Briana , Barratt, Joel , Lane, Meredith , Talundzic, Eldin , Bradbury, Richard
- Date: 2021
- Type: Text , Journal article
- Relation: Microbiome Vol. 9, no. 1 (2021), p.
- Full Text:
- Reviewed:
- Description: Background: Targeted amplicon deep sequencing (TADS) has enabled characterization of diverse bacterial communities, yet the application of TADS to communities of parasites has been relatively slow to advance. The greatest obstacle to this has been the genetic diversity of parasitic agents, which include helminths, protozoa, arthropods, and some acanthocephalans. Meanwhile, universal amplification of conserved loci from all parasites without amplifying host DNA has proven challenging. Pan-eukaryotic PCRs preferentially amplify the more abundant host DNA, obscuring parasite-derived reads following TADS. Flaherty et al. (2018) described a pan-parasitic TADS method involving amplification of eukaryotic 18S rDNA regions possessing restriction sites only in vertebrates. Using this method, host DNA in total DNA extracts could be selectively digested prior to PCR using restriction enzymes, thereby increasing the number of parasite-derived reads obtained following NGS. This approach showed promise though was only as sensitive as conventional PCR. Results: Here, we expand on this work by designing a second set of pan-eukaryotic primers flanking the priming sites already described, enabling nested PCR amplification of the established 18S rDNA target. This nested approach facilitated introduction of a second restriction digestion between the first and second PCR, reducing the proportional mass of amplifiable host-derived DNA while increasing the number of PCR amplification cycles. We applied this method to blood specimens containing Babesia, Plasmodium, various kinetoplastids, and filarial nematodes and confirmed its limit of detection (LOD) to be approximately 10-fold lower than previously described, falling within the range of most qPCR methods. Conclusions: The assay detects and differentiates the major malaria parasites of humans, along with several other clinically important blood parasites. This represents an important step towards a TADS-based universal parasite diagnostic (UPDx) test with a sufficient LOD for routine applications. [MediaObject not available: see fulltext.]. © 2021, The Author(s).
Strongyloides fuelleborni kellyi in New Guinea : neglected, ignored and unexplored
- Authors: Bradbury, Richard
- Date: 2021
- Type: Text , Journal article
- Relation: Microbiology Australia Vol. 42, no. 4 (2021), p. 169-172
- Full Text:
- Reviewed:
- Description: Strongyloidiasis remains endemic throughout the Island of New Guinea. While many infections are caused by Strongyloides stercoralis, a second human-infecting Strongyloides species, Strongyloides fuelleborni kellyi, is also present. S. f. kellyi infections are most common in infants and young children, and those with high-intensity infections might develop a potentially fatal protein-losing enteropathy, swollen belly syndrome. Surprisingly little work has been performed on S. f. kellyi. Unlike S. stercoralis, S. f. kellyi is passed in faeces as eggs rather than rhabditiform larvae. There is no specific diagnostic test. This review summarises what is currently known about the biology, epidemiology, and clinical impact of S. f. kellyi infections. Features that might be used to differentiate S. f. kellyi from hookworm and S. stercoralis are also discussed. S. f. kellyi remains a neglected, ignored, and unexplored human helminth infection, worthy of further research. © 2021 Journal Compilation
- Authors: Bradbury, Richard
- Date: 2021
- Type: Text , Journal article
- Relation: Microbiology Australia Vol. 42, no. 4 (2021), p. 169-172
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- Description: Strongyloidiasis remains endemic throughout the Island of New Guinea. While many infections are caused by Strongyloides stercoralis, a second human-infecting Strongyloides species, Strongyloides fuelleborni kellyi, is also present. S. f. kellyi infections are most common in infants and young children, and those with high-intensity infections might develop a potentially fatal protein-losing enteropathy, swollen belly syndrome. Surprisingly little work has been performed on S. f. kellyi. Unlike S. stercoralis, S. f. kellyi is passed in faeces as eggs rather than rhabditiform larvae. There is no specific diagnostic test. This review summarises what is currently known about the biology, epidemiology, and clinical impact of S. f. kellyi infections. Features that might be used to differentiate S. f. kellyi from hookworm and S. stercoralis are also discussed. S. f. kellyi remains a neglected, ignored, and unexplored human helminth infection, worthy of further research. © 2021 Journal Compilation
Strongyloides genotyping: a review of methods and application in public health and population genetics
- Bradbury, Richard, Pafčo, Barbora, Nosková, Eva, Hasegawa, Hideo
- Authors: Bradbury, Richard , Pafčo, Barbora , Nosková, Eva , Hasegawa, Hideo
- Date: 2021
- Type: Text , Journal article , Review
- Relation: International Journal for Parasitology Vol. 51, no. 13-14 (2021), p. 1153-1166
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- Reviewed:
- Description: Strongyloidiasis represents a major medical and veterinary helminthic disease. Human infection is caused by Strongyloides stercoralis, Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi, with S. stercoralis accounting for the majority of cases. Strongyloides f. fuelleborni likely represents a zoonosis acquired from non-human primates (NHPs), while no animal reservoir for S. f. kellyi infection has been found. Whether S. stercoralis represents a zoonosis acquired from dogs and cats remains unanswered. Over the past two decades various tools have been applied to genotype Strongyloides spp. The most commonly sequenced markers have been the hyper-variable regions I and IV of the 18S rRNA gene and selected portions of the cytochrome c oxidase subunit I gene. These markers have been sequenced and compared in Strongyloides from multiple hosts and geographical regions. More recently, a machine learning algorithm multi-locus sequence typing approach has been applied using these markers, while others have applied whole genome sequencing. Genotyping of Strongyloides from dogs, cats, NHPs and humans has identified that S. stercoralis likely originated in dogs and adapted to human hosts. It has also been demonstrated that S. stercoralis is distinct from S. f. fuelleborni and S. f. kellyi. Two distinct genetic clades of S. stercoralis exist, one restricted to dogs and another infecting humans, NHPs, dogs and cats. Genotyping of S. f. fuelleborni has identified two separate clades, one associated with African isolates and another Indochinese peninsular clade. This review summarises the history and development of genotyping tools for Strongyloides spp. It describes the findings of major studies to date in the context of the epidemiology and evolutionary biology of these helminths, with a specific focus on human-infecting species. © 2021 Australian Society for Parasitology
- Authors: Bradbury, Richard , Pafčo, Barbora , Nosková, Eva , Hasegawa, Hideo
- Date: 2021
- Type: Text , Journal article , Review
- Relation: International Journal for Parasitology Vol. 51, no. 13-14 (2021), p. 1153-1166
- Full Text:
- Reviewed:
- Description: Strongyloidiasis represents a major medical and veterinary helminthic disease. Human infection is caused by Strongyloides stercoralis, Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi, with S. stercoralis accounting for the majority of cases. Strongyloides f. fuelleborni likely represents a zoonosis acquired from non-human primates (NHPs), while no animal reservoir for S. f. kellyi infection has been found. Whether S. stercoralis represents a zoonosis acquired from dogs and cats remains unanswered. Over the past two decades various tools have been applied to genotype Strongyloides spp. The most commonly sequenced markers have been the hyper-variable regions I and IV of the 18S rRNA gene and selected portions of the cytochrome c oxidase subunit I gene. These markers have been sequenced and compared in Strongyloides from multiple hosts and geographical regions. More recently, a machine learning algorithm multi-locus sequence typing approach has been applied using these markers, while others have applied whole genome sequencing. Genotyping of Strongyloides from dogs, cats, NHPs and humans has identified that S. stercoralis likely originated in dogs and adapted to human hosts. It has also been demonstrated that S. stercoralis is distinct from S. f. fuelleborni and S. f. kellyi. Two distinct genetic clades of S. stercoralis exist, one restricted to dogs and another infecting humans, NHPs, dogs and cats. Genotyping of S. f. fuelleborni has identified two separate clades, one associated with African isolates and another Indochinese peninsular clade. This review summarises the history and development of genotyping tools for Strongyloides spp. It describes the findings of major studies to date in the context of the epidemiology and evolutionary biology of these helminths, with a specific focus on human-infecting species. © 2021 Australian Society for Parasitology
Surveillance for soil-transmitted helminths in high-risk county, Mississippi, USA
- Bradbury, Richard, Martin, Lora, Malloch, Lacy, Martin, Maygan, Williams, John, Patterson, Kayla, Sanders, Cameron, Singh, Gurbaksh, Arguello, Irene, Rodriguez, Eduardo, Byers, Paul, Haynie, Lisa, Qvarnstrom, Yvonne, Hobbs, Charlotte
- Authors: Bradbury, Richard , Martin, Lora , Malloch, Lacy , Martin, Maygan , Williams, John , Patterson, Kayla , Sanders, Cameron , Singh, Gurbaksh , Arguello, Irene , Rodriguez, Eduardo , Byers, Paul , Haynie, Lisa , Qvarnstrom, Yvonne , Hobbs, Charlotte
- Date: 2023
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 29, no. 12 (2023), p. 2533-2537
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- Description: Recent reports of hookworm infection in Alabama, USA, has prompted surveillance in Mississippi, given the states’ similar environmental conditions. We collected stool specimens from 277 children in Rankin County, Mississippi. Kato–Katz microscopic smear, agar plate culture, and quantitative PCR indicated no soil-transmitted helminths. Nevertheless, further surveillance in other high-risk Mississippi counties is warranted. © 2023 Centers for Disease Control and Prevention (CDC). All rights reserved.
- Authors: Bradbury, Richard , Martin, Lora , Malloch, Lacy , Martin, Maygan , Williams, John , Patterson, Kayla , Sanders, Cameron , Singh, Gurbaksh , Arguello, Irene , Rodriguez, Eduardo , Byers, Paul , Haynie, Lisa , Qvarnstrom, Yvonne , Hobbs, Charlotte
- Date: 2023
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 29, no. 12 (2023), p. 2533-2537
- Full Text:
- Reviewed:
- Description: Recent reports of hookworm infection in Alabama, USA, has prompted surveillance in Mississippi, given the states’ similar environmental conditions. We collected stool specimens from 277 children in Rankin County, Mississippi. Kato–Katz microscopic smear, agar plate culture, and quantitative PCR indicated no soil-transmitted helminths. Nevertheless, further surveillance in other high-risk Mississippi counties is warranted. © 2023 Centers for Disease Control and Prevention (CDC). All rights reserved.