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Yanmaz B, Özgen EK, Sayı O, Erdoğan Y, Aslan MH, İba Yılmaz S, Karadeniz Pütür E, Polat N, Özmen M, Şerifoğlu Bağatır P, Ildız S. Phylogenetic Analysis of Brucella melitensis Strains Isolated from Humans Using 16S rRNA Sequencing and Multiple Locus Variable Number of Tandem Repeats Analysis-16. Vector Borne Zoonotic Dis 2024. [PMID: 38608219 DOI: 10.1089/vbz.2023.0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] Open
Abstract
Background: Brucellosis is the most important public health problem worldwide, and the annual incidence of the disease in humans is 2.1 million. The Brucella genome is highly conserved, with over 90% similarity among species. The aim of this study was to perform species-level identification of Brucella spp. strains isolated from humans diagnosed with brucellosis and to further investigate the phylogenetic relationships using multiple locus variable number of tandem repeats analysis (MLVA)-16 and 16S rRNA sequencing analysis. Materials and Methods: Brucella spp. was isolated from the blood cultures of 54 patients who tested positive for brucellosis through serological examinations. Real-time PCR was used to identify the isolates in species, and the genus level of Brucella was confirmed with 16S rRNA. All isolates were subjected to phylogenetic analysis using variable number of tandem repeat analysis with multiple loci. Results: Subsequent analysis via real-time PCR confirmed these isolates to be of the Brucella melitensis species. The 16S rRNA sequence analysis showed 100% homogeneity among the isolates. MLVA revealed the formation of five different genotypic groups. While two groups were formed based on the 16S rRNA sequence analysis, five groups were formed in the MLVA. Conclusions: The study concluded that 16S rRNA sequence analysis alone did not provide sufficient discrimination for phylogenetic analysis but served as a supportive method for identification. MLVA exhibited higher phylogenetic power. The widespread isolation of B. melitensis from human brucellosis cases highlights the importance of controlling brucellosis in small ruminants to prevent human infections.
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Affiliation(s)
- Berna Yanmaz
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Burdur Mehmet Akif Ersoy University, Burdur, Türkiye
| | - Ediz Kağan Özgen
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Atatürk University, Erzurum, Türkiye
| | - Orbay Sayı
- Veterinary Control Institute, Republic of Türkiye Ministry of Agriculture and Forestry, İzmir, Türkiye
| | - Yasemin Erdoğan
- Veterinary Control Institute, Republic of Türkiye Ministry of Agriculture and Forestry, Erzurum, Türkiye
| | - Mehtap Hülya Aslan
- Department of Microbiology, Health Sciences University Erzurum Regional Education and Research Hospital, Erzurum, Türkiye
| | - Sibel İba Yılmaz
- Department of Infection Diseases and Clinical Microbiology, Health Sciences University Erzurum Regional Education and Research Hospital, Erzurum, Türkiye
| | - Elif Karadeniz Pütür
- Veterinary Control Institute, Republic of Türkiye Ministry of Agriculture and Forestry, Erzurum, Türkiye
| | - Nebahat Polat
- Veterinary Control Institute, Republic of Türkiye Ministry of Agriculture and Forestry, Erzurum, Türkiye
| | - Murat Özmen
- Veterinary Control Institute, Republic of Türkiye Ministry of Agriculture and Forestry, Erzurum, Türkiye
| | - Perihan Şerifoğlu Bağatır
- Veterinary Control Institute, Republic of Türkiye Ministry of Agriculture and Forestry, Erzurum, Türkiye
| | - Sedat Ildız
- Graduate School of Health Sciences of Ankara University and General Directorate of Food and Control, Republic of Türkiye Ministry of Agriculture and Forestry, Ankara, Türkiye
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Hu L, Tiesinga J. Case report: Primary vulvar adenocarcinoma of mammary gland type-its genetic characteristics by focused next-generation sequencing. Pathol Oncol Res 2024; 30:1611376. [PMID: 38572338 PMCID: PMC10989740 DOI: 10.3389/pore.2024.1611376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/09/2024] [Indexed: 04/05/2024]
Abstract
Mammary-like vulvar adenocarcinoma (MLVA) is an exceedingly rare subtype of vulvar adenocarcinoma that shares features with mammary gland tissue. Due to its rarity and lack of consensus, MLVA presents diagnostic challenges to pathologists. We present the case of a 59-year-old female with an ulcerated mass on the right side of the external genitalia, diagnosed as MLVA. Comprehensive immunohistochemistry (IHC) and gene sequencing studies were performed to characterize the tumor. IHC analysis revealed triple expression of hormonal receptors (estrogen receptor, progesterone receptor, and HER2), supporting the mammary gland origin of the tumor. Gene sequencing identified unique genetic mutations associated with the expression of hormonal markers. One fusion gene (ERBB2-NAGLU) has not been reported in any tumors, and other mutations with unique mutation types have not been previously reported in MLVA. Our findings shed light on the molecular characteristics of MLV and may help improve the diagnosis and treatment of this rare type of vulvar adenocarcinoma.
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Affiliation(s)
- Lina Hu
- Alaska Native Medical Center, Department of Pathology, Anchorage, AK, United States
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Liu G, Ma X, Zhang R, Lü J, Zhou P, Liu B, Liu T, Ren H, Liu Z, Li Z, Jiang X. Epidemiological changes and molecular characteristics of Brucella strains in Ningxia, China. Front Microbiol 2024; 15:1320845. [PMID: 38314436 PMCID: PMC10835715 DOI: 10.3389/fmicb.2024.1320845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024] Open
Abstract
Objective Human brucellosis causes serious public health concerns in Ningxia, China. Methods This study employed epidemiological, bacteriological, and multiple-locus variable-number tandem repeat analysis (MLVA) methods to conduct an epidemiological investigation, which is necessary for devising tailored control strategies. Results Between 1958 and 2022, 29,892 cases were reported, with an average annual number of cases and incidence of 467 and 7.1/100,000, respectively. The epidemic situation gradually worsened, with cases escalating from 26 cases in 2005 to 6,292 in 2022, with the incidence rate rising from 0.441 in 2005 to 86.83 in 2022. Geographically, the disease spread from a single affected county in 2004 to encompass all 22 counties in 2022. Yanchi County had the highest incidence, followed by the Hongsibao and Tongxin counties. These data suggest that Brucella infection has become a rampant regional concern in human brucellosis. Between 1958 and 2019, a total of 230 Brucella strains were identified across four studied hosts. These strains comprised four species with 12 biovars, including B. melitensis bv. 1, bv. 2, bv. 3, B. abortus bv. 1, bv. 3, bv. 4, bv. 5, bv. 6, bv. 7, B. suis bv. 1 and bv. 3, and B. canis. These data highlight the high species/biovars and host diversity of the Brucella population, posing a substantial challenge to brucellosis surveillance. There was an apparent transition from multiple species/biovars historically to the current dominance of a single species, B. melitensis, emphasizing the requirement for strengthening surveillance of B. melitensis. Genotypes 42 and 116, constituting 96.2% of the total number of genotypes, predominated in panel 1 and MLVA-11, indicating that all strains belong to the East Mediterranean lineage. MLVA cluster analysis revealed persistent transmission of dominant circulating genotypes, presenting an epidemic pattern characterized primarily by epidemiologically related cases with a few sporadic cases. Strains in this study exhibited high genetic homogeneity with strains from the Northwest, and those from Kazakhstan and Mongolia. Conclusion The epidemic situation of human brucellosis has gradually worsened; the rampant epidemic of the disease has become a regional concern. The present study highlights that implementing the of targeted surveillance and intervention strategies is urge.
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Affiliation(s)
- Guangtian Liu
- The Fourth People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Xueping Ma
- Ningxia Hui Autonomous Region Center for Disease Control and Prevention, Yinchuan, China
| | - Ruiqing Zhang
- The Fourth People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Jufen Lü
- The College of Public Health, Ningxia Medical University, Yinchuan, China
| | - Pan Zhou
- The Fourth People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Bofei Liu
- The Fourth People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Tao Liu
- The Fourth People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Hui Ren
- The Fourth People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Zhiguo Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuefeng Jiang
- The Fourth People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
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Xue H, Li J, Ma L, Yang X, Ren L, Zhao Z, Wang J, Zhao Y, Zhao Z, Zhang X, Liu Z, Li Z. Seroprevalence and Molecular Characterization of Brucella abortus from the Himalayan Marmot in Qinghai, China. Infect Drug Resist 2023; 16:7721-7734. [PMID: 38144222 PMCID: PMC10749113 DOI: 10.2147/idr.s436950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 12/26/2023] Open
Abstract
Objective Brucellosis is a serious public health issue in Qinghai (QH), China. Surveying the seroprevalence and isolation of B. abortus strains from marmots is key to understanding the role of wildlife in the maintenance and spread of brucellosis. Methods In this study, a set of methods, including a serology survey, bacteriology, antibiotic susceptibility, molecular genotyping (MLST and MLVA), and genome sequencing, were employed to characterize the two B. abortus strains. Results The seroprevalence of brucellosis in marmots was 7.0% (80/1146) by serum tube agglutination test (SAT); one Brucella strain was recovered from these positive samples, and another Brucella strain from a human. Two strains were identified as B. abortus bv. 1 and were susceptible to all eight drugs examined. The distribution patterns of the accessory genes, virulence associated genes, and resistance genes of the two strains were consistent, and there was excellent collinearity between the two strains on chromosome I, but they had significant SVs in chromosome II, including inversions and translocations. MLST genotyping identified two B. abortus strains as ST2, and MLVA-16 analysis showed that the two strains clustered with strains from northern China. WGS-SNP phylogenetic analysis showed that the strains were genetically homogeneous with strains from the northern region, implying that strains from a common lineage were spread continuously in different regions and hosts. Conclusion Seroprevalence and molecular clues demonstrated frequent direct or indirect contact between sheep/goats, cattle, and marmots, implying that wildlife plays a vital role in the maintenance and spread of B. abortus in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Hongmei Xue
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Jiquan Li
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Li Ma
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Xuxin Yang
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Lingling Ren
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Zhijun Zhao
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Jianling Wang
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Yuanbo Zhao
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Zhongzhi Zhao
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Xuefei Zhang
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, People’s Republic of China
| | - Zhiguo Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Zhenjun Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
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Rahimi H, Tukmechi A, Rashidian E. Genetic diversity of Brucella melitensis isolates from sheep and goat milk in Iran. Vet Res Forum 2023; 14:649-657. [PMID: 38174090 PMCID: PMC10759773 DOI: 10.30466/vrf.2023.1988859.3768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/20/2023] [Indexed: 01/05/2024]
Abstract
The genetic diversity of Brucella strains has not been fully understood. To investigate this, the genetic characteristics of 64 isolates of Brucella melitensis from sheep and goats' milk were studied using random fragment length polymorphism (RFLP) and multiple locus variable-number tandem repeat analysis (MLVA-16) methods developed in Orsay, France (MLVA-16Orsay). The RFLP analysis revealed that all 64 isolates were of biovar one. The MLVA-typing showed that one sample was simultaneously infected with two strains of B. melitensis and the genotype of 65 isolate was analyzed. Four genotypes (47, 42, 43, and 63) were identified using MLVA-8 (panel 1), whereas six genotypes (138, 125, 116, 108, and two unknown genotypes) were identified using MLVA11 (panels 1 and 2A). From the review of MLVA-16 (panels 1, 2A, and 2B), panel 2B showed a very high discriminatory power. Two loci of Bruc04 and Bruc30 from this panel had diversity index values higher than 0.71 and the average diversity index was 0.619. So MLVA-16Orsay 34 showed the genotype indicating a low genetic homogeneity among the isolates. The findings of MLVA genotyping of the isolates suggest that strains of B. melitensis isolated from the milk of small ruminants in Iran are most closely related to the isolates from neighboring countries of the Eastern Mediterranean group. To the best of our knowledge, this is the first study to indicate the potential use of MLVA genotyping for simultaneous detection of specimen contamination using two different B. melitensis biovars.
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Affiliation(s)
- Heidar Rahimi
- Department of Microbiology, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran;
| | - Amir Tukmechi
- Department of Microbiology, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran;
| | - Ehsan Rashidian
- Department of Microbiology, Faculty of Veterinary Medicine, Lorestan University, Khorramabad, Iran.
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Buni D, Kovács ÁB, Földi D, Bányai K, Bali K, Domán M, Wehmann E, Bradbury J, Bottinelli M, Catania S, Stefani E, Lysnyansky I, Kovács L, Grózner D, Gyuranecz M, Kreizinger Z. Development of molecular assays for the analysis of genetic relationships of Mycoplasma iowae. Vet Microbiol 2023; 287:109909. [PMID: 37925876 DOI: 10.1016/j.vetmic.2023.109909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Mycoplasma iowae is a worldwide spread and economically important avian pathogen that mostly infects turkeys. Currently, multi-locus sequence typing (MLST) serves as the gold standard method for strain identification in M. iowae. However, additional robust genotyping methods are required to effectively monitor M. iowae infections and conduct epidemiological investigations. The first aim of this study was to develop genotyping assays with high resolution, that specifically target M. iowae, namely a multiple-locus variable number of tandem-repeats analysis (MLVA) and a core genome multi-locus sequence typing (cgMLST) schema. The second aim was the determination of relationships among a diverse selection of M. iowae strains and clinical isolates with a previous and the newly developed assays. The MLVA was designed based on the analyses of tandem-repeat (TR) regions in the six serotype reference strains (I, J, K, N, Q and R). The cgMLST schema was developed based on the coding sequences (CDSs) common in 95% of the examined 99 isolates. The samples were submitted for a previously published MLST assay for comparison with the developed methods. Out of 94 TR regions identified, 17 alleles were selected for further evaluation by PCR. Finally, seven alleles were chosen to establish the MLVA assay. Additionally, whole genome sequence analyses identified a total of 676 CDSs shared by 95% of the isolates, all of which were included into the developed cgMLST schema. The MLVA discriminated 19 distinct genotypes (GT), while with the cgMLST assay 79 sequence types (ST) could be determined with Simpson's diversity indices of 0.810 (MLVA) and 0.989 (cgMLST). The applied assays consistently identified the same main clusters among the diverse selection of isolates, thereby demonstrating their suitability for various genetic analyses and their ability to yield congruent results.
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Affiliation(s)
- Dominika Buni
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary
| | - Áron Botond Kovács
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Dorottya Földi
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Krisztián Bányai
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary; University of Veterinary Medicine Budapest, István utca 2., Budapest 1078, Hungary
| | - Krisztina Bali
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Marianna Domán
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Enikő Wehmann
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Janet Bradbury
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, Wirral CH64 7TE, United Kingdom
| | - Marco Bottinelli
- Mycoplasma Unit, WOAH Reference Laboratory for Avian Mycoplasmosis, SCT-1, Istituto Zooprofilattico Sperimentale delle Venezie, Via Bovolino 1/C, Buttapietra, Verona 37060, Italy
| | - Salvatore Catania
- Mycoplasma Unit, WOAH Reference Laboratory for Avian Mycoplasmosis, SCT-1, Istituto Zooprofilattico Sperimentale delle Venezie, Via Bovolino 1/C, Buttapietra, Verona 37060, Italy
| | - Elisabetta Stefani
- Mycoplasma Unit, WOAH Reference Laboratory for Avian Mycoplasmosis, SCT-1, Istituto Zooprofilattico Sperimentale delle Venezie, Via Bovolino 1/C, Buttapietra, Verona 37060, Italy
| | - Inna Lysnyansky
- Department of Avian Diseases, Kimron Veterinary Institute, Beit Dagan, Israel
| | - László Kovács
- University of Veterinary Medicine Budapest, István utca 2., Budapest 1078, Hungary; Poultry-Care Kft., Lehel út 21., Újszász 5052, Hungary
| | - Dénes Grózner
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary
| | - Miklós Gyuranecz
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary; University of Veterinary Medicine Budapest, István utca 2., Budapest 1078, Hungary; MolliScience Kft., Március 15. utca 1, Biatorbágy 2051, Hungary
| | - Zsuzsa Kreizinger
- Veterinary Medical Research Institute, Hungarian Research Network, Hungária körút 21, Budapest 1143, Hungary; MolliScience Kft., Március 15. utca 1, Biatorbágy 2051, Hungary.
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Gcebe N, Pierneef RE, Michel AL, Hlokwe MT. Mycobacteriosis in slaughter pigs from South Africa from 1991 to 2002: Mycobacterium spp. diversity and Mycobacterium avium complex genotypes. Front Microbiol 2023; 14:1284906. [PMID: 38033580 PMCID: PMC10687471 DOI: 10.3389/fmicb.2023.1284906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Mycobacterium avium complex (MAC) bacteria are the most prominent etiological agents of lymphadenitis in pigs. M. avium subspecies hominissuis (MAH) is a member of MAC and has been reported in many parts of the world to be the most prevalent non-tuberculous mycobacteria (NTM) to cause mycobacteriosis in humans, mainly in children. Thus, the economic and zoonotic impact of MAC species are increasingly being recognized. In South Africa, little is known about the distribution of NTM and the molecular epidemiology of M. avium in pigs. Materials and methods In this study, lymph nodes including mandibular, mesenteric, submandibular, and retropharyngeal, with tuberculosis-like lesions were collected during routine meat inspection of slaughter pigs with no disease symptoms (n = 132), between 1991 and 2002. These pigs were slaughtered at 44 abattoirs distributed across seven of the nine South African provinces. Mycobacterial culture, polymerase chain reaction (PCR), and sequencing of the Mycobacterium specific 577 bp 16S rRNA gene fragment were performed for species and subspecies identification. Results The majority of the isolates (each per sample); 114 (86.4%) were identified as MAH, 8 (6%) as MAA/M. avium subsp. silvaticum, 4 (3%) were Mycobacterium tuberculosis, 2 (1.5%) as Mycobacterium intracellulare, and 1 (0.75%) as Mycobacterium bovis. The other isolates were identified as Mycobacterium lentiflavum (0.75%), Mycobacterium novocastrense (0.75%), and a Micrococcus spp. (0.75%). Using an eight-marker MLVA typing tool, we deciphered at least nine MIRU VNTR INMV types of MAH and MAA. Discussion Identification of known zoonotic mycobacteria, including MAH, MAA, M. intracellulare, M. bovis, and M. tuberculosis, from slaughter pigs has a potential public health impact and also strengthens recognition of the potential economic impact of MAC. This study has also for the first time in South Africa, revealed MAC MIRU VNTR INMV genotypes which will aid in the future epidemiological investigation of MAC in South Africa.
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Affiliation(s)
- Nomakorinte Gcebe
- Bacteriology Laboratory, Agricultural Research Council–Onderstepoort Veterinary Research, Pretoria, South Africa
| | - Rian Ewald Pierneef
- Agricultural Research Council–Biotechnology Platform, Pretoria, South Africa
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
- Microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anita Luise Michel
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Motlatso Tiny Hlokwe
- Bacteriology Laboratory, Agricultural Research Council–Onderstepoort Veterinary Research, Pretoria, South Africa
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Legouge C, Bidet P, Gits-Muselli M, Cointe A, Courroux C, Birgy A, Bonacorsi S. Rapid, simple multi-locus variable number tandem repeat analysis: a reliable tool for Klebsiella pneumoniae outbreak screening. J Hosp Infect 2023; 141:41-48. [PMID: 37634603 DOI: 10.1016/j.jhin.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Klebsiella pneumoniae causing nosocomial infections is increasingly multi-drug-resistant. Rapid and efficient typing tools are required for monitoring. AIM To assess a simple, rapid (<5 h) multiplex polymerase chain reaction method based on multi-locus variable number tandem repeat analysis (MLVA) as a screening tool to determine whether or not K. pneumoniae strains are related. METHODS The global discriminatory power of the method was assessed on 72 unrelated K. pneumoniae isolates, including community carriage isolates, highly virulent strains causing liver abscess, and extended-spectrum beta-lactamase- and carbapenemase-producing strains. Suspected related strains from a suspected outbreak and a relapsed meningitis case were also studied. MLVA results were compared with whole-genome sequencing (WGS) analysis and multi-locus sequence typing (MLST). FINDINGS MLVA and MLST had similar discriminatory power, each distinguishing 54 profiles among the 72 unrelated isolates (Hunter-Gaston index 0.989). Each strain belonging to one sequence type (ST) or ST complex had its own MLVA type, with few exceptions. Two strains of ST268 and ST1119 shared the same MLVA profile, and two unrelated strains of ST307, ST86, ST45 and ST37 exhibited two different MLVA types each. Moreover, investigation of seven grouped cases of K. pneumoniae neonatal sepsis pointed to strong suspicion of a common source for five isolates, while two isolates with a different MLVA profile were excluded from this cluster. CONCLUSION The MLVA approach is a useful, rapid and reliable tool for epidemiological investigation requiring only basic molecular biology equipment, and permits identification of sporadic isolates that are not part of an outbreak. However, analysis of strains sharing the same MLVA type by a highly discriminatory technique, such as WGS, remains necessary.
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Affiliation(s)
- C Legouge
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - P Bidet
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France; Université Paris Cité, IAME, INSERM, Paris, France.
| | - M Gits-Muselli
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France; Université Paris Cité, IAME, INSERM, Paris, France
| | - A Cointe
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France; Université Paris Cité, IAME, INSERM, Paris, France
| | - C Courroux
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - A Birgy
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France; Université Paris Cité, IAME, INSERM, Paris, France
| | - S Bonacorsi
- Service de Microbiologie, Centre National de Référence Associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France; Université Paris Cité, IAME, INSERM, Paris, France
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Guo P, Mei S, Wang Y, Zheng X, Li L, Cheng Y. Molecular typing of Mycoplasma pneumoniae and its correlation with macrolide resistance in children in Henan of China. Indian J Med Microbiol 2023; 46:100435. [PMID: 37945129 DOI: 10.1016/j.ijmmb.2023.100435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND/PURPOSE As a major causative pathogen of community-acquired pneumonia, Mycoplasma pneumoniae (M. pneumoniae) can cause both upper and lower respiratory tract inflammation as well as extrapulmonary syndromes, especially in infants and the elderly. The emergence of macrolide-resistance has significant effects on the treatment of relevant diseases in children. This study aimed to analyze the genotypes and the macrolide resistance-associated mutations in M. pneumoniae sampled from the pediatric patients in Henan, China. METHODS A segment of gene on the 23S rRNA was amplified and sequenced to detect the mutations related to macrolide resistance. Molecular typing was performed by the method named multiple locus variable-number tandem repeat analysis (MLVA) for macrolide-susceptible and macrolide-resistant specimens. RESULTS Among the M. pneumoniae-positive samples, 95.7% (111/116) had macrolide-resistant mutation, and all of them consisted of the A2063G mutation. There were only two MLVA types identified in this study, type 4-5-7-2 (51/92, 55.4%) and type 3-5-6-2 (41/92, 44.6%). CONCLUSION There was no correlation between MLVA types and macrolide resistance (P > 0.05).
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Affiliation(s)
- Pengbo Guo
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, China.
| | - Shiyue Mei
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, China.
| | - Yanhong Wang
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, China.
| | - Xuan Zheng
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, China.
| | - Lifeng Li
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, China; Henan International Joint Laboratory of Children's Infectious Disease, China.
| | - Yibing Cheng
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, China.
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Risby H, Robinson G, Chandra N, King G, Vivancos R, Smith R, Thomas D, Fox A, McCarthy N, Chalmers RM. Application of a new multi-locus variable number tandem repeat analysis ( MLVA) scheme for the seasonal investigation of Cryptosporidium parvum cases in Wales and the northwest of England, spring 2022. Curr Res Parasitol Vector Borne Dis 2023; 4:100151. [PMID: 38021189 PMCID: PMC10665698 DOI: 10.1016/j.crpvbd.2023.100151] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023]
Abstract
The protozoan Cryptosporidium parvum is an important cause of gastroenteritis in humans and livestock, and cryptosporidiosis outbreaks are common. However, a multi-locus genotyping scheme is not widely adopted. We describe the further development and application of a seven-locus multi-locus variable number of tandem repeats analysis (MLVA) scheme. From 28th March to 31st July 2022, confirmed C. parvum stools (n = 213) from cryptosporidiosis patients (cases) in Wales (n = 95) and the north west of England (n = 118) were tested by MLVA. Typability (defined as alleles identified at all seven loci in a sample) was 81.2% and discriminatory power estimated by Hunter Gaston Discriminatory Index was 0.99. A MLVA profile was constructed from the alleles, expressed in chromosomal order. Profiles were defined as simple (single allele at each locus) or mixed (more than one allele at any locus). A total of 161 MLVA profiles were identified; 13 were mixed, an additional 38 simple profiles contained null records, and 110 were complete simple profiles. A minimum spanning tree was constructed of simple MLVA profiles and those identical at all seven loci defined genetic clusters of cases (here, null records were considered as an allele); 77 cases formed 25 clusters, ranging from two to nine (mode = two) cases. The largest cluster, following epidemiological investigation, signalled a newly-identified outbreak. Two other cases with mixed profiles that contained the outbreak alleles were included in the outbreak investigation. In another epidemiologically-identified outbreak of six initial cases, MLVA detected two additional cases. In a third, small outbreak of three cases, identical MLVA profiles strengthened the microbiological evidence. Review of the performance characteristics of the individual loci and of the seven-locus scheme suggested that two loci might be candidates for review, but a larger dataset over a wider geographical area and longer timeframe will help inform decision-making about the scheme by user laboratories and stakeholders (such as public health agencies). This MLVA scheme is straightforward in use, fast and cheap compared to sequence-based methods, identifies mixed infections, provides an important tool for C. parvum surveillance, and can enhance outbreak investigations and public health action.
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Affiliation(s)
- Harriet Risby
- Cryptosporidium Reference Unit, Public Health Wales Microbiology and Health Protection, Singleton Hospital, Swansea, SA2 8QA, UK
| | - Guy Robinson
- Cryptosporidium Reference Unit, Public Health Wales Microbiology and Health Protection, Singleton Hospital, Swansea, SA2 8QA, UK
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK
| | - Nastassya Chandra
- United Kingdom Health Security Agency, Field Service North West, Suite 3B, 3rd Floor, Cunard Building, Water Street, Liverpool, L3 1DS, UK
| | - Grace King
- Communicable Disease Surveillance Centre, Public Health Wales, 2 Capital Quarter, Tyndall Street, Cardiff, CF10 4BZ, UK
| | - Roberto Vivancos
- United Kingdom Health Security Agency, Field Service North West, Suite 3B, 3rd Floor, Cunard Building, Water Street, Liverpool, L3 1DS, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, L69 3GL, UK
- Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Robert Smith
- Communicable Disease Surveillance Centre, Public Health Wales, 2 Capital Quarter, Tyndall Street, Cardiff, CF10 4BZ, UK
| | - Daniel Thomas
- Communicable Disease Surveillance Centre, Public Health Wales, 2 Capital Quarter, Tyndall Street, Cardiff, CF10 4BZ, UK
| | - Andrew Fox
- United Kingdom Health Security Agency, Field Service North West, Suite 3B, 3rd Floor, Cunard Building, Water Street, Liverpool, L3 1DS, UK
| | - Noel McCarthy
- University of Warwick, Coventry, CV4 7AL, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, L69 3GL, UK
- Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Rachel M. Chalmers
- Cryptosporidium Reference Unit, Public Health Wales Microbiology and Health Protection, Singleton Hospital, Swansea, SA2 8QA, UK
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK
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11
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Andrews N, McCabe E, Wall P, Buckley JF, Fanning S. Validating the Utility of Multilocus Variable Number Tandem-repeat Analysis ( MLVA) as a Subtyping Strategy to Monitor Listeria monocytogenes In-built Food Processing Environments. J Food Prot 2023; 86:100147. [PMID: 37619693 DOI: 10.1016/j.jfp.2023.100147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Listeria monocytogenes is a serious human pathogen and an enduring challenge to control for the ready-to-eat food processing industry. Cost-effective tools that can be deployed by commercial or in-house laboratories to rapidly investigate and resolve contamination events in the built food processing environment are of value to the food industry. Multilocus variable number tandem-repeat analysis (MLVA) is a molecular subtyping method, which along with other same-generation methods such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) is being superseded in disease tracking and outbreak investigations by whole-genome sequencing (WGS). In this paper, it is demonstrated that MLVA can continue to play a valuable role as a valid, fast, simple, and cost-effective method to identify and track Listeria monocytogenes subtypes in factory environments, with the method being highly congruent with MLST. Although MLVA does not have the discriminatory power of WGS to identify truly persistent clones, with careful interpretation of results alongside isolate metadata, it remains a powerful tool in situations and locations where WGS may not be readily available to food business operators.
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Affiliation(s)
- Nicholas Andrews
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Evonne McCabe
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Patrick Wall
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - James F Buckley
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; Institute for Global Food Security, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT5 6AG, United Kingdom.
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Xue H, Zhao Z, Wang J, Ma L, Li J, Yang X, Ren L, Xu L, Liu Z, Li Z. Native circulating Brucella melitensis lineages causing a brucellosis epidemic in Qinghai, China. Front Microbiol 2023; 14:1233686. [PMID: 37799605 PMCID: PMC10547896 DOI: 10.3389/fmicb.2023.1233686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/25/2023] [Indexed: 10/07/2023] Open
Abstract
Since 2010, the cases and incidences of human brucellosis have been increasing annually in Qinghai (QH) Province. Molecular epidemiology and phylogenetic analyses of strains from this region are crucial to better understand the transmission of the disease and the evolutionary patterns of Brucella strains. In this study, classical bio-typing assay, multilocus variable-number tandem repeat analysis, and the whole-genome sequencing-single-nucleotide polymorphism approach were used to illustrate the epidemiological and evolutionary patterns of Brucella melitensis. A total of 54 B. melitensis bv. 3 strains were isolated and molecularly characterized, with all strains belonging to the East Mediterranean lineages. Cross-regional transmission events (i.e., between counties) were caused by common sources of infection, suggesting that predominant circulating genotypes are endemic in different regions. Strengthening surveillance in animal brucellosis and controlling infected animals' cross-border movement are necessary. Two strains isolated from humans and marmots were clustered in the same sub-clade, implying the possible existence of direct and/or indirect contact between sheep (and goats) and wildlife (marmots), but this needs to be verified by further investigations. The global-scale phylogenetic analysis indicated that 54 strains sorted into six subclades, four of which formed independent lineages, suggesting that the increase in the incidence rate of human brucellosis may be caused by local circulating lineages. Further strengthening the serology and pathogen surveillance of animals (wildlife) and humans will contribute to an in-depth understanding of the transmission chain of human brucellosis in this region.
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Affiliation(s)
- Hongmei Xue
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Zhijun Zhao
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Jianling Wang
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Li Ma
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Jiquan Li
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Xuxin Yang
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Lingling Ren
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Liqing Xu
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Zhiguo Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Vocational and Technical College, Inner Mongolia Agricultural University, Baotou, China
| | - Zhenjun Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Gonuguntla HN, Surendra KSNL, Prasad A, Sarangi LN, Rana SK, Manasa G, Muthappa PN, Harikumar AV, Sharma GK. Brucella melitensis: Divergence Among Indian Strains and Genetic Characterization of a Strain Isolated from Cattle. Indian J Microbiol 2023; 63:272-280. [PMID: 37781017 PMCID: PMC10533427 DOI: 10.1007/s12088-023-01081-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/17/2023] [Indexed: 10/03/2023] Open
Abstract
Brucella melitensis primarily affects sheep, goats and is associated with brucellosis in humans, which is one of the world's most widespread neglected zoonotic disease. The current study attempted the determination of genetic diversity through comparative genome analysis of B. melitensis strains reported from India with other countries. The study also reports the isolation and identification of B. melitensis BMNDDB8664 from a cow with a history of abortion, whole-genome sequencing (WGS), determination of virulence factors, genotyping, and comparative genome analysis. Multilocus sequence typing, Multiple locus variable number of tandem repeats analysis (MLVA), and WGS based phylogeny revealed the predominance of ST-8 and genotypes (116 and II respectively) that clustered to the East Mediterranean lineage. Identification of hitherto unreported genotypes by MLVA also indicated the existence and circulation of West Mediterranean and American lineages in India. Though the AMOS-PCR results suggest the BMNDDB8664 isolate as Brucella abortus, the outcomes from multiplex PCR, ribosomal multilocus sequence typing, and WGS analysis confirmed it as B. melitensis. The analysis revealed the presence of adeF gene (aids conferring resistance to fluoro-quinolone and tetracyclines). The isolate lacked two important T4SS genes virB2 and virB7 genes (roles in infection and rifampicin resistance respectively) and also lacked the Brucella suis mprF gene that aids intracellular survival. Further, BMNDDB8664 lacked some of the genes associated with LPS synthesis (wbkB, wbkC) and transport (wzm, wzt) and hence, is most likely a rough strain. WGS-based phylogenetic analysis revealed close genetic relatedness of this BMNDDB8664 with a sheep isolate and two human isolates. The results prompt systematic, broad-based epidemiological studies on brucella infection at the species level. For effective control of human brucellosis, a concerted One Health approach with studies encircling the identification of aetiology at species, strain level to find their prevalence, spread, and inter-host transmission patterns need to be understood, for better design and implementation of effective control strategies in India and other endemic regions. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01081-w.
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Affiliation(s)
- Hariprasad Naidu Gonuguntla
- National Dairy Development Board Research and Development Laboratory, IIL Campus, Gachibowli, Hyderabad, Telangana 500032 India
| | - Kota Sri Naga Leela Surendra
- National Dairy Development Board Research and Development Laboratory, IIL Campus, Gachibowli, Hyderabad, Telangana 500032 India
| | - Amitesh Prasad
- National Dairy Development Board Research and Development Laboratory, IIL Campus, Gachibowli, Hyderabad, Telangana 500032 India
| | - Laxmi Narayan Sarangi
- National Dairy Development Board Research and Development Laboratory, IIL Campus, Gachibowli, Hyderabad, Telangana 500032 India
| | | | - Gujjala Manasa
- National Dairy Development Board Research and Development Laboratory, IIL Campus, Gachibowli, Hyderabad, Telangana 500032 India
| | - Ponnanna Nadikerianda Muthappa
- National Dairy Development Board Research and Development Laboratory, IIL Campus, Gachibowli, Hyderabad, Telangana 500032 India
| | - A. V. Harikumar
- National Dairy Development Board, Anand, Gujarat 388001 India
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Özgen EK, Yanmaz B, Bağatir PŞ. Investigation of virulence factors, phylogenetic grouping, multiple-locus variable number tandem repeat analysis, and antimicrobial susceptibility of E. coli isolated from aborted bovine fetal tissue. Lett Appl Microbiol 2023; 76:ovad100. [PMID: 37660240 DOI: 10.1093/lambio/ovad100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/26/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
Escherichia coli is an important microorganism for cattle breeding. The aim of this study was to investigate the presence of phylogenetic groups, virulence factors, genotyping with multi-locus variable tandem repeat analysis (MLVA), and susceptibility to commonly used antimicrobial agents in E. coli strains isolated from aborted bovine fetal samples. In this study, phylogrouping and various virulence genes were analyzed by PCR in E. coli strains isolated from 637 bovine fetal tissue samples. Consequently, E. coli was isolated and identified in 24 samples in culture. Of the 24 isolates identified as positive, 12.5% were defined as group A, 83.3% as B1, and 4.2% as group B2. Of the E. coli isolates, virulence factor fimH was identified in eight (33.3%), traT in 15 (62.5%), ompT in five (20.8%), CNF1 in one (4.16%), and CNF2 in six (25%). Seven genotypic groups were determined as a result of the analysis with the MLVA 10 method. According to the antimicrobial susceptibility test results, high resistance was determined against amoxicillin/clavulanic acid and oxytetracycline. In conclusion, strains of E. coli containing CNF1, CNF2, fimH, traT, and ompT virulence factors can be associated with bovine abortions. It is noteworthy that the dominant phylogenetic group B1 has been observed in cases of cattle abortions.
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Affiliation(s)
- Ediz Kağan Özgen
- Erzurum Veterinary Control Institute, Republic of Turkey Ministry of Agriculture and Forestry, Erzurum 25080, Turkey
| | - Berna Yanmaz
- Faculty of Veterinary Medicine, Department of Veterinary Public Health, Burdur Mehmet Akif Ersoy University, Burdur 15030, Turkey
| | - Perihan Şerifoğlu Bağatir
- Erzurum Veterinary Control Institute, Republic of Turkey Ministry of Agriculture and Forestry, Erzurum 25080, Turkey
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Abad-Fau A, Sevilla E, Martín-Burriel I, Moreno B, Bolea R. Update on Commonly Used Molecular Typing Methods for Clostridioides difficile. Microorganisms 2023; 11:1752. [PMID: 37512924 PMCID: PMC10384772 DOI: 10.3390/microorganisms11071752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
This review aims to provide a comprehensive overview of the significant Clostridioides difficile molecular typing techniques currently employed in research and medical communities. The main objectives of this review are to describe the key molecular typing methods utilized in C. difficile studies and to highlight the epidemiological characteristics of the most prevalent strains on a global scale. Geographically distinct regions exhibit distinct strain types of C. difficile, with notable concordance observed among various typing methodologies. The advantages that next-generation sequencing (NGS) offers has changed epidemiology research, enabling high-resolution genomic analyses of this pathogen. NGS platforms offer an unprecedented opportunity to explore the genetic intricacies and evolutionary trajectories of C. difficile strains. It is relevant to acknowledge that novel routes of transmission are continually being unveiled and warrant further investigation, particularly in the context of zoonotic implications and environmental contamination.
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Affiliation(s)
- Ana Abad-Fau
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Eloísa Sevilla
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Inmaculada Martín-Burriel
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Bernardino Moreno
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Rosa Bolea
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
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Tan Q, Wang Y, Liu Y, Tao Z, Yu C, Huang Y, Yang X, Ying X, Hu Y, Li S. Molecular epidemiological characteristics of Brucella in Guizhou Province, China, from 2009 to 2021. Front Microbiol 2023; 14:1188469. [PMID: 37426016 PMCID: PMC10326899 DOI: 10.3389/fmicb.2023.1188469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction Brucellosis was made statutorily notifiable in 1955, in China, while in Guizhou Province, the pathogen of human brucellosis was isolated for the first time in 2011. However, currently, the brucellosis epidemic is becoming more and more severe in Guizhou Province. The type distribution and genetic characteristics of Brucella in Guizhou Province, as well as its evolutionary relationship with domestic and foreign strains, are still unclear. Methods MLST, MLVA, and rpoB typing techniques were used for the molecular epidemiological study of the 83 Brucella isolates in Guizhou province. Results Among the 83 Brucella strains, MLST identified three ST genotypes, of which ST39 is a newly reported type in China. MLVA-16 generated 49 genotypes, and MLVA-11 generated 5 known genotypes and 2 unreported genotypes. Six genotypes were identified by rpoB technology. Discussion MLVA has a high resolution, but differences at the Bruce 04 and 16 loci cannot exclude associations between epidemics, and combining MLST and rpoB typing methods for epidemiologic tracing can avoid erroneous judgments. Moreover, through the combined analysis of the three typing techniques, the possible origin of the new Brucella can be reasonably inferred, which is also conducive to promoting the subsequent research of the novel Brucella.
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Affiliation(s)
- Qinqin Tan
- Laboratory Center, Center for Disease Control and Prevention of Guizhou Provincial, Guiyang, Guizhou, China
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, University of Guizhou Medical, Guiyang, Guizhou, China
| | - Yue Wang
- Laboratory Center, Center for Disease Control and Prevention of Guizhou Provincial, Guiyang, Guizhou, China
| | - Ying Liu
- Laboratory Center, Center for Disease Control and Prevention of Guizhou Provincial, Guiyang, Guizhou, China
| | - Zhongfa Tao
- Center for Disease Control and Prevention of Guizhou Provincial, Institute of Infectious Disease Control, Guiyang, Guizhou, China
| | - Chun Yu
- Center for Disease Control and Prevention of Guizhou Provincial, Institute of Infectious Disease Control, Guiyang, Guizhou, China
| | - Yan Huang
- Center for Disease Control and Prevention of Guizhou Provincial, Institute of Infectious Disease Control, Guiyang, Guizhou, China
| | - Xinggui Yang
- Laboratory Center, Center for Disease Control and Prevention of Guizhou Provincial, Guiyang, Guizhou, China
| | - Xia Ying
- Laboratory Center, Center for Disease Control and Prevention of Guizhou Provincial, Guiyang, Guizhou, China
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, University of Guizhou Medical, Guiyang, Guizhou, China
| | - Yong Hu
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, University of Guizhou Medical, Guiyang, Guizhou, China
| | - Shijun Li
- Laboratory Center, Center for Disease Control and Prevention of Guizhou Provincial, Guiyang, Guizhou, China
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, University of Guizhou Medical, Guiyang, Guizhou, China
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Pereira CR, Neia RC, Silva SB, Williamson CHD, Gillece JD, O'Callaghan D, Foster JT, Oliveira IRC, Filho JSSB, Lage AP, Azevedo VAC, Dorneles EMS. Comparison of Brucella abortus population structure based on genotyping methods with different levels of resolution. J Microbiol Methods 2023:106772. [PMID: 37343840 DOI: 10.1016/j.mimet.2023.106772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/18/2023] [Accepted: 06/18/2023] [Indexed: 06/23/2023]
Abstract
Numerous genotyping techniques based on different principles and with different costs and levels of resolution are currently available for understanding the transmission dynamics of brucellosis worldwide. We aimed to compare the population structure of the genomes of 53 Brazilian Brucella abortus isolates using eight different genotyping methods: multiple-locus variable-number tandem-repeat analysis (MLVA8, MLVA11, MLVA16), multilocus sequence typing (MLST9, MLST21), core genome MLST (cgMLST) and two techniques based on single nucleotide polymorphism (SNP) detection (parSNP and NASP) from whole genomes. The strains were isolated from six different Brazilian states between 1977 and 2008 and had previously been analyzed using MLVA8, MLVA11, and MLVA16. Their whole genomes were sequenced, assembled, and subjected to MSLT9 MLST21, cgMLST, and SNP analyses. All the genotypes were compared by hierarchical grouping method based on the average distances between the correlation matrices of each technique. MLST9 and MLST21 had the lowest level of resolution, both revealing only four genotypes. MLVA8, MLVA11, and MLVA16 had progressively increasing levels of resolution as more loci were analyzed, identifying 6, 16, and 44 genotypes, respectively. cgMLST showed the highest level of resolution, identifying 45 genotypes, followed by the SNP-based methods, both of which had 44 genotypes. In the assessed population, MLVA was more discriminatory than MLST and was easier and cheaper to perform. SNP techniques and cgMLST provided the highest levels of resolution and the results from the two methods were in close agreement. In conclusion, the choice of genotyping technique can strongly affect one's ability to make meaningful epidemiological conclusions but is dependent on available resources: while the VNTR based techniques are more indicated to high prevalence scenarios, the WGS methods are the ones with the best discriminative power and therefore recommended for outbreaks investigation.
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Affiliation(s)
- Carine R Pereira
- Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Raquel C Neia
- Faculdade de Ciências Básicas, Universidade Federal Fluminense, Nova Friburgo, Rio de Janeiro, Brazil
| | - Saulo B Silva
- Escola de Ciências da Saúde, Univali, Itajaí, Santa Catarina, Brazil
| | | | - John D Gillece
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - David O'Callaghan
- Bacterial Virulence and Infectious Disease, University of Montpellier, Nimes, France
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Izabela R C Oliveira
- Departamento de Estatística, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Júlio S S B Filho
- Departamento de Estatística, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Andrey P Lage
- Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco A C Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elaine M S Dorneles
- Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil.
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Esnault E, Rouault A, Labbé A, Houdayer C, Bailly Y, Houard E, Bougeard S, Paboeuf F, Eterradossi N, Chemaly M, Denis M. Controlled Experimental Infection in Pigs with a Strain of Yersinia enterocolitica Harboring Genetic Markers for Human Pathogenicity: Colonization and Stability. Infect Immun 2023:e0015723. [PMID: 37255474 DOI: 10.1128/iai.00157-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
Yersinia enterocolitica (Ye) is one of the major causes of foodborne zoonosis. The BT4/O:3 bioserotype is most commonly isolated in human infections. Pigs are considered the main reservoir of Ye, and hence, understanding the dynamics of infection by this pathogen at the individual and group levels is crucial. In the present study, an experimental model was validated in Large White pigs infected with a BT4/O:3 strain. This study showed that Ye contamination in pigs may occur via the introduction of the bacteria not only by mouth but also by snout, with a colonization process consisting of three periods corresponding to three contamination statuses of pigs: P1, corresponding to the 24 h following ingestion or inhalation of Ye with the appearance of bacteria in tonsils or in feces; P2, from 2 days postinoculation (dpi), corresponding to expansion of Ye and colonization of the digestive system and extraintestinal organs associated with an IgG serological response; and P3, after 21 dpi, corresponding to regression of colonization with intermittent Ye detection in tonsils and feces. Although the inoculated strain persisted up to 56 dpi in all pigs, genetic variations with the loss of the gene yadA (a gene involved in human infection) and the emergence of two new multilocus variable-number tandem-repeat analysis (MLVA) profiles were observed in 33% of the 30 isolates studied. This experimental infection model of pigs by Ye provides new insights into the colonization steps in pigs in terms of bacterial distribution over time and bacterial genetic stability.
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Affiliation(s)
- Emilie Esnault
- Unit for Hygiene of Poultry and Pork Products, ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Alicia Rouault
- Unit for Hygiene of Poultry and Pork Products, ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Annie Labbé
- Unit for Hygiene of Poultry and Pork Products, ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Catherine Houdayer
- Unit for Hygiene of Poultry and Pork Products, ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Yann Bailly
- Unit for SPF Pig Production and Experimentation, ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Emmanuelle Houard
- Unit for Hygiene of Poultry and Pork Products, ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Stéphanie Bougeard
- Unit for Epidemiology, Health and Welfare Research, ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Frédéric Paboeuf
- Unit for SPF Pig Production and Experimentation, ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | | | - Marianne Chemaly
- Unit for Hygiene of Poultry and Pork Products, ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Martine Denis
- Unit for Hygiene of Poultry and Pork Products, ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
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Sørgaard M, Sveinsson K, Patel S, Nilsen HK, Olsen AB, Vaagnes Ø, Colquhoun DJ, Gulla S. MLVA genotyping of Moritella viscosa reveals serial emergence of novel, host-specific clonal complexes in Norwegian salmon farming. J Fish Dis 2023; 46:535-543. [PMID: 36787245 DOI: 10.1111/jfd.13766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
A Multi-Locus Variable number of tandem repeat Analysis (MLVA) genotyping scheme was developed for the epidemiological study of Moritella viscosa, which causes 'winter ulcer' predominantly in sea-reared Atlantic salmon (Salmo salar L.). The assay involves multiplex PCR amplification of six Variable Number of Tandem Repeat (VNTR) loci, followed by capillary electrophoresis and data interpretation. A collection of 747 spatiotemporally diverse M. viscosa isolates from nine fish species was analysed, the majority from farmed Norwegian salmon. MLVA distributed 76% of the isolates across three major clonal complexes (CC1, CC2 and CC3), with the remaining forming minor clusters and singletons. While 90% of the salmon isolates belong to either CC1, CC2 or CC3, only 20% of the isolates recovered from other fish species do so, indicating a considerable degree of host specificity. We further highlight a series of 'clonal shifts' amongst Norwegian salmon isolates over the 35-year sampling period, with CC1 showing exclusive predominance prior to the emergence of CC2, which was later supplanted by CC3, before the recent re-emergence of CC1. Apparently, these shifts have rapidly swept the entire Norwegian coastline and conceivably, as suggested by typing of a small number of non-Norwegian isolates, the Northeast Atlantic region as a whole.
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Affiliation(s)
| | | | - Sonal Patel
- Norwegian Veterinary Institute, Ås, Norway
- Vaxxinova Norway AS, Bergen, Norway
| | | | | | - Øyvind Vaagnes
- Vaxxinova Norway AS, Bergen, Norway
- Blue Analytics AS, Bergen, Norway
| | - Duncan J Colquhoun
- Norwegian Veterinary Institute, Ås, Norway
- University of Bergen, Bergen, Norway
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20
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Boeri EJ, Ruybal P, Dominguez ML, Fernandez NM, Becker P, Elena S, Escobar GI, Ayala SM, Hassan DB, Trangoni MD. Higher diversity of Brucella canis in Latin America, according to an MLVA_13 Bc analysis. Acta Trop 2023; 243:106914. [PMID: 37062420 DOI: 10.1016/j.actatropica.2023.106914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/03/2023] [Accepted: 03/28/2023] [Indexed: 04/18/2023]
Abstract
Brucella canis is the main causative agent of canine brucellosis, which affects domestic and wild canids and leads to clinical signs and symptoms of the reproductive and locomotor systems. Owing to the scarce information on this pathogen, here we addressed the genetic diversity of the circulating strains of this species in Argentina by following an MVLA_13 Bc scheme. The analyzed sample set consisted of 101 strains of B. canis isolates collected between 2006 and 2020 from canines of the Autonomous City of Buenos Aires (CABA) and other regions of Argentina, as well as 235 isolates from North America. . The analysis yielded 336 variants (Hunter-Gaston Diversity Index, HGDI equal to 1.0) showing high diversity on a global scale. The analysis of the six most variable markers also reveled high diversity and allowed further analysis regarding variant relationships. Although the diversity obtained using both schemes (all or the 6 most variable markers) was higher for the Latin American than for the North American strains, we cannot discard that this was due to biases in the sampling methodology or to the different health policies employed in these regions regarding the management of infected individuals. Altogether, the Argentine circulating strains are genetically diverse, but with no apparent geographical association. The markers used in the MLVA_13 Bc are variable and highly useful for the evaluation of outbreaks. Furthermore, the reduced panel of 6 markers (MLVA_6 Bc) proposed in this study is convenient for the study of B. canis strain diversity.
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Affiliation(s)
- Eduardo Jorge Boeri
- Instituto de Zoonosis Luis Pasteur, Av. Diaz Velez 4821 (1.405), División Inmunología y Diagnóstico, Laboratorio Sección Serología y Diagnóstico, Buenos Aires, Argentina.
| | - Paula Ruybal
- Universidad de Buenos Aires, Facultad de Medicina, Paraguay 2155, Departamento de Microbiología, Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Paraguay 2157, Buenos Aires, Argentina.
| | - María Luz Dominguez
- Instituto de Zoonosis Luis Pasteur, Av. Diaz Velez 4821 (1.405), División Inmunología y Diagnóstico, Laboratorio Sección Serología y Diagnóstico, Buenos Aires, Argentina.
| | - Natalia Mercedes Fernandez
- Instituto de Zoonosis Luis Pasteur, Av. Diaz Velez 4821 (1.405), División Inmunología y Diagnóstico, Laboratorio Sección Serología y Diagnóstico, Buenos Aires, Argentina.
| | - Paula Becker
- Instituto de Zoonosis Luis Pasteur, Av. Diaz Velez 4821 (1.405), División Inmunología y Diagnóstico, Laboratorio Sección Serología y Diagnóstico, Buenos Aires, Argentina.
| | - Sebastián Elena
- Laboratorio de Referencia de la OIE para Brucelosis, Dirección General de Laboratorio y Control Técnico (DiLab), Servicio Nacional de Sanidad y Calidad Agroalimentaria (SENASA), Martínez, 1640 Buenos Aires, Argentina.
| | - Gabriela Ileana Escobar
- Laboratorio de Brucelosis Laboratorio Nacional de Referencia INEI-ANLIS Dr. Carlos G. Malbrán. Av. Vélez Sarsfield 563, Ciudad Autónoma de Buenos Aires, Argentina..
| | - Sandra Marcela Ayala
- Laboratorio de Brucelosis Laboratorio Nacional de Referencia INEI-ANLIS Dr. Carlos G. Malbrán. Av. Vélez Sarsfield 563, Ciudad Autónoma de Buenos Aires, Argentina..
| | - Deborah Beatriz Hassan
- Laboratorio de Brucelosis Laboratorio Nacional de Referencia INEI-ANLIS Dr. Carlos G. Malbrán. Av. Vélez Sarsfield 563, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcos David Trangoni
- Laboratorio de Brucella, Campylobacter y Microbiota del rumen. Instituto de Biotecnología/Instituto de Agrobiotecnología y Biología Molecular (IB/IABIMO), UEDD INTA-CONICET, CICVyA, CNIA, INTA Hurlingham, Argentina.
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Shiralizadeh S, Keramat F, Hashemi SH, Majzoobi MM, Azimzadeh M, Alikhani MS, Karami P, Rahimi Z, Alikhani MY. Investigation of antimicrobial resistance patterns and molecular typing of Pseudomonas aeruginosa isolates among Coronavirus disease-19 patients. BMC Microbiol 2023; 23:84. [PMID: 36991311 PMCID: PMC10052215 DOI: 10.1186/s12866-023-02825-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is a common co-infecting pathogen recognized among COVID-19 patients. We aimed to investigate the antimicrobial resistance patterns and molecular typing of Pseudomonas aeruginosa isolates among Coronavirus disease-19 patients. METHODS Between December 2020 and July 2021, 15 Pseudomonas aeruginosa were isolated from COVID-19 patients in the intensive care unit at Sina Hospital in Hamadan, west of Iran. The antimicrobial resistance of the isolates was determined by disk diffusion and broth microdilution methods. The double-disk synergy method, Modified Hodge test, and polymerase chain reaction were utilized to detect Pseudomonas aeruginosa extended spectrum beta-lactamase and carbapenemase producers. Microtiter plate assay was performed to evaluate the biofilm formation ability of the isolates. The isolates phylogenetic relatedness was revealed using the multilocus variable-number tandem-repeat analysis method. RESULTS The results showed Pseudomonas aeruginosa isolates had the most elevated resistance to imipenem (93.3%), trimethoprim-sulfamethoxazole (93.3%), ceftriaxone (80%), ceftazidime (80%), gentamicin (60%), levofloxacin (60%), ciprofloxacin (60%), and cefepime (60%). In the broth microdilution method, 100%, 100%, 20%, and 13.3% of isolates showed resistance to imipenem, meropenem, polymyxin B, and colistin, respectively. Ten (66.6%) isolates were identified as multiple drug resistance. Carbapenemase enzymes and extended spectrum beta-lactamases were identified in 66.6% and 20% of the isolates, respectively and the biofilm formation was detected in 100% of the isolates. The blaOXA-48, blaTEM, blaIMP, blaSPM, blaPER, blaVEB, blaNDM, blaSHV, and blaCTX-M genes were detected in 100%, 86.6%, 86.6%, 40%, 20%, 20%, 13.3%, 6.6%, and 6.6% of the isolates, respectively. The blaVIM, blaGIM, blaGES, and blaMCR-1 genes were not identified in any of the isolates. The MLVA typing technique showed 11 types and seven main clusters and most isolates belong to cluster I, V and VII. CONCLUSION Due to the high rate of antimicrobial resistance, as well as the genetic diversity of Pseudomonas aeruginosa isolates from COVID-19 patients, it is indispensable to monitor the antimicrobial resistance pattern and epidemiology of the isolates on a regular basis.
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Affiliation(s)
- Somaye Shiralizadeh
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, IR, Iran
| | - Fariba Keramat
- Department of Infectious Diseases, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, IR, Iran
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, IR , Iran
| | - Seyyed Hamid Hashemi
- Department of Infectious Diseases, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, IR, Iran
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, IR , Iran
| | - Mohammad Mehdi Majzoobi
- Department of Infectious Diseases, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, IR, Iran
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, IR , Iran
| | - Masoud Azimzadeh
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, IR, Iran
| | | | - Pezhman Karami
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, IR, Iran
| | - Zahra Rahimi
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, IR, Iran
| | - Mohammad Yousef Alikhani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, IR, Iran.
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, IR , Iran.
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22
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İnce SS, Müştak HK. Genotyping and antimicrobial resistance profiles of chicken originated Salmonella Enteritidis isolates. Braz J Microbiol 2023; 54:499-507. [PMID: 36752945 PMCID: PMC9944479 DOI: 10.1007/s42770-023-00914-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
Salmonellosis is a common foodborne zoonosis worldwide. The most common Salmonella serovar in humans is Salmonella enterica subsp. enterica serovar Enteritidis (50.3%) in the world. The main transmission route for S. Enteritidis is consumption of contaminated poultry products. Therefore, it is important to determine the diversity and spread of chicken-originated S. Enteritidis isolates in order to monitor and control salmonellosis. Pulsed-field gel electrophoresis (PFGE) and multiple locus variable number of tandem repeats analysis (MLVA) are frequently used for typing of S. Enteritidis isolates. This study aimed to determine the antimicrobial resistance (AMR) profiles and MLVA and PFGE genotypes of chicken-originated S. Enteritidis isolates. A total of 200 S. Enteritidis isolated from chicken broiler, layer, and breeder flocks from different locations in Turkey were investigated by Kirby-Bauer disk diffusion method, PFGE, and MLVA. The AMR test indicated that 57% of the S. Enteritidis isolates were susceptible to all antimicrobials, while 39% were resistant to at least one antimicrobial. The highest resistance (25%) was against ampicillin. Multi-drug resistance rate was low (21%) and mostly from broiler flocks (93%). All isolates were genotyped into 32 different PFGE genotypes (PT) and 34 different MLVA genotypes (MT). The dominant genotypes were PT6 (12.5%) and MT22 (50%). In specific sample groups, there was a correlation between genotypes, breeding type, geographic location, and isolation years of the isolates. There was no significant difference in the discrimination power of PFGE and MLVA. However, MLVA was more suitable for large sample groups and routine genotyping because it was easier, quicker, and less labor-intensive to use.
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Affiliation(s)
- Seyyide Sarıçam İnce
- Department of Microbiology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey.
| | - Hamit Kaan Müştak
- Department of Microbiology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
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23
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Kong N, Shu S, Zhang C, Li C, Luo Y, Fang S, Bi S. Intergenic region polymorphism analysis: a novel genotyping method for Klebsiella pneumoniae. J Appl Microbiol 2023; 134:7044773. [PMID: 36801995 DOI: 10.1093/jambio/lxad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/07/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023]
Abstract
AIMS The ability to distinguish between Klebsiella pneumoniae strains is critical for outbreak investigations. A new typing method, intergenic region polymorphism analysis (IRPA), was developed, validated, and the discriminatory power was determined by comparison with multiple-locus variable-number tandem repeat analysis (MLVA) in this study. METHODS AND RESULTS This method is based on the idea that every IRPA locus (polymorphic fragment of intergenic regions present in one strain but not in other strains or different fragment sizes in other strains) could divide strains into different genotypes. A 9-loci IRPA scheme was designed to type 64 K. pneumoniae isolates. Five IRPA loci were identified that conferred the same level of discrimination as the 9-loci initially examined. Among these K. pneumoniae isolates, 7.81% (5/64), 6.25% (4/64), 4.96% (3/64), 9.38% (6/64), and 1.56% (1/64) were capsular serotypes K1, K2, K5, K20, and K54, respectively. The discriminatory power of the IRPA method was better than that of MLVA expressed in Simpson's index of diversity (SI) at 0.997 and 0.988, respectively. The congruent analysis of the IRPA method and MLVA showed moderate congruence between the two methods (AR = 0.378). The AW indicated that if IRPA data are availabl, one can accurately predict the MLVA cluster. CONCLUSION The IRPA method was found to have higher discriminatory power than MLVA and allowed for simpler band profile interpretation. The IRPA method is a rapid, simple, and high-resolution technique for molecular typing of K. pneumoniae.
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Affiliation(s)
- Nianqing Kong
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan, Guangdong Province 528458, China.,College of Public Health, Guangdong Pharmaceutical University, Guangzhou, Guangdong Province 510220, China
| | - Shenghuang Shu
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan, Guangdong Province 528458, China
| | - Cangyun Zhang
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan, Guangdong Province 528458, China
| | - Chuyi Li
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan, Guangdong Province 528458, China
| | - Yongwen Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Shuying Fang
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan, Guangdong Province 528458, China
| | - Shuilian Bi
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan, Guangdong Province 528458, China
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Donchev D, Ivanov IN, Stoikov I, Sabtcheva S, Kalchev Y, Murdjeva M, Dobreva E, Hristova R. Improvement and Validation of a Multi-Locus Variable Number of Tandem Repeats Analysis ( MLVA8+) for Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. Microorganisms 2023; 11:microorganisms11020444. [PMID: 36838409 PMCID: PMC9965953 DOI: 10.3390/microorganisms11020444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The genotyping of the multidrug-resistant Klebsiella pneumoniae species complex is essential to identify outbreaks and to track their source and spread. The aim of this study was to improve and extend the typeability, availability, cost and time efficiency of an existing multi-locus VNTR analysis (MLVA). A modified scheme (MLVA8+) was adopted and validated for strain-level differentiation of the three Klebsiella species involved in human pathology. A diverse set of 465 K. pneumoniae clinical isolates from 22 hospitals and 3 outpatient laboratories in Bulgaria were studied, where 315 were carbapenem-resistant. The MLVA8+ typeability was significantly improved and the typing data were validated against 158 isolates which were previously typed by WGS. The MLVA8+ results were highly concordant with the classic 7-locus MLST and the novel K. variicola MLST, but had greater congruency coefficients (adjusted Wallace). A major advantage was the differentiation of the hybrid cluster ST258 into its corresponding clades. Furthermore, the applicability of MLVA8+ was demonstrated by conducting a retrospective investigation of the intra-hospital spread of blaKPC-, blaNDM- and blaOXA-48-like producers. The MLVA8+ has improved utility and extended typing scope to K. variicola and K. quasipneumoniae, while its cost and time-to-result were reduced.
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Affiliation(s)
- Deyan Donchev
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
- Correspondence:
| | - Ivan N. Ivanov
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Ivan Stoikov
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
- Laboratory for Clinical Microbiology, National Oncology Center, 6 Plovdivsko pole Str., 1797 Sofia, Bulgaria
| | - Stefana Sabtcheva
- Laboratory for Clinical Microbiology, National Oncology Center, 6 Plovdivsko pole Str., 1797 Sofia, Bulgaria
| | - Yordan Kalchev
- Department of Medical Microbiology and Immunology, “Prof. Dr. Elissay Yanev”, Medical University—Plovdiv, 15-A Vasil Aprilov Blvd., 4002 Plovdiv, Bulgaria
| | - Marianna Murdjeva
- Department of Medical Microbiology and Immunology, “Prof. Dr. Elissay Yanev”, Medical University—Plovdiv, 15-A Vasil Aprilov Blvd., 4002 Plovdiv, Bulgaria
| | - Elina Dobreva
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Rumyana Hristova
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
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Manqele A, Gcebe N, Pierneef RE, Moerane R, Adesiyun AA. Identification of Listeria species and Multilocus Variable-Number Tandem Repeat Analysis ( MLVA) Typing of Listeria innocua and Listeria monocytogenes Isolates from Cattle Farms and Beef and Beef-Based Products from Retail Outlets in Mpumalanga and North West Provinces, South Africa. Pathogens 2023; 12. [PMID: 36678495 DOI: 10.3390/pathogens12010147] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/17/2023] Open
Abstract
In this study, Listeria isolates (214) were characterized as follows: L. innocua (77.10%), L. monocytogenes (11.21%), L. welshimeri (5.61%), L. grayi (1.40%), L. seeligeri (0.93%), and L. species (3.73%) that were not identified at the species level, from beef and beef based products from retail and farms in Mpumalanga and North West provinces of South Africa. MLVA was further used to type Listeria innocua isolates (165) and Listeria monocytogenes isolates (24). The L. monocytogenes isolates were also serogrouped using PCR. The MLVA protocol for L. monocytogenes typing included six tandem repeat primer sets, and the MLVA protocol for L. innocua included the use of three tandem repeats primer sets. The L. monocytogenes serogroups were determined as follows: 4b-4d-4e (IVb) (37.50%), 1/2a-3a (IIa) (29.16%), 1/2b-3b (IIb) (12.50%), 1/2c-3c (IIc) (8.33%), and IVb-1 (4.16%). MLVA could cluster isolates belonging to each specie, L. monocytogenes, and L. innocua isolates, into MLVA-related strains. There were 34 and 10 MLVA types obtained from the MLVA typing of L. innocua and L. monocytogenes, respectively. MLVA clustered the L. monocytogenes isolates irrespective of sample category, serogroups, and geographical origin. Similarly, the L. innocua isolates clustered irrespective of meat category and geographical origin. MLVA was able to cluster isolates based on MLVA relatedness. The clustering of isolates from farms and retailers indicates transmission of Listeria spp. MLVA is an affordable, simple, and discriminatory method that can be used routinely to type L. monocytogenes and L. innocua isolates.
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Asgharzadeh S, Golmoradi Zadeh R, Taati Moghadam M, Farahani Eraghiye H, Sadeghi Kalani B, Masjedian Jazi F, Mirkalantari S. Distribution and expression of virulence genes (hlyA, sat) and genotyping of Escherichia coli O25b/ST131 by multi-locus variable number tandem repeat analysis in Tehran, Iran. Acta Microbiol Immunol Hung 2022; 69:314-322. [PMID: 36129793 DOI: 10.1556/030.2022.01826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/01/2022] [Indexed: 12/13/2022]
Abstract
Escherichia coli ST131 is a pandemic clone with high antibiotic resistance, and it is a major causative agent of urinary tract infection (UTI) and bloodstream infections. This study evaluated the distribution and expression of virulence genes and genotyping of E. coli O25b/ST131 by Multi-locus variable number tandem repeat analysis (MLVA) method among UTI in patients at Tehran hospitals, Iran.A total of 107 E. coli isolates were collected from UTI patients. Polymerase chain reaction (PCR) amplification of the pabB gene was used to identify E. coli O25b/ST131 and the prevalence of sat and hlyA virulence genes was also analyzed. The microtiter method quantified biofilm formation ability in E. coli O25b/ST131. The Real-Time PCR (qRT-PCR) was performed to evaluate the expression of sat and hlyA genes. Finally, MLVA was performed for E. coli O25b/ST131 genotyping by targeting seven tandem repeats. SPSS-16 software was used for statistical analysis. Molecular study showed that 71% of isolates carried the pabB gene and were considered E. coli O25b/ST131 strains. Also, 45.8% and 17.8% of isolates carried sat and hlyA genes, respectively. The 57.9% isolates had biofilm formation ability. Expression of the studied virulence genes showed an increase in strong biofilm producing E. coli O25b/ST131 strains. A total of 76 (100%) E. coli O25b/ST131 strains were typed by the MLVA method.High prevalence of E. coli O25b/ST131 isolates in UTI patients can be a serious warning to the treatment due to the high antibiotic resistance rate, expression of virulence genes, and biofilm formation.
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Affiliation(s)
- Sajjad Asgharzadeh
- 1Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rezvan Golmoradi Zadeh
- 1Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Taati Moghadam
- 1Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamed Farahani Eraghiye
- 1Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Behrooz Sadeghi Kalani
- 2Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Faramarz Masjedian Jazi
- 1Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shiva Mirkalantari
- 1Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Brangsch H, Singha H, Laroucau K, Elschner M. Sequence-based detection and typing procedures for Burkholderia mallei: Assessment and prospects. Front Vet Sci 2022; 9:1056996. [PMID: 36452150 PMCID: PMC9703372 DOI: 10.3389/fvets.2022.1056996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/26/2022] [Indexed: 10/28/2023] Open
Abstract
Although glanders has been eradicated in most of the developed world, the disease still persists in various countries such as Brazil, India, Pakistan, Bangladesh, Nepal, Iran, Bahrain, UAE and Turkey. It is one of the notifiable diseases listed by the World Organization for Animal Health. Occurrence of glanders imposes restriction on equestrian events and restricts equine movement, thus causing economic losses to equine industry. The genetic diversity and global distribution of the causing agent, Burkholderia (B.) mallei, have not been assessed in detail and are complicated by the high clonality of this organism. Among the identification and typing methods, PCR-based methods for distinguishing B. mallei from its close relative B. pseudomallei as well as genotyping using tandem repeat regions (MLVA) are established. The advent and continuous advancement of the sequencing techniques and the reconstruction of closed genomes enable the development of genome guided epidemiological tools. For achieving a higher genomic resolution, genotyping methods based on whole genome sequencing data can be employed, like genome-wide single nucleotide polymorphisms. One of the limitations in obtaining complete genomic sequences for further molecular characterization of B. mallei is its high GC content. In this review, we aim to provide an overview of the widely used detection and typing methods for B. mallei and illustrate gaps that still require development. The genomic features of Burkholderia, their high homology and clonality will be first described from a comparative genomics perspective. Then, the commonly used molecular detection (PCR systems) and typing systems (e.g., multilocus sequence typing, variable number of tandem repeat analysis) will be presented and put in perspective with recently developed genomic methods. Also, the increasing availability of B. mallei genomic sequences and evolution of the sequencing methods offers exciting prospects for further refinement of B. mallei typing, that could overcome the difficulties presently encountered with this particular bacterium.
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Affiliation(s)
- Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut – Federal Research Institute for Animal Health, Jena, Germany
| | | | - Karine Laroucau
- Bacterial Zoonosis Unit, Animal Health Laboratory, French Food Agency (Anses), Maisons-Alfort, France
| | - Mandy Elschner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut – Federal Research Institute for Animal Health, Jena, Germany
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Holzer K, Wareth G, El-Diasty M, Abdel-Hamid NH, Hamdy MER, Moustafa SA, Linde J, Bartusch F, Abdel-Glil MY, Sayour AE, Elbauomy EM, Elhadidy M, Melzer F, Beyer W. Tracking the distribution, genetic diversity and lineage of Brucella melitensis recovered from humans and animals in Egypt based on core-genome SNP analysis and in silico MLVA-16. Transbound Emerg Dis 2022; 69:3952-3963. [PMID: 36383491 DOI: 10.1111/tbed.14768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/07/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022]
Abstract
Brucellosis is one of the most common neglected zoonotic diseases globally, with a public health significance and a high economic loss in the livestock industry caused by the bacteria of the genus Brucella. In this study, 136 Egyptian Brucella melitensis strains isolated from animals and humans between 2001 and 2020 were analysed by examining the whole-core-genome single-nucleotide polymorphism (cgSNP) in comparison to the in silico multilocus variable number of tandem repeat analysis (MLVA-16). Almost all Egyptian isolates were belonging to the West Mediterranean clade, except two isolates from buffalo and camel were belonging to the American and East Mediterranean clades, respectively. A significant correlation between the human case of brucellosis and the possible source of infection from animals was found. It seems that several outbreak strains already existing for many years have been spread over long distances and between many governorates. The cgSNP analysis, in combination with epidemiological metadata, allows a better differentiation than the MLVA-16 genotyping method and, hence, the source definition and tracking of outbreak strains. The MLVA based on the currently used 16 markers is not suitable for this task. Our results revealed 99 different cgSNP genotypes with many different outbreak strains, both older and widely distributed ones and rather newly introduced ones as well. This indicates several different incidents and sources of infections, probably by imported animals from other countries to Egypt. Comparing our panel of isolates to public databases by cgSNP analysis, the results revealed near relatives from Italy. Moreover, near relatives from the United States, France, Austria and India were found by in silico MLVA.
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Affiliation(s)
- Katharina Holzer
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Gamal Wareth
- Friedrich-Loeffler Institut, Institute for Bacterial Infections and Zoonoses, Jena, Germany.,Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh, Moshtohor, Egypt
| | - Mohamed El-Diasty
- Animal Health Research Institute, Agricultural Research Center, Cairo, Egypt
| | - Nour H Abdel-Hamid
- Animal Health Research Institute, Agricultural Research Center, Cairo, Egypt
| | - Mahmoud E R Hamdy
- Animal Health Research Institute, Agricultural Research Center, Cairo, Egypt
| | - Shawky A Moustafa
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh, Moshtohor, Egypt
| | - Jörg Linde
- Friedrich-Loeffler Institut, Institute for Bacterial Infections and Zoonoses, Jena, Germany
| | - Felix Bartusch
- IT Center (ZDV), High-Performance and Cloud Computing Group, University of Tuebingen, Tuebingen, Germany
| | - Mostafa Y Abdel-Glil
- Friedrich-Loeffler Institut, Institute for Bacterial Infections and Zoonoses, Jena, Germany
| | - Ashraf E Sayour
- Animal Health Research Institute, Agricultural Research Center, Cairo, Egypt
| | - Essam M Elbauomy
- Animal Health Research Institute, Agricultural Research Center, Cairo, Egypt
| | - Mohamed Elhadidy
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.,Department of Bacteriology, Mycology, and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Falk Melzer
- Friedrich-Loeffler Institut, Institute for Bacterial Infections and Zoonoses, Jena, Germany
| | - Wolfgang Beyer
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
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Tsai BY, Chien CC, Huang SH, Zheng JY, Hsu CY, Tsai YS, Hung YP, Ko WC, Tsai PJ. The emergence of Clostridioides difficile PCR ribotype 127 at a hospital in northeastern Taiwan. J Microbiol Immunol Infect 2022; 55:896-909. [PMID: 35042668 DOI: 10.1016/j.jmii.2021.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/27/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Several studies have highlighted the incidence of Clostridioides difficile infections (CDIs) in Taiwan and certain ribotypes have been related to severe clinical diseases. A study was conducted to investigate the polymerase chain reaction (PCR) ribotypes and genetic relatedness of clinical C. difficile strains collected from January 2009 to December 2015 at a hospital in northeastern Taiwan. MATERIAL AND METHODS A modified two-step typing algorithm for C. difficile was used by combining a modified 8-plex and 3'-truncated tcdA screening PCR. In addition, MLVA typing was adopted for investigation of bacterial clonality and transmission. RESULTS Among a total of 86 strains, 24 (28%) were nontoxigenic and 62 (72%) had both tcdA and tcdB (A + B+). No tcdA-negative and tcdB-positive (A-B+) strains were identified. Binary toxin (CDT)-producing (cdtA+/cdtB+) strains were started to be identified in 2013. The 21 (34%) A+B+ clinical strains with binary toxin and tcdC deletion were identified as RT127 strains, which contained both RT078-lineage markers and fluoroquinolone (FQ)-resistant mutations (Thr82Ile in gyrA). Multiple loci variable-number tandem repeat analysis (MLVA) for phylogenetic relatedness of RT127 strains indicated that 20 of 21 strains belonged to a clonal complex that was identical to a clinical strain collected from southern Taiwan in 2011, suggestive of a clonal expansion in Taiwan. CONCLUSION A two-step typing method could rapidly confirm species identification and define the toxin gene profile of C. difficile isolates. The clonal expansion of RT127 strains in Taiwan indicates monitoring and surveillance of toxigenic C. difficile isolates from human, animal, and environment are critical to develop One Health prevention strategies.
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Affiliation(s)
- Bo-Yang Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Chun-Chih Chien
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Kaohsiung, Kaohsiung, Taiwan.
| | - Shu-Huan Huang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Kee-Lung, Keelung, Taiwan.
| | - Jun-Yuan Zheng
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Kee-Lung, Kee-Lung, Taiwan.
| | - Chih-Yu Hsu
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
| | - Yau-Sheng Tsai
- Institute of Clinical Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Yuan-Pin Hung
- Departments of Internal Medicine, Tainan Hospital, Ministry of Health & Welfare, Tainan, Taiwan; Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Pei-Jane Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan; Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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30
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Bidet P, Birgy A, Brethon B, Dalle JH, Mariani-Kurkdjian P, Courroux C, Monjault A, Gits-Museli M, Bonacorsi S. Epidemiological investigation of Pseudomonas aeruginosa isolates including Multidrug-Resistant serogroup O12 isolates, by use of a rapid and simplified Multiple-Locus Variable-Number of Tandem Repeats Analysis and Whole Genome Sequencing. J Hosp Infect 2022; 130:56-62. [PMID: 36181986 DOI: 10.1016/j.jhin.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/05/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Clustered cases of Pseudomonas aeruginosa infection in immunocompromised patients' wards require rapid characterization of a potential epidemic to guide investigations and identify the potential source of contamination. AIM To design and evaluate a rapid and simple typing method for P. aeruginosa in comparison to whole genome sequencing (WGS). METHODS We designed and used a simplified PCR based on multiple locus tandem variable number analysis (MLVA) to investigate cases of P. aeruginosa infection and colonization in a paediatric haematology department. The method was compared to WGS by using Illumina method. FINDINGS On the 17 isolates recovered from 15 children (8 from blood cultures, 3 from urinary tract infections, 1 from sputum and 5 stool isolates) MLVA distinguished 10 different profiles and 7 isolates from 6 children shared the same profile. Analysis by WGS revealed that these 7 isolates belonged to sequence type ST111 and serotype O12 and permitted to further distinguish at least 3 different genotypes among them. Five environmental strains had 3 MLVA profiles, one shared with a clinical isolate but WGS excluded any relationship. CONCLUSION The simplified and inexpensive MLVA method permitted to exclude, in less than five hours, most of unrelated isolates and to focus investigations on a small number of cases while WGS, taking several days of work, drew definitive conclusions concerning the outbreak and the genetic relationships of the ST111 isolates circulating in the department. We conclude that sequential use of both methods is the optimal strategy to investigate grouped cases of P. aeruginosa infections.
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Affiliation(s)
- P Bidet
- Université Paris Cité, IAME, INSERM, F-75018 Paris, France; Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France.
| | - A Birgy
- Université Paris Cité, IAME, INSERM, F-75018 Paris, France; Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France
| | - B Brethon
- Service d'Hémato-immunologie, Hôpital Robert-Debré, AP-HP, Paris, France
| | - J H Dalle
- Service d'Hémato-immunologie, Hôpital Robert-Debré, AP-HP, Paris, France
| | - P Mariani-Kurkdjian
- Université Paris Cité, IAME, INSERM, F-75018 Paris, France; Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France
| | - C Courroux
- Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France
| | - A Monjault
- Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France
| | - M Gits-Museli
- Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France
| | - S Bonacorsi
- Université Paris Cité, IAME, INSERM, F-75018 Paris, France; Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France
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31
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Vasini B, Farace P, Ariel A, Cirone K, Mendez L, Morsella C, Fresia P, Iraola G, Gioffré A, Paolicchi F. Phylogenetic and Multiple-Locus Variable number tandem repeat analysis of Mycobacterium avium subsp. paratuberculosis isolates from Argentina. Vet Res Commun 2022. [PMID: 35948855 DOI: 10.1007/s11259-022-09983-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/03/2022] [Indexed: 10/15/2022]
Abstract
Paratuberculosis is a worldwide chronic enteric disease of ruminants, caused by Mycobacterium avium subsp. paratuberculosis (MAP). While MAP has been widely investigated all around the world, little is known about the different strains that circulate in each country. This study describes the genetic diversity of MAP isolates from different bovine and deer herds from Argentina, analyzed by Multiple-Locus Variable number tandem repeat Analysis (MLVA), as well as the phylogenetic relatedness between geographically distant isolates through Whole Genome Sequencing (WGS) and core-genome analysis. A total of 90 MAP isolates were analyzed. The results showed seven different MLVA genotypes, with almost 75% of them belonging to pattern INMV 1, described in all the herds studied. WGS results suggested the presence of a common INMV 1 strain circulating throughout the country. Our results allow confirming the coexistence of different strains in time and space and the mixed infections identified in some animals. These observations suggest the absence of animal monitoring prior to introduction to the herds and the need for a control program in the country. This study represents the first to report WGS of MAP strains in Argentina.
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Katsiolis A, Papadopoulos DK, Giantsis IA, Papageorgiou K, Zdragas A, Giadinis ND, Petridou E. Brucella spp. distribution, hosting ruminants from Greece, applying various molecular identification techniques. BMC Vet Res 2022; 18:202. [PMID: 35624476 PMCID: PMC9137169 DOI: 10.1186/s12917-022-03295-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/13/2022] [Indexed: 12/02/2022] Open
Abstract
Background Brucellosis still remains an endemic disease for both livestock and human in Greece, influencing the primary sector and national economy in general. Although farm animals and particularly ruminants constitute the natural hosts of the disease, transmission to humans is not uncommon, thus representing a serious occupational disease as well. Under this prism, knowledge concerning Brucella species distribution in ruminants is considered a high priority. There are various molecular methodologies for Brucella detection with however differential discriminant capacity. Hence, the aim of this survey was to achieve nationally Brucella epidemiology baseline genotyping data at species and subtype level, as well as to evaluate the pros and cons of different molecular techniques utilized for detection of Brucella species. Thirty-nine tissue samples from 30 domestic ruminants, which were found positive applying a screening PCR, were tested by four different molecular techniques i.e. sequencing of the 16S rRNA, the BP26 and the OMP31 regions, and the MLVA typing panel 1 assay of minisatellite markers. Results Only one haplotype was revealed from the 16S rRNA sequencing analysis, indicating that molecular identification of Brucella bacteria based on this marker might be feasible solely up to genus level. BP26 sequencing analysis and MLVA were in complete agreement detecting both B. melitensis and B. abortus. An interesting exception was observed in 11 samples, of lower quality extracted DNA, in which not all expected MLVA amplicons were produced and identification was based on the remaining ones as well as on BP26. On the contrary OMP31 failed to provide a clear band in any of the examined samples. Conclusions The present study reveals the constant circulation of Brucella bacteria in ruminants throughout Greece. Further, according to our results, BP26 gene represents a very good alternative to MLVA minisatellite assay, particularly in lower quality DNA samples. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03295-4.
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Affiliation(s)
- Aristomenis Katsiolis
- Department of Microbiology and Infectious Diseases, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dimitrios K Papadopoulos
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100, Florina, Greece
| | - Ioannis A Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100, Florina, Greece.
| | - Konstantinos Papageorgiou
- Department of Microbiology and Infectious Diseases, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Antonis Zdragas
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organization DEMETER (former NAGREF), Thessaloniki, Greece
| | - Nektarios D Giadinis
- Clinic of Farm Animals, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Evanthia Petridou
- Department of Microbiology and Infectious Diseases, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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Fu M, He P, OuYang X, Yu Y, Wen B, Zhou D, Xiong X, Yuan Q, Jiao J. Novel genotypes of Coxiella burnetii circulating in rats in Yunnan Province, China. BMC Vet Res 2022; 18:204. [PMID: 35624449 PMCID: PMC9137106 DOI: 10.1186/s12917-022-03310-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coxiella burnetii (Cb) is the causative agent of the zoonotic disease Q fever which is distributed worldwide. Molecular typing of Cb strains is essential to find out the infectious source and prevent Q fever outbreaks, but there has been a lack of typing data for Cb strains in China. The aim of this study was to investigate the genotypes of Cb strains in wild rats in Yunnan Province, China. RESULTS Eighty-six wild rats (Rattus flavipectus) were collected in Yunnan Province and 8 of the 86 liver samples from the wild rats were positive in Cb-specific quantitative PCR (qPCR). The Cb strains from the 8 rats were then typed into 3 genotypes using 10-spacer multispacer sequence typing (MST), and 2 of the 3 genotypes were recognized as novel ones. Moreover, the Cb strains in the wild rats were all identified as genotype 1 using 6-loci multilocus variable number of tandem repeat analysis (MLVA). CONCLUSIONS This is the first report of genotypic diversity of Cb strains from wild rats in China. Further studies are needed to explore the presence of more genotypes and to associate the genotypes circulating in the wildlife-livestock interaction with those causing human disease to further expand on the epidemiological aspects of the pathogen.
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Affiliation(s)
- Mengjiao Fu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Peisheng He
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.,Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, People's Republic of China
| | - Xuan OuYang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Yonghui Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Bohai Wen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Xiaolu Xiong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Qinghong Yuan
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory of Natural Focal Disease Control and Prevention, Yunnan, People's Republic of China.
| | - Jun Jiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
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Heidari R, Farajzadeh Sheikh A, Hashemzadeh M, Farshadzadeh Z, Salmanzadeh S, Saki M. Antibiotic resistance, biofilm production ability and genetic diversity of carbapenem-resistant Pseudomonas aeruginosa strains isolated from nosocomial infections in southwestern Iran. Mol Biol Rep 2022; 49:3811-3822. [PMID: 35169997 PMCID: PMC8853202 DOI: 10.1007/s11033-022-07225-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/02/2022] [Indexed: 12/14/2022]
Abstract
Background This study was aimed to evaluate the antibiotic resistance, biofilm formation, and genetic diversity of carbapenem-resistant Pseudomonas aeruginosa (CRPA) strains isolated from four types of nosocomial infections (NIs) including urinary tract infection (UTI), ventilator-associated pneumonia (VAP), surgical site infection (SSI), and bloodstream infection (BSI). Methods and results In total, 115 isolates of NIs-causing P. aeruginosa were collected from NIs. Antibiotic susceptibility testing (AST) was performed using disk diffusion method and minimum inhibitory concentrations. Biofilm formation was tested on 96-well polystyrene microtiter plates (MTP). CRPA isolates were genotyped using multiple-locus variable number of tandem repeat analysis (MLVA). The most resistance and susceptibility rates were observed to amikacin (70.6%) and colistin (96.1%), respectively. Colistin and meropenem were the most active antimicrobial agents in VAP, SSI, and BSI. While, colistin and cefepime were the most active in UTIs. In total, 52.2% (n = 60/115) of P. aeruginosa isolates were carbapenem resistant, of which 95.0%, 55.0%, and 5.0% were multidrug-resistant, extensively drug-resistant, and pandrug-resistant, respectively. There was a significant association between resistance to carbapenem and resistance to other antibiotics except for piperacillin/tazobactam. The biofilm production of CRPA isolates was 95.0%, of which 23.3% were strong biofilm producers. Based on MLVA, there were 34 different types of CRPA isolates classified into three main clusters and 5 sub clusters. Conclusion The association of CRPA with other antibiotic resistance, the high rates of biofilm production, and the high genetic diversity of the isolates may be a warning of the need for a careful surveillance program.
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Affiliation(s)
- Reza Heidari
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ahmad Farajzadeh Sheikh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Zahra Farshadzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shokrollah Salmanzadeh
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Tropical Medicine Ward, Razi Teaching Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Morteza Saki
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Pelerito A, Nunes A, Grilo T, Isidro J, Silva C, Ferreira AC, Valdezate S, Núncio MS, Georgi E, Gomes JP. Genetic Characterization of Brucella spp.: Whole Genome Sequencing-Based Approach for the Determination of Multiple Locus Variable Number Tandem Repeat Profiles. Front Microbiol 2021; 12:740068. [PMID: 34867857 PMCID: PMC8633399 DOI: 10.3389/fmicb.2021.740068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022] Open
Abstract
Brucellosis is an important zoonosis that is emerging in some regions of the world, gaining increased relevance with the inclusion of the causing agent Brucella spp. in the class B bioterrorism group. Until now, multi-locus VNTR Analysis (MLVA) based on 16 loci has been considered as the gold standard for Brucella typing. However, this methodology is laborious, and, with the rampant release of Brucella genomes, the transition from the traditional MLVA to whole genome sequencing (WGS)-based typing is on course. Nevertheless, in order to avoid a disruptive transition with the loss of massive genetic data obtained throughout the last decade and considering that the transition timings will vary considerably among different countries, it is important to determine WGS-based MLVA alleles of the nowadays sequenced genomes. On this regard, we aimed to evaluate the performance of a Python script that had been previously developed for the rapid in silico extraction of the MLVA alleles, by comparing it to the PCR-based MLVA procedure over 83 strains from different Brucella species. The WGS-based MLVA approach detected 95.3% of all possible 1,328 hits (83 strains×16 loci) and showed an agreement rate with the PCR-based MLVA procedure of 96.4% for MLVA-16. According to our dataset, we suggest the use of a minimal depth of coverage of ~50x and a maximum number of ~200 contigs as guiding “boundaries” for the future application of the script. In conclusion, the evaluated script seems to be a very useful and robust tool for the in silico determination of MLVA profiles of Brucella strains, allowing retrospective and prospective molecular epidemiological studies, which are important for maintaining an active epidemiological surveillance of brucellosis.
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Affiliation(s)
- Ana Pelerito
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.,CBIOS - Universidade Lusófona's Research Center for Biosciences & Health Technologies, Lisbon, Portugal.,Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Teresa Grilo
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Catarina Silva
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal.,Centre for Toxicogenomics and Human Health (ToxOmics), Faculdade de Ciências Médicas, Nova Medical School, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Ana Cristina Ferreira
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal.,National Institute for Agrarian and Veterinary Research, I.P. (INIAV, IP), Oeiras, Portugal
| | - Sylvia Valdezate
- ISCIII Reference and Research Laboratory for Taxonomy, National Centre of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Sofia Núncio
- Emergency Response and Biopreparedness Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Enrico Georgi
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.,Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
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Usein CR, Oprea M, Ciontea AS, Dinu S, Cristea D, Zota LC, Kotila S. A Snapshot of the Genetic Diversity of Salmonella Enteritidis Population Involved in Human Infections in Romania Taken in the European Epidemiological Context. Pathogens 2021; 10:pathogens10111490. [PMID: 34832645 PMCID: PMC8621327 DOI: 10.3390/pathogens10111490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/12/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
In the absence of consistent national molecular typing data to enhance the surveillance of Salmonella Enteritidis, it was considered useful to collect baseline information on the genetic diversity and antibiotic susceptibility of strains isolated in Romania between January 2016 and April 2020 and compare them to strains described in major international outbreaks of the same period. A collection of 245 clinical isolates were genotyped by a standardised multiple-locus variable-number of tandem repeats analysis (MLVA) 5-loci protocol and screened for antimicrobial resistance against 15 compounds. Twenty strains were further subjected to whole genome sequencing (WGS) and compared to epidemiologically relevant high-throughput sequencing data available in European databases. Twenty-seven MLVA genotypes were identified, of which three, commonly reported in Europe between 2016–2020, covered 72% of the collection. Antibiotic resistance was detected in 30% of the strains, with resistance to nalidixic acid and ciprofloxacin as the most common phenotype, and also associated with two prevalent MLVA clones. WGS-derived multilocus sequence typing (MLST) revealed a single sequence type (ST11) further resolved into 10 core-genome MLST complex types. The minimum spanning tree constructed from the cgMLST data clustered Romanian and international strains, which shared more than 95% of the core genes, revealing links with a contemporaneous multi-country outbreak. This study could be regarded as a forerunner to the advent of using this integrative approach in the public health practice at a national level and thus contribute to the concerted actions at a European level to stop outbreaks.
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Affiliation(s)
- Codruta-Romanita Usein
- “Cantacuzino” National Military Medical Institute for Research and Development, 050096 Bucharest, Romania; (A.S.C.); (S.D.); (D.C.)
- Correspondence: (C.-R.U.); (M.O.)
| | - Mihaela Oprea
- “Cantacuzino” National Military Medical Institute for Research and Development, 050096 Bucharest, Romania; (A.S.C.); (S.D.); (D.C.)
- Correspondence: (C.-R.U.); (M.O.)
| | - Adriana Simona Ciontea
- “Cantacuzino” National Military Medical Institute for Research and Development, 050096 Bucharest, Romania; (A.S.C.); (S.D.); (D.C.)
| | - Sorin Dinu
- “Cantacuzino” National Military Medical Institute for Research and Development, 050096 Bucharest, Romania; (A.S.C.); (S.D.); (D.C.)
| | - Daniela Cristea
- “Cantacuzino” National Military Medical Institute for Research and Development, 050096 Bucharest, Romania; (A.S.C.); (S.D.); (D.C.)
| | - Lavinia Cipriana Zota
- National Center for Surveillance and Control of Communicable Diseases, National Institute of Public Health, 050463 Bucharest, Romania;
| | - Saara Kotila
- European Centre for Disease Prevention and Control, 16973 Solna, Sweden;
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Jodełko A, Szymańska-Czerwińska M, Rola JG, Niemczuk K. Molecular detection of Coxiella burnetii in small ruminants and genotyping of specimens collected from goats in Poland. BMC Vet Res 2021; 17:341. [PMID: 34711239 PMCID: PMC8554849 DOI: 10.1186/s12917-021-03051-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 10/08/2021] [Indexed: 11/30/2022] Open
Abstract
Background Coxiella burnetii is the etiological agent of Q fever, a zoonosis affecting many animal species including sheep and goats. The aims of this study were to evaluate the shedding of Coxiella burnetii in small ruminant herds and to identify the pathogen’s genotypes and sequence types (STs) using multiple-locus variable number tandem repeat analysis (MLVA) and multispacer sequence typing (MST) methods. Results Overall, 165 samples from 43 herds of goats and 9 flocks of sheep were collected including bulk tank milk (BTM), individual milk samples, vaginal swabs, tissue sections from stillborn kids, feces and placentas. These were tested by real-time PCR targeting the IS1111 element. C. burnetii infection was confirmed in 51.16% of the herds of goats and 22.2% of the flocks of sheep. Six out of nine samples originating from goats were successfully genotyped using the MLVA method. The presence was confirmed of two widely distributed MLVA genotypes (I and J) and genotype PL1 previously reported only in cattle. Only one sequence type (ST61) was identified; however, the majority of specimens represented partial STs and some of them may belong to ST61. Other partial STs could possibly be ST74. Conclusion This study confirmed the relatively common occurrence of Coxiella burnetii in small ruminant herds in Poland. Interestingly, all genotyped samples represent cattle-associated MLVA genotypes.
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Affiliation(s)
- Agnieszka Jodełko
- Department of Cattle and Sheep Diseases, National Veterinary Research Institute, Pulawy, Poland.
| | | | - Jolanta Grażyna Rola
- Department of Hygiene of Food of Animal Origin, National Veterinary Research Institute, Pulawy, Poland
| | - Krzysztof Niemczuk
- Department of Cattle and Sheep Diseases, National Veterinary Research Institute, Pulawy, Poland
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Kim J, Seo MR, Kim B, Kim J, Bae MH, Pai H. Genetic Relatedness of 5-Year Isolates of Clostridioides difficile Polymerase Chain Reaction Ribotype 017 Strains in a Hospital. Antibiotics (Basel) 2021; 10:1229. [PMID: 34680810 DOI: 10.3390/antibiotics10101229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/29/2021] [Accepted: 10/07/2021] [Indexed: 11/24/2022] Open
Abstract
The objective of this study was to analyse the genetic relatedness of Clostridioides difficile polymerase chain reaction ribotype 017 (RT017) strains from patients with hospital-acquired C. difficile infection (HA-CDI) in a hospital with a high RT017 prevalence. From 2009 to 2013, 200 RT017 strains (26.8%) were collected from 745 HA-CDI patient isolates. They comprised 64 MLVA types, and 197 (98.5%) strains were genetically related to 5 clonal complexes (CCs). The largest cluster, CC-A, included 163 isolates of 40 MLVA types. CC-A accounted for 20% of RT017 strains in 2009 and sharply increased to 94.9% in 2010, 94% in 2011, 86.2% in 2012, and 73.5% in 2013. The other 4 CCs included 20 isolates with 7 MLVA types. The resistance rates of antimicrobials were as follows: clindamycin 100%, moxifloxacin 99%, rifaximin 88.5%, and vancomycin 1%. All isolates were susceptible to metronidazole and piperacillin/tazobactam. Comparing antibiotic resistance among CCs, the geometric mean of the minimum inhibitory concentrations of moxifloxacin, vancomycin, and piperacillin/tazobactam were significantly higher for CC-A isolates than for the other CCs. RT017 clones constantly evolved over the 5 years studied with regard to genetic relatedness. The levels of antibiotic resistance may contribute to the persistence of organisms in the institution.
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Jiao J, Zhang J, He P, OuYang X, Yu Y, Wen B, Sun Y, Yuan Q, Xiong X. Identification of Tick-Borne Pathogens and Genotyping of Coxiella burnetii in Rhipicephalus microplus in Yunnan Province, China. Front Microbiol 2021; 12:736484. [PMID: 34621258 PMCID: PMC8491607 DOI: 10.3389/fmicb.2021.736484] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
Rhipicephalus microplus, a vector that can transmit many pathogens to humans and domestic animals, is widely distributed in Yunnan province, China. However, few reports on the prevalence of tick-borne pathogens (TBPs) in Rh. microplus in Yunnan are available. The aim of this study was to detect TBPs in Rh. microplus in Yunnan and to analyze the phylogenetic characterization of TBPs detected in these ticks. The adult Rh. microplus (n = 516) feeding on cattle were collected. The pooled DNA samples of these ticks were evaluated using metagenomic next-generation sequencing (mNGS) and then TBPs in individual ticks were identified using genus- or group-specific nested polymerase chain reaction (PCR) combined with DNA sequencing assay. As a result, Candidatus Rickettsia jingxinensis (24.61%, 127/516), Anaplasma marginale (13.18%, 68/516), Coxiella burnetii (3.10%, 16/516), and Coxiella-like endosymbiont (CLE) (8.33%, 43/516) were detected. The dual coinfection with Ca. R. jingxinensis and A. marginale and the triple coinfection with Ca. R. jingxinensis, A. marginale, and CLE were most frequent and detected in 3.68% (19/516) and 3.10% (16/516) of these ticks, respectively. The results provide insight into the diversity of TBPs and their coinfections in Rh. microplus in Yunnan province of China, reporting for the first time that C. burnetii had been found in Rh. microplus in China. Multilocus variable number tandem repeat analysis with 6 loci (MLVA-6) discriminated the C. burnetii detected in Rh. microplus in Yunnan into MLVA genotype 1, which is closely related to previously described genotypes found primarily in tick and human samples from different regions of the globe, indicating a potential public health threat posed by C. burnetii in Rh. microplus in Yunnan.
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Affiliation(s)
- Jun Jiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jianing Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Peisheng He
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xuan OuYang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yonghui Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bohai Wen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Qinghong Yuan
- Yunnan Provincial Key Laboratory of Natural Focal Disease Control and Prevention, Yunnan Institute of Endemic Diseases Control and Prevention, Dali, China
| | - Xiaolu Xiong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Wu TH, Wang NM, Liu FC, Pan HH, Huang FL, Fang YP, Chiang TW, Yang YY, Song CS, Wu HC, Lee CY. Macrolide Resistance, Clinical Features, and Cytokine Profiles in Taiwanese Children With Mycoplasma pneumoniae Infection. Open Forum Infect Dis 2021; 8:ofab416. [PMID: 34557557 PMCID: PMC8454522 DOI: 10.1093/ofid/ofab416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/09/2021] [Indexed: 12/30/2022] Open
Abstract
Background The factors that predict the progression of Mycoplasma pneumoniae infection remain inconclusive. Therefore, we investigated macrolide resistance prevalence, M pneumoniae genotype, and clinical characteristics of childhood M pneumoniae respiratory tract infections in Taiwan. Methods A total of 295 children hospitalized with respiratory tract infections with positive serological M pneumoniae immunoglobulin M test results were enrolled in this 3-year prospective study. Oropharyngeal swabs were obtained for M pneumoniae cultures and polymerase chain reaction tests. All M pneumoniae specimens were further characterized by P1 typing, multilocus variable-number tandem-repeat analysis (MLVA), and macrolide resistance genotyping. The clinical characteristics and blood cytokine profiles were analyzed accordingly. Results Of 138 M pneumoniae specimens, type I P1 was the predominant (136 of 138, 98.6%). The MLVA type P (4-4-5-7-2) was the leading strain (42 of 138, 30.4%), followed by type J, U, A, and X. The overall macrolide-resistant rate was 38.4% (53 of 138); the resistance rate increased dramatically yearly: 10.6% in 2017, 47.5% in 2018, and 62.5% in 2019 (P < .001). All macrolide-resistant M pneumoniae (MRMP) harbored the A2063G mutation and were MLVA type 4-5-7-2 (49 of 53, 92.5%), especially type U and X. No significant differences in clinical symptoms, duration of hospital stay, and radiographic findings were identified among patients between MRMP and macrolide-sensitive M pneumoniae (MSMP) groups. Patients with MRMP infection had more febrile days before and during hospitalization and higher interleukin (IL)-13 and IL-33 levels than patients with MSMP infection (P < .05). Conclusions Macrolide-resistant M pneumoniae surged in Taiwan throughout the study period, but macrolide resistance was not a determinant factor of clinical severity.
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Affiliation(s)
- Tsung-Hua Wu
- Department of Pediatrics, Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Nancy M Wang
- Department of Biology, National Changhua University of Education, Changhua, Taiwan
| | - Fang-Ching Liu
- Department of Pediatrics, Jen-Ai Hospital, Taichung, Taiwan
| | - Hui-Hsien Pan
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Fang-Liang Huang
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Ping Fang
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Ting-Wei Chiang
- Department of Biology, National Changhua University of Education, Changhua, Taiwan
| | - Yu-Ying Yang
- Department of Clinical Laboratory, Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Chiah-Sing Song
- Department of Clinical Laboratory, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Hsiang-Chin Wu
- Department of Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chun-Yi Lee
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
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Holzer K, El-Diasty M, Wareth G, Abdel-Hamid NH, Hamdy MER, Moustafa SA, Linde J, Bartusch F, Sayour AE, Elbauomy EM, Elhadidy M, Melzer F, Beyer W. Tracking the Distribution of Brucella abortus in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16. Microorganisms 2021; 9:microorganisms9091942. [PMID: 34576838 PMCID: PMC8469952 DOI: 10.3390/microorganisms9091942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Brucellosis, caused by the bacteria of the genus Brucella, is one of the most neglected common zoonotic diseases globally with a public health significance and a high economic loss among the livestock industry worldwide. Since little is known about the distribution of B. abortus in Egypt, a total of 46 B. abortus isolates recovered between 2012–2020, plus one animal isolate from 2006, were analyzed by examining the whole core genome single nucleotide polymorphism (cgSNP) in comparison to the in silico multilocus variable number of tandem repeat analysis (MLVA). Both cgSNP analysis and MLVA revealed three clusters and one isolate only was distantly related to the others. One cluster identified a rather widely distributed outbreak strain which is repeatedly occurring for at least 16 years with marginal deviations in cgSNP analysis. The other cluster of isolates represents a rather newly introduced outbreak strain. A separate cluster comprised RB51 vaccine related strains, isolated from aborted material. The comparison with MLVA data sets from public databases reveals one near relative from Argentina to the oldest outbreak strain and a related strain from Spain to a newly introduced outbreak strain in Egypt. The distantly related isolate matches with a strain from Portugal in the MLVA profile. Based on cgSNP analysis the oldest outbreak strain clusters with strains from the UK. Compared to the in silico analysis of MLVA, cgSNP analysis using WGS data provides a much higher resolution of genotypes and, when correlated to the associated epidemiological metadata, cgSNP analysis allows the differentiation of outbreaks by defining different outbreak strains. In this respect, MLVA data are error-prone and can lead to incorrect interpretations of outbreak events.
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Affiliation(s)
- Katharina Holzer
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany;
- Correspondence: ; Tel.: +49-711-4592-2428
| | - Mohamed El-Diasty
- Agricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (N.H.A.-H.); (M.E.R.H.); (A.E.S.); (E.M.E.)
| | - Gamal Wareth
- Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, Egypt; (G.W.); (S.A.M.)
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.)
| | - Nour H. Abdel-Hamid
- Agricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (N.H.A.-H.); (M.E.R.H.); (A.E.S.); (E.M.E.)
| | - Mahmoud E. R. Hamdy
- Agricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (N.H.A.-H.); (M.E.R.H.); (A.E.S.); (E.M.E.)
| | - Shawky A. Moustafa
- Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, Egypt; (G.W.); (S.A.M.)
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.)
| | - Felix Bartusch
- High-Performance and Cloud Computing Group, IT Center (ZDV), University of Tuebingen, Waechterstrasse 76, 72074 Tübingen, Germany;
| | - Ashraf E. Sayour
- Agricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (N.H.A.-H.); (M.E.R.H.); (A.E.S.); (E.M.E.)
| | - Essam M. Elbauomy
- Agricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (N.H.A.-H.); (M.E.R.H.); (A.E.S.); (E.M.E.)
| | - Mohamed Elhadidy
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza 12578, Egypt;
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.)
| | - Wolfgang Beyer
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany;
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Kumari G, Doimari S, Suman Kumar M, Singh M, Singh DK. MLVA typing of Brucella melitensis and B. abortus isolates of animal and human origin from India. Anim Biotechnol 2021; 34:375-383. [PMID: 34487479 DOI: 10.1080/10495398.2021.1971685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Brucellosis is a widely prevalent zoonotic disease of major public health significance. A collection of Brucella melitensis and Brucella abortus field isolates of animal and human origin were subjected to MLVA-15 typing followed by phylogeography studies. The MLVA-15 analysis of B. melitensis (n = 65) field isolates resulted in 48 different profiles. The panel I marker bruce45 was found to be most conserved, while the rest of the panel I markers showed low to moderate length polymorphism. Among the panel II markers, bruce04, bruce16 and bruce30 showed a high discriminatory index. The MLVA-15 typing of 13 B. abortus field isolates revealed 13 different genotypes with panel II markers showing higher discriminatory ability vis-à-vis panel I. The minimum spanning tree analysis (MST) in comparison with isolates from the international database revealed that all B. melitensis and B. abortus isolates from this study belonged to the 'Eastern Mediterranean' and the 'abortus C' lineage, respectively. The MLVA-15 typing could differentiate field isolates of B. abortus and B. melitensis originating from different regions, reaffirming the technique's potential of high resolution and suitability for local epidemiological studies. The MLVA scheme also has the advantage of comparison of local isolates with a worldwide database, allowing for phylogeographical studies.
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Affiliation(s)
- Gita Kumari
- ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Soni Doimari
- ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - M Suman Kumar
- ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Maninder Singh
- Faculty of Veterinary Science, Sher-e-Kashmir University of Agricultural Sciences and Technology, Chatha, Jammu, India
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Zahli R, Soliveri J, Abrini J, Copa-Patiño JL, Nadia A, Scheu AK, Nadia SS. Prevalence, typing and antimicrobial resistance of Salmonella isolates from commercial shellfish in the North coast of Morocco. World J Microbiol Biotechnol 2021; 37:170. [PMID: 34487261 DOI: 10.1007/s11274-021-03136-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
Salmonellosis is one of the most common foodborne illnesses in the world. The irrational use of antibiotics in medicine and in animal nutrition has greatly favored the emergence and spread of resistant strains of non-typhoid Salmonella. This study aims the determination of the prevalence of Salmonella in bivalve mollusks in Northern Morocco, as well as the molecular typing and antibiotic susceptibility testing of the strains isolated from positive samples. In total, 150 samples from shellfish composed of mussels (Mytilus galloprovincialis), clams (Callista chione and Ruditapes descussatus) and oysters (Magallana gigas). Isolated Salmonella were characterized by Molecular techniques PCR, MLST and MLVA, phylogenetically grouped by MLSA, and susceptibilities were determined for 30 antimicrobial drugs using microdilution method by the BD Phoenix Automated Microbiology System. Prevalence of Salmonella enterica subsp. enterica was 12.67%, grouped in four serovars identified as Chester, Hadar, Typhimurium and Kentucky. Five different MLST STs (sequence types) were detected, ST1954 being the most common, which was mostly found in Chester isolates. Forty-two percent of the isolates showed resistance to more than one antibiotic, especially trimethoprim, sulfa drugs, quinolones and β-lactam. There was a marked change in the serovars and antimicrobial resistance profiles of the Salmonella isolates in this study compared to those in previous studies.
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Affiliation(s)
- Rajae Zahli
- Biotechnology and Applied Microbiology Laboratory (BMA), Department of Biology, Abdelmalek Essadi University, Tétouan, Morocco.
| | - Juan Soliveri
- Department of Biomedicine and Biotechnology, Faculty of Farmacy, University of Alcalá, 28805, Madrid, Spain
| | - Jamal Abrini
- Biotechnology and Applied Microbiology Laboratory (BMA), Department of Biology, Abdelmalek Essadi University, Tétouan, Morocco
| | - José L Copa-Patiño
- Department of Biomedicine and Biotechnology, Faculty of Farmacy, University of Alcalá, 28805, Madrid, Spain
| | - Amajoud Nadia
- Regional Environmental Laboratory of the Urban Community of Tetouan, Tétouan, Morocco
| | - Ann-Karolin Scheu
- Department of Biomedicine and Biotechnology, Faculty of Farmacy, University of Alcalá, 28805, Madrid, Spain
| | - Skali Senhaji Nadia
- Biotechnology and Applied Microbiology Laboratory (BMA), Department of Biology, Abdelmalek Essadi University, Tétouan, Morocco
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Kabała M, Gofron Z, Aptekorz M, Sacha K, Harmanus C, Kuijper E, Martirosian G. Clostridioides difficile Ribotype 027 (RT027) Outbreak Investigation Due to the Emergence of Rifampicin Resistance Using Multilocus Variable-Number Tandem Repeat Analysis ( MLVA). Infect Drug Resist 2021; 14:3247-3254. [PMID: 34429622 PMCID: PMC8380304 DOI: 10.2147/idr.s324745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/24/2021] [Indexed: 12/29/2022] Open
Abstract
Objective The aim of this study was Clostridioides difficile outbreak investigation due to the emergence of rifampicin resistant ribotype 027 (RT 027) fecal isolates from patients of Polish tertiary care hospital between X. 2017 and II. 2018 using multilocus variable tandem repeat analysis (MLVA). Materials and Methods Twenty-nine C. difficile fecal isolates from patients of tertiary care hospital in Southern Poland were ribotyped and analyzed by MLVA. Multiplex PCR (mPCR) for genes encoding GDH (gluD), toxins A (tcdA)/ B (tcdB), 16S rDNA and binary toxin genes (ctdA and ctdB) was performed. The antibiotic susceptibility profile was determined by E-test. Results The A, B and binary toxins encoding genes were detected in all 29 C. difficile strains which were sensitive to metronidazole, vancomycin and were resistant to erythromycin, clindamycin, and moxifloxacin; resistance to imipenem demonstrated 97%, to rifampicin – 45% isolates. C. difficile strains could be grouped by MLVA into 5 distinct clusters, and the largest cluster II contains 16 strains. The comparison of rifampicin GM MIC of cluster II (n=16 strains) with all others (n=13) showed that strains from clusters I, III, IV and V possessed significantly (p <0.005) higher GM MIC and were more resistant to rifampicin. Conclusion MLVA analysis proved transmission and recognized outbreak due to multidrug-resistant RT 027 C. difficile among patients of tertiary care hospital in Southern Poland. The reason for this is probably the widespread occurrence of spores in the hospital environment, which includes, among others, neglect of hygienic procedures and epidemic supervision. High resistance to imipenem (97%) and to rifampicin (45%) among C. difficile RT 027 Silesian isolates is threatening and requires further studies to elucidate this phenomenon.
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Affiliation(s)
- Monika Kabała
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
| | - Zygmunt Gofron
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
| | - Małgorzata Aptekorz
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
| | - Krzysztof Sacha
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
| | - Celine Harmanus
- Department of Medical Microbiology Leiden University Medical Center, Leiden, the Netherlands
| | - Ed Kuijper
- Department of Medical Microbiology Leiden University Medical Center, Leiden, the Netherlands
| | - Gayane Martirosian
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
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Ghielmetti G, Kupca AM, Hanczaruk M, Friedel U, Weinberger H, Revilla-Fernández S, Hofer E, Riehm JM, Stephan R, Glawischnig W. Mycobacterium microti Infections in Free-Ranging Red Deer (Cervus elaphus). Emerg Infect Dis 2021; 27:2025-2032. [PMID: 34286688 PMCID: PMC8314804 DOI: 10.3201/eid2708.210634] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Infections with Mycobacterium microti, a member of the M. tuberculosis complex, have been increasingly reported in humans and in domestic and free-ranging wild animals. At postmortem examination, infected animals may display histopathologic lesions indistinguishable from those caused by M. bovis or M. caprae, potentially leading to misidentification of bovine tuberculosis. We report 3 cases of M. microti infections in free-ranging red deer (Cervus elaphus) from western Austria and southern Germany. One diseased animal displayed severe pyogranulomatous pleuropneumonia and multifocal granulomas on the surface of the pericardium. Two other animals showed alterations of the lungs and associated lymph nodes compatible with parasitic infestation. Results of the phylogenetic analysis including multiple animal strains from the study area showed independent infection events, but no host-adapted genotype. Personnel involved in bovine tuberculosis–monitoring programs should be aware of the fastidious nature of M. microti, its pathogenicity in wildlife, and zoonotic potential.
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Zhu Z, Wang W, Cao M, Zhu Q, Ma T, Zhang Y, Liu G, Zhou X, Li B, Shi Y, Zhang J. Virulence factors and molecular characteristics of Shigella flexneri isolated from calves with diarrhea. BMC Microbiol 2021; 21:214. [PMID: 34271864 PMCID: PMC8285881 DOI: 10.1186/s12866-021-02277-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/28/2021] [Indexed: 11/10/2022] Open
Abstract
Background The natural hosts of Shigella are typically humans and other primates, but it has been shown that the host range of Shigella has expanded to many animals. Although Shigella is becoming a major threat to animals, there is limited information on the genetic background of local strains. The purpose of this study was to assess the presence of virulence factors and the molecular characteristics of S. flexneri isolated from calves with diarrhea. Results Fifty-four S. flexneri isolates from Gansun, Shanxi, Qinghai, Xinjiang and Tibet obtained during 2014 to 2016 possessed four typical biochemical characteristics of Shigella. The prevalences of ipaH, virA, ipaBCD, ial, sen, set1A, set1B and stx were 100 %, 100 %, 77.78 %, 79.63 %, 48.15 %, 48.15 and 0 %, respectively. Multilocus variable number tandem repeat analysis (MLVA) based on 8 variable number of tandem repeat (VNTR) loci discriminated the isolates into 39 different MLVA types (MTs), pulsed field gel electrophoresis (PFGE) based on NotI digestion divided the 54 isolates into 31 PFGE types (PTs), and multilocus sequence typing (MLST) based on 15 housekeeping genes differentiated the isolates into 7 MLST sequence types (STs). Conclusions The findings from this study enrich our knowledge of the molecular characteristics of S. flexneri collected from calves with diarrhea, which will be important for addressing clinical and epidemiological issues regarding shigellosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02277-0.
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Affiliation(s)
- Zhen Zhu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China.,College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Weiwei Wang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China
| | - Mingze Cao
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Qiqi Zhu
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Tenghe Ma
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Yongying Zhang
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Guanhui Liu
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Xuzheng Zhou
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China
| | - Bing Li
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China
| | - Yuxiang Shi
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Jiyu Zhang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China.
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Akhtar R, Ali MM, Ullah A, Muttalib A, Mehboob K, Ullah A, Ahmad N, Chohan TZ. Genotyping of Brucella strains isolated from humans and cattle of different geographical regions of Pakistan using MLVA-15. Vet Med Sci 2021; 7:1688-1695. [PMID: 34245235 PMCID: PMC8464260 DOI: 10.1002/vms3.550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background Prevalence of brucellosis and MLVA genotyping in animals and humans, isolated from different regions of Pakistan was performed. Animals having history of brucellosis from the field and local farms of Bannu, Mardan, Peshawar, Swat, Lahore and Islamabad were selected for blood collection. Humans that work with them were also selected for sampling in this study. Total of 600 samples were taken from cattle and humans and subjected to Rose Bengal plate Test (RBPT) for the initial screening of positive samples. Designed primers of B.abortus for cattle and B.melitensis for humans were utilised to perform PCR. Culturing and isolation was carried to further to perform MLVA genotyping assay through the selection of two panels of primer markers. Results RBPT showed more number of cases of brucellosis in animals and humans compared to the PCR findings. Genotyping findings based upon MLVA‐15 set of markers demonstrated that the isolated strains of B.abortus fall in the same clade with strain A1, P8 and A2 from Pakistan and also similar with BCCN#02‐45 strain from India. On the other hand, B.melitensis isolated from different districts of Pakistan shared the same clade with BwIM‐AFG 63, BwIM‐AFG 44 strains from Afghanistan and BwIM IRN 37 strain from Iran. Selected VNTR alleles were sequenced for calibration purposes. Conclusion It is concluded that Brucella is prevalent in animals and humans in studied districts of Pakistan. Moreover, A1, P8, BwIM‐AFG 63, BwIM‐AFG 44 and A2 were found the common genotypes in Pakistan.
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Affiliation(s)
- Raheela Akhtar
- Department of Pathology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Muddassir Ali
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Asad Ullah
- Department of Pathology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Abdul Muttalib
- Department of Pathology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Kashan Mehboob
- Department of Pathology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Arif Ullah
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Nasim Ahmad
- Department of Theriogenology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Tahir Zahoor Chohan
- Planning and Development Division, Pakistan Agriculture Research Council, Islamabad, Pakistan
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Souillard R, Grosjean D, Le Gratiet T, Poezevara T, Rouxel S, Balaine L, Macé S, Martin L, Anniballi F, Chemaly M, Le Bouquin S, Le Maréchal C. Asymptomatic Carriage of C. botulinum Type D/C in Broiler Flocks as the Source of Contamination of a Massive Botulism Outbreak on a Dairy Cattle Farm. Front Microbiol 2021; 12:679377. [PMID: 34276611 PMCID: PMC8279769 DOI: 10.3389/fmicb.2021.679377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/07/2021] [Indexed: 12/03/2022] Open
Abstract
In winter 2018, a massive type D/C cattle botulism outbreak occurred on a mixed dairy and broiler farm in France. An investigation was conducted based on the hypothesis of asymptomatic carriage in poultry. We set out to identify the source of contamination of the dairy cattle and to monitor the contamination of broilers over time, including the hatchery delivering chicks to the farm. Environmental samples were collected on the farm during the cattle outbreak (n = 40), after the outbreak for three successive broiler flocks (n = 128), and once in the hatchery delivering the chicks (n = 58). These samples were analyzed using real-time PCR after an enrichment step to detect Clostridium botulinum type D/C. The results showed contamination in the manure from the broilers raised just before the onset of the cattle outbreak (5 + /5), as well as in some of the components of the cattle ration (3 + /17). This latter contamination is likely due to the use of the same tractor bucket to remove litter from the poultry house and to prepare the cattle ration on the same day. Contamination monitoring over several months revealed continuous asymptomatic carriage in the broilers (4 + /20 and 17 + /20 cloacal swabs in 2 successive flocks), a persistence of C. botulinum type D/C in the ventilation system of the poultry house (8 + /14), and contamination of the equipment coming from the hatchery used for delivering the chicks (3 + /18). Further investigations conducted in the hatchery demonstrated contamination in the hatchery by C. botulinum type D/C (6 + /58). Comparison of samples using a multilocus variable number tandem repeat analysis showed the same profile for samples collected on broilers, cattle and in the hatchery. This study highlighted the crucial role of the implementation of biosecurity measures in mixed farms to avoid cross-contamination between production units given the potential asymptomatic carriage of poultry. This study also revealed the contamination of the poultry hatchery. Further investigations are required to better understand the role of hatcheries in the epidemiology of animal botulism.
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Affiliation(s)
- Rozenn Souillard
- ANSES, French Agency for Food, Environmental and Occupational Health Safety, Epidemiology, Health and Welfare Unit, Ploufragan, France
| | - Daniel Grosjean
- DDCSPP de la Meuse, Departmental Authority in Charge of Veterinary Services for Meuse Department, Bar-le-Duc, France
| | - Thibault Le Gratiet
- ANSES, French Agency for Food, Environmental and Occupational Health Safety, Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan, France
| | - Typhaine Poezevara
- ANSES, French Agency for Food, Environmental and Occupational Health Safety, Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan, France
| | - Sandra Rouxel
- ANSES, French Agency for Food, Environmental and Occupational Health Safety, Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan, France
| | - Loïc Balaine
- ANSES, French Agency for Food, Environmental and Occupational Health Safety, Epidemiology, Health and Welfare Unit, Ploufragan, France
| | - Sabrina Macé
- ANSES, French Agency for Food, Environmental and Occupational Health Safety, Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan, France
| | - Laure Martin
- ANSES, French Agency for Food, Environmental and Occupational Health Safety, Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan, France
| | - Fabrizio Anniballi
- Department of Veterinary Public Health and Food Safety, National Reference Centre for Botulism, Istituto Superiore di Sanità, Rome, Italy
| | - Marianne Chemaly
- ANSES, French Agency for Food, Environmental and Occupational Health Safety, Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan, France
| | - Sophie Le Bouquin
- ANSES, French Agency for Food, Environmental and Occupational Health Safety, Epidemiology, Health and Welfare Unit, Ploufragan, France
| | - Caroline Le Maréchal
- ANSES, French Agency for Food, Environmental and Occupational Health Safety, Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan, France
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Mwaba J, Debes AK, Murt KN, Shea P, Simuyandi M, Laban N, Kazimbaya K, Chisenga C, Li S, Almeida M, Meisel JS, Shibemba A, Kantenga T, Mukonka V, Kwenda G, Sack DA, Chilengi R, Stine OC. Three transmission events of Vibrio cholerae O1 into Lusaka, Zambia. BMC Infect Dis 2021; 21:570. [PMID: 34126945 PMCID: PMC8200794 DOI: 10.1186/s12879-021-06259-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/27/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Cholera has been present and recurring in Zambia since 1977. However, there is a paucity of data on genetic relatedness and diversity of the Vibrio cholerae isolates responsible for these outbreaks. Understanding whether the outbreaks are seeded from existing local isolates or if the outbreaks represent separate transmission events can inform public health decisions. RESULTS Seventy-two V. cholerae isolates from outbreaks in 2009/2010, 2016, and 2017/2018 in Zambia were characterized using multilocus variable number tandem repeat analysis (MLVA) and whole genome sequencing (WGS). The isolates had eight distinct MLVA genotypes that clustered into three MLVA clonal complexes (CCs). Each CC contained isolates from only one outbreak. The results from WGS revealed both clustered and dispersed single nucleotide variants. The genetic relatedness of isolates based on WGS was consistent with the MLVA, each CC was a distinct genetic lineage and had nearest neighbors from other East African countries. In Lusaka, isolates from the same outbreak were more closely related to themselves and isolates from other countries than to isolates from other outbreaks in other years. CONCLUSIONS Our observations are consistent with i) the presence of random mutation and alternative mechanisms of nucleotide variation, and ii) three separate transmission events of V. cholerae into Lusaka, Zambia. We suggest that locally, case-area targeted invention strategies and regionally, well-coordinated plans be in place to effectively control future cholera outbreaks.
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Affiliation(s)
- John Mwaba
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Department of Biomedical Sciences, University of Zambia School of Health Sciences, Lusaka, Zambia
- Department of Pathology and Microbiology, University Teaching Hospitals, Lusaka, Zambia
| | - Amanda K Debes
- Johns Hopkins Bloomberg School of Public Health, MD, Baltimore, USA
| | - Kelsey N Murt
- Johns Hopkins Bloomberg School of Public Health, MD, Baltimore, USA
| | - Patrick Shea
- Johns Hopkins Bloomberg School of Public Health, MD, Baltimore, USA
| | | | - Natasha Laban
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Katayi Kazimbaya
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Department of Biomedical Sciences, University of Zambia School of Health Sciences, Lusaka, Zambia
| | | | - Shan Li
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mathieu Almeida
- University of Maryland, College Park, College Park, MD, USA
- Université Paris-Saclay, INRAE, MGP, 78350, Jouy-en-Josas, France
| | | | - Aaron Shibemba
- Department of Pathology and Microbiology, University Teaching Hospitals, Lusaka, Zambia
| | - Timothy Kantenga
- Department of Biomedical Sciences, University of Zambia School of Health Sciences, Lusaka, Zambia
- Department of Pathology and Microbiology, University Teaching Hospitals, Lusaka, Zambia
| | | | - Geoffrey Kwenda
- Department of Biomedical Sciences, University of Zambia School of Health Sciences, Lusaka, Zambia
| | - David A Sack
- Johns Hopkins Bloomberg School of Public Health, MD, Baltimore, USA
| | - Roma Chilengi
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - O Colin Stine
- University of Maryland School of Medicine, Baltimore, MD, USA.
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Frangoulidis D, Kahlhofer C, Said AS, Osman AY, Chitimia-Dobler L, Shuaib YA. High Prevalence and New Genotype of Coxiella burnetii in Ticks Infesting Camels in Somalia. Pathogens 2021; 10:741. [PMID: 34204648 PMCID: PMC8231198 DOI: 10.3390/pathogens10060741] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 12/30/2022] Open
Abstract
Coxiella burnetii is the causative agent of Q fever. It can infect animals, humans, and birds, as well as ticks, and it has a worldwide geographical distribution. To better understand the epidemiology of C. burnetii in Somalia, ticks infesting camels were collected from five different regions, including Bari, Nugaal, Mudug, Sool, and Sanaag, between January and March 2018. Collected ticks were tested for C. burnetii and Coxiella-like endosymbiont DNA by using IS1111, icd, and Com1-target PCR assays. Moreover, sequencing of the 16S-rRNA was conducted. Molecular characterization and typing were done by adaA-gene analysis and plasmid-type identification. Further typing was carried out by 14-marker Multi-Locus Variable-Number Tandem Repeats (MLVA/VNTR) analysis. The investigated ticks (n = 237) were identified as Hyalomma spp. (n = 227, 95.8%), Amblyomma spp. (n = 8, 3.4%), and Ripicephalus spp. (n = 2, 0.8%), and 59.1% (140/237) of them were positive for Coxiella spp. While Sanger sequencing and plasmid-type identification revealed a C. burnetii that harbours the QpRS-plasmid, MLVA/VNTR genotyping showed a new genotype which was initially named D21. In conclusion, this is the first report of C. burnetii in ticks in Somalia. The findings denote the possibility that C. burnetii is endemic in Somalia. Further epidemiological studies investigating samples from humans, animals, and ticks within the context of "One Health" are warranted.
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Affiliation(s)
- Dimitrios Frangoulidis
- Bundeswehr Medical Service Headquarters VI-2, Medical Intelligence & Information, Dachauer Str. 128, 80637 Munich, Germany;
- Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany;
| | - Claudia Kahlhofer
- Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany;
| | - Ahmed Shire Said
- College of Veterinary Medicine, East Africa University, Bosaso P.O. Box 111, Somalia;
| | - Abdinasir Yusuf Osman
- The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK;
| | - Lidia Chitimia-Dobler
- Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany;
- Department of Parasitology, Institute of Zoology, University of Hohenheim, Emil Wolff-Strasse 34, 70599 Stuttgart, Germany
| | - Yassir Adam Shuaib
- College of Veterinary Medicine, Sudan University of Science and Technology, P.O. Box 204 Hilat Kuku, Khartoum North 13321, Sudan
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