1
|
Hoque MN, Faisal GM, Jerin S, Moyna Z, Islam MA, Talukder AK, Alam MS, Das ZC, Isalm T, Hossain MA, Rahman ANMA. Unveiling distinct genetic features in multidrug-resistant Escherichia coli isolated from mammary tissue and gut of mastitis induced mice. Heliyon 2024; 10:e26723. [PMID: 38434354 PMCID: PMC10904246 DOI: 10.1016/j.heliyon.2024.e26723] [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: 10/26/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Escherichia coli is one of the major pathogens causing mastitis in lactating mammals. We hypothesized that E. coli from the gut and mammary glands may have similar genomic characteristics in the causation of mastitis. To test this hypothesis, we used whole genome sequencing to analyze two multidrug resistant E. coli strains isolated from mammary tissue (G2M6U) and fecal sample (G6M1F) of experimentally induced mastitis mice. Both strains showed resistance to multiple (>7) antibiotics such as oxacillin, aztreonam, nalidixic acid, streptomycin, gentamicin, cefoxitin, ampicillin, tetracycline, azithromycin and nitrofurantoin. The genome of E. coli G2M6U had 59 antimicrobial resistance genes (ARGs) and 159 virulence factor genes (VFGs), while the E. coli G6M1F genome possessed 77 ARGs and 178 VFGs. Both strains were found to be genetically related to many E. coli strains causing mastitis and enteric diseases originating from different hosts and regions. The G6M1F had several unique ARGs (e.g., QnrS1, sul2, tetA, tetR, emrK, blaTEM-1/105, and aph(6)-Id, aph(3″)-Ib) conferring resistance to certain antibiotics, whereas G2M6U had a unique heat-stable enterotoxin gene (astA) and 7192 single nucleotide polymorphisms. Furthermore, there were 43 and 111 unique genes identified in G2M6U and G6M1F genomes, respectively. These results indicate distinct differences in the genomic characteristics of E. coli strain G2M6U and G6M1F that might have important implications in the pathophysiology of mammalian mastitis, and treatment strategies for mastitis in dairy animals.
Collapse
Affiliation(s)
- M. Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Shobnom Jerin
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Zannatara Moyna
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Md Aminul Islam
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, 2310, Bangladesh
| | - Anup Kumar Talukder
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | | | - Ziban Chandra Das
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Tofazzal Isalm
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, 1706, Bangladesh
| | - M. Anwar Hossain
- Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Abu Nasar Md Aminoor Rahman
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| |
Collapse
|
2
|
Geiping L, Detlefsen H, Trittmacher S, Baums CG, Bergmann R, Hennig-Pauka I. Streptococcus equi subspecies zooepidemicus - a case report of sudden death in a German sow farm. Porcine Health Manag 2023; 9:48. [PMID: 37875963 PMCID: PMC10594803 DOI: 10.1186/s40813-023-00344-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023] Open
Abstract
A farm in North-West Germany experienced a high morbidity and mortality in their sow herd. Sows showed fever, lethargy, oedema, mucosal discharge and dyspnoea. Necropsy revealed a severe fibrinous and purulent polyserositis. Haematological and histological examinations confirmed septicaemia. Streptococcus equi subspecies zooepidemicus was isolated in high yields from major organs. Sequence typing of this isolate (21/455) revealed a new sequence type showing a significantly higher proliferation rate in comparison to two other isolates. Other infectious agents (influenza A virus, Porcine Reproductive and Respiratory Syndrome Virus, Porcine Circovirus 2, african swine fever virus, classical swine fever virus, Actinobacillus pleuropneumoniae) were excluded by routine diagnostic examinations. A climate check revealed an insufficient air supply in the area for the gestating sows. This case describes the first disease outbreak in swine due to S. zooepidemicus in Germany.
Collapse
Affiliation(s)
- Lukas Geiping
- Field Station for Epidemiology in Bakum, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Henrik Detlefsen
- Tierarztpraxis Bethen, Heideweg 7, 49661, Cloppenburg/Bethen, Germany
| | - Sara Trittmacher
- Field Station for Epidemiology in Bakum, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Christoph Georg Baums
- Institute of Bacteriology and Mycology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - René Bergmann
- Institute of Bacteriology and Mycology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Isabel Hennig-Pauka
- Field Station for Epidemiology in Bakum, University of Veterinary Medicine Hannover, Foundation, Germany.
| |
Collapse
|
3
|
Abdo SM, El-Adawy H, Farag HF, El-Taweel HA, Elhadad H, El-Badry AAM. Detection and molecular identification of Blastocystis isolates from humans and cattle in northern Egypt. J Parasit Dis 2021; 45:738-745. [PMID: 34475655 DOI: 10.1007/s12639-021-01354-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 01/19/2021] [Indexed: 11/28/2022] Open
Abstract
Blastocystis is one of the less well-understood waterborne protozoa of medical and veterinary importance. The present study aimed to detect, identify, and subtype Blastocystis in cattle and humans in northern Egypt and to investigate the potential for zoonotic transmission. Fecal samples were collected from 136 humans (68 in contact with animals and 68 no animal contact) and 190 cattle from a rural area in Kafr El-Sheikh Province, Egypt. All samples were microscopically examined by direct wet mount technique and cultured in Jones' medium. Genomic DNA was extracted from positive cultures. A region of the Blastocystis small subunit ribosomal ribonucleic acid (SSU rRNA) gene was amplified using PCR. Blastocystis subtypes were identified by sequencing of the amplified SSU rRNA gene. The relatedness of sequence types obtained in this study and others submitted in GenBank was compared according to their genetic relatedness. Out of 136 human and 190 cattle samples, Blastocystis was detected in 53 (38.9%) and 37 (19.4%), respectively using either culture or direct wet mount. Blastocystis SSU rRNA gene was amplified in 55 samples (32 humans and 23 animals). Six subtypes were identified (STs 1-3 in humans and ST4, ST10 and ST14 in cattle) and were distinguishable with inter (up to 0.075) and intra (up to 0.024) subtype variations. A close phylogenetic relationship between human and animal isolated STs 1-4 was demonstrated. To the best of our knowledge, this is the first study to investigate the the potentiality for zoonotic transmission of certain Blastocystis subtypes in northern Egypt.
Collapse
Affiliation(s)
- Sarah Mohamed Abdo
- Department of Medical Parasitology, Faculty of Medicine, Kafrelsheikh University, Kafr El-Sheikh, 35516 Egypt
| | - Hosny El-Adawy
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany.,Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, 35516 Egypt
| | - Hoda Fahmy Farag
- Parasitology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Hend Aly El-Taweel
- Parasitology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Heba Elhadad
- Parasitology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Ayman Abdel-Moamen El-Badry
- Department of Microbiology-Medical Parasitology Section, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| |
Collapse
|
4
|
Xiong D, Zhang X, Xiong J, Yu J, Wei H. Rapid genome-wide sequence typing of African swine fever virus based on alleles. Virus Res 2021; 297:198357. [PMID: 33667625 DOI: 10.1016/j.virusres.2021.198357] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 04/15/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 11/26/2022]
Abstract
Rapid and accurate molecular typing of African swine fever virus (ASFV) during outbreaks is important to reveal diversity and sourcing of ASFV. Here we present a new way to perform rapid genome-wide multi-locus sequence typing of ASFV using an allele calling based on gene by gene approach. Using open-accessed chewBBACA software, 41 publicly available ASFV genomes were analyzed to optimize the parameters to find the alleles. Alleles as many as 127 were found for building the phylogenetic trees, which covered more than 60 % of the whole genome. Then the method was used to analyze two ASFV genomes assembled from two metagenomic sequences of a swine whole blood and a swine spleen tissue collected in Wuhan, China. It reveals that the two ASFV genomes are the closest to that of Pig/HLJ/2018 strain and DB/LN/2018 strain, which were isolated earlier in China. This proved that the ASFV in Wuhan originated from the same source causing the earlier outbreaks in Heilongjiang and Liaoning province of China. This method could identify more informative genome regions that could be used for accurate typing than other genome-wide analysis, and with less demand on computing resources. It also showed tolerance to analyze ASFV draft genomes assembled directly from metagenomic sequences. Furthermore, the ASFV-specific genetic markers found by the allele calling could be translated into clinical diagnostics or can be used broadly to identify conserved putative therapeutic candidates.
Collapse
Affiliation(s)
- Dongyan Xiong
- Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxu Zhang
- Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin Xiong
- Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; African Swine Fever Regional Laboratory of China (Wuhan), Jinglong Street, Jiangxia District, Wuhan, China
| | - Junping Yu
- Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; African Swine Fever Regional Laboratory of China (Wuhan), Jinglong Street, Jiangxia District, Wuhan, China.
| | - Hongping Wei
- Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; African Swine Fever Regional Laboratory of China (Wuhan), Jinglong Street, Jiangxia District, Wuhan, China.
| |
Collapse
|
5
|
Wang JT, Meng DQ, Guo JE, Yan GD, Zhang L, Wan ZT, Li Q, Gao L, Gao RH, Zhao LF, Wang H. [Isolation and Identification of two Escherichia albertii strains in Shanxi Province, China]. Zhonghua Yu Fang Yi Xue Za Zhi 2020; 54:1121-1126. [PMID: 33115199 DOI: 10.3760/cma.j.cn112150-20200429-00667] [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] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Objective: To investigate the prevalence of Escherchia albertii in Shanxi province. Methods: The chicken intestines were enriched in EC broth. The eae gene was detected by PCR, and the eae-positive EC enrichments were inoculated in MacConkey agar plate. The eae-positive lactose non-fermenting isolates were presumed as Escherchia albertii, and then analyzed by triplex-PCR, 16S rDNA sequencing and MLST. Results: Two suspected Escherchia albertii were isolated from 250 samples of chicken intestines. It was identified as Escherchia albertii by phenotypic, specific genes,16S rDNA sequencing, and MLST analyses. The cytolethal distending toxin B (cdtB) showed positive by PCR,and they were clusted to Ⅱ/Ⅲ/Ⅴ group by sequencing. Conclusion: This study showed that the Escherchia albertii was existed in Shanxi province, China.
Collapse
Affiliation(s)
- J T Wang
- Department of Microbiology Test, Taiyuan Center for Disease Control and Prevention, Taiyuan 030001, China
| | - D Q Meng
- Department of Microbiology Test, Taiyuan Center for Disease Control and Prevention, Taiyuan 030001, China
| | - J E Guo
- Department of Microbiology Test, Taiyuan Center for Disease Control and Prevention, Taiyuan 030001, China
| | - G D Yan
- Institute of Microbiology, Zigong Center for Disease Control and Prevention, Zigong 643000, China
| | - L Zhang
- Institute of Microbiology, Zigong Center for Disease Control and Prevention, Zigong 643000, China
| | - Z T Wan
- Institute of Microbiology, Zigong Center for Disease Control and Prevention, Zigong 643000, China
| | - Q Li
- Institute of Microbiology, Zigong Center for Disease Control and Prevention, Zigong 643000, China
| | - L Gao
- Department of Microbiology Test, Taiyuan Center for Disease Control and Prevention, Taiyuan 030001, China
| | - R H Gao
- Department of Microbiology Test, Taiyuan Center for Disease Control and Prevention, Taiyuan 030001, China
| | - L F Zhao
- Department of Microbiology Test, Taiyuan Center for Disease Control and Prevention, Taiyuan 030001, China
| | - H Wang
- Institute of Microbiology, Zigong Center for Disease Control and Prevention, Zigong 643000, China
| |
Collapse
|
6
|
Blanchard AM, Billenness R, Warren J, Glanvill A, Roden W, Drinkall E, Maboni G, Robinson RS, Rees CED, Pfarrer C, Tötemeyer S. Characterisation of Listeria monocytogenes isolates from cattle using a bovine caruncular epithelial cell model. Heliyon 2020; 6:e04476. [PMID: 32743095 PMCID: PMC7385464 DOI: 10.1016/j.heliyon.2020.e04476] [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: 04/03/2020] [Revised: 05/22/2020] [Accepted: 07/13/2020] [Indexed: 11/18/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen in human and veterinary health, causing significant morbidity and mortality including abortion. It has a particular tropism for the gravid uterus, however, the route of infection in reproductive tissues of ruminants (i.e. placentome), is much less clear. In this study, we aimed to investigate a bovine caruncular epithelial cell (BCEC) line as a model for L. monocytogenes infection of the bovine reproductive tract. The BCEC infection model was used to assess the ability of 14 different L. monocytogenes isolates to infect these cells. Lysozyme sensitivity and bacterial survival in 580 μg lysozyme/ml correlated with attenuated ability to proliferate in BCEC (p = 0.004 and p = 0.02, respectively). Four isolates were significantly attenuated compared to the control strain 10403S. One of these strains (AR008) showed evidence of compromised cell wall leading to increased sensitivity to ß-lactam antibiotics, and another (7644) had compromised cell membrane integrity leading to increased sensitivity to cationic peptides. Whole genome sequencing followed by Multi Locus Sequence Type analysis identified that five invasive isolates had the same sequence type, ST59, despite originating from three different clinical conditions. Virulence gene analysis showed that the attenuated isolate LM4 was lacking two virulence genes (uhpT, virR) known to be involved in intracellular growth and virulence. In conclusion, the BCEC model was able to differentiate between the infective potential of different isolates. Moreover, resistance to lysozyme correlated with the ability to invade and replicate within BCEC, suggesting co-selection for surviving challenging environments as the abomasum.
Collapse
Affiliation(s)
- Adam M Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Rosemarie Billenness
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Jessica Warren
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Amy Glanvill
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - William Roden
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Emma Drinkall
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Grazieli Maboni
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK.,Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Robert S Robinson
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | | | - Christiane Pfarrer
- Department of Anatomy, University of Veterinary Medicine, Hannover, Germany
| | - Sabine Tötemeyer
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| |
Collapse
|
7
|
Mills JP, Kaye KS, Evans R, Salzman E, Pogue J, Hayakawa K, Marchaim D, Awasthy P, Salim M, Martin ET. Clinical and Molecular Epidemiology of Extended-Spectrum Beta-Lactamase-Producing Escherichia Coli Infections in Metro Detroit: Early Dominance of the ST-131 Clone. Infect Dis Ther 2020; 9:683-90. [PMID: 32683600 DOI: 10.1007/s40121-020-00321-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Indexed: 11/01/2022] Open
Abstract
INTRODUCTION Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli infections have become endemic worldwide. We aimed to describe the molecular and clinical epidemiology of ESBL-producing E. coli infections during a period of rising global prevalence. METHODS Three hundred sixty-nine consecutive ESBL-producing E. coli infections in Detroit from 2010-2011 were analyzed. Sequence typing (ST) and CH typing were performed. Clinical characteristics and outcomes were compared between patients infected with ST131 and non-ST131 isolates. RESULTS Ninety-six percent of isolates were ST 131, and 78.6% of ST 131 isolates produced blaCTX-M-15. Median time to effective therapy was 48 h vs. 35 h (P = 0.38) in the ST131 vs. non-ST131 groups. Ninety-day mortality rates (8% vs. 8%, P = 1.0) were similar between the two groups. CONCLUSION blaCTX-M-15 ST131 E. coli predominated in Detroit during an early period of global ST131 dissemination. Patients with ST131 E. coli infections had similar clinical outcomes to those with non-ST131 E. coli infections.
Collapse
|
8
|
Tan S, Dvorak CMT, Estrada AA, Gebhart C, Marthaler DG, Murtaugh MP. MinION sequencing of Streptococcus suis allows for functional characterization of bacteria by multilocus sequence typing and antimicrobial resistance profiling. J Microbiol Methods 2020; 169:105817. [PMID: 31881288 DOI: 10.1016/j.mimet.2019.105817] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 01/31/2023]
Abstract
In recent years, high-throughput sequencing has revolutionized disease diagnosis by its powerful ability to provide high resolution genomic information. The Oxford Nanopore MinION sequencer has unparalleled potential as a rapid disease diagnostic tool due to its high mobility, accessibility, and short turnaround time. However, there is a lack of rigorous quality assessment and control processes standardizing the testing on the MinION, which is necessary for incorporation into a diagnostic workflow. Thus, our study examined the use of the MinION sequencer for bacterial whole genome generation and characterization. Using Streptococcus suis as a model, we optimized DNA isolation and treatments to be used for MinION sequencing and standardized de novo assembly to quickly generate a full-length consensus sequence achieving a 99.4% average accuracy. The consensus genomes from MinION sequencing were able to accurately predict the multilocus sequence type in 8 out of 10 samples and identified antimicrobial resistance profiles for 100% of the samples, despite the concern of a high error rate. The inability to unequivocally predict sequence types was due to difficulty in differentiating high identity alleles, which was overcome by applying additional error correction methods to increase consensus accuracy. This manuscript provides methods for the use of MinION sequencing for identification of S. suis genome sequence, sequence type, and antibiotic resistance profile that can be used as a framework for identification and classification of other pathogens.
Collapse
|
9
|
de Azevedo FKSF, Dutra V, Nakazato L, Mello CM, Pepato MA, de Sousa ATHI, Takahara DT, Hahn RC, Souto FJD. Molecular epidemiology of multidrug-resistant Acinetobacter baumannii infection in two hospitals in Central Brazil: the role of ST730 and ST162 in clinical outcomes. J Med Microbiol 2018; 68:31-40. [PMID: 30516469 DOI: 10.1099/jmm.0.000853] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 12/11/2022] Open
Abstract
PURPOSE Acinetobacter baumannii is a major cause of multidrug-resistant nosocomial infections. The characteristics of A. baumannii at two hospitals in a city in Central Brazil are described by analysing the phenotypes and molecular profiles of isolates recovered from 87 patients. METHODOLOGY The isolates were identified and their antimicrobial susceptibility was evaluated using the the Bact/Alert 3D and Vitek2 methods. Patients' clinical data were obtained from medical files. Genes associated with resistance to carbapenems were analysed by multilocus sequence typing, clinical and bacteriological variables were analysed by descriptive statistics, and logistic models were generated to adjust the associations. RESULTS Sixty-four (73.5 %) out of 87 A. baumannii isolates analysed were from patients in intensive care. The mortality rate was 43.7 %. Eighty (91.9 %) isolates were resistant to imipenem and 86 were susceptible to colistin (98.8 %). The blaOXA-23 gene (78.2 %) and its upstream insertion ISAba1 (55.2 %) were predominant, followed by blaOXA-24 (55.2 %) and blaOXA-143 (28.7 %). The blaOXA-23 gene and ISAba1 were independently associated with resistance to imipenem (P<0.05). There were 13 different sequence types (STs) among the 35 isolates. ST1 (nine; 25.7 %), ST162 (eight; 22.8 %) and ST730 (six; 17.1 %) were the most common, and four new STs were identified. The isolates were grouped into five clonal complexes (CC1, CC15, CC79, CC108 and CC162) plus a singleton using eburst. CONCLUSION Respiratory infection, age >60 years and use of noradrenaline were factors associated with fatality. ST730 (CC79) was associated with higher mortality (P<0.05) and ST162 (CC162) was associated with increased survival probability (P<0.05).
Collapse
Affiliation(s)
| | - Valéria Dutra
- 2Laboratory of Veterinary Microbiology and Molecular Biology, College of Veterinary Medicine, Federal University of Mato Grosso, Mato Grosso, Brazil
| | - Luciano Nakazato
- 2Laboratory of Veterinary Microbiology and Molecular Biology, College of Veterinary Medicine, Federal University of Mato Grosso, Mato Grosso, Brazil
| | - Camila Martines Mello
- 1College of Medicine, Júlio Muller Hospital University, Federal University of Mato Grosso, Mato Grosso State, Brazil
| | - Marco Andrey Pepato
- 1College of Medicine, Júlio Muller Hospital University, Federal University of Mato Grosso, Mato Grosso State, Brazil
| | | | - Doracilde Terume Takahara
- 1College of Medicine, Júlio Muller Hospital University, Federal University of Mato Grosso, Mato Grosso State, Brazil
| | - Rosane Christine Hahn
- 1College of Medicine, Júlio Muller Hospital University, Federal University of Mato Grosso, Mato Grosso State, Brazil
| | - Francisco José Dutra Souto
- 1College of Medicine, Júlio Muller Hospital University, Federal University of Mato Grosso, Mato Grosso State, Brazil
| |
Collapse
|
10
|
Helmy YA, Spierling NG, Schmidt S, Rosenfeld UM, Reil D, Imholt C, Jacob J, Ulrich RG, Aebischer T, Klotz C. Occurrence and distribution of Giardia species in wild rodents in Germany. Parasit Vectors 2018; 11:213. [PMID: 29587877 PMCID: PMC5870188 DOI: 10.1186/s13071-018-2802-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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: 11/24/2017] [Accepted: 03/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Giardiasis is an important gastrointestinal parasitic disease in humans and other mammals caused by the protozoan Giardia duodenalis. This species complex is represented by genetically distinct groups (assemblages A-H) with varying zoonotic potential and host preferences. Wild rodents can harbor potentially zoonotic assemblages A and B, and the rodent-specific assemblage G. Other Giardia spp. found in these animals are Giardia muris and Giardia microti. For the latter, only limited information on genetic typing is available. It has been speculated that wild rodents might represent an important reservoir for parasites causing human giardiasis. The aim of this study was to investigate the occurrence and distribution of Giardia spp. and assemblage types in wild rodents from different study sites in Germany. RESULTS Screening of 577 wild rodents of the genera Apodemus, Microtus and Myodes, sampled at eleven study sites in Germany, revealed a high overall Giardia prevalence. Giardia species determination at the SSU rDNA gene locus revealed that Apodemus mice, depending on species, were predominantly infected with one of two distinct G. muris sequence types. Giardia microti was the predominant parasite species found in voles of the genera Microtus and Myodes. Only a few animals were positive for potentially zoonotic G. duodenalis. Subtyping at the beta-giardin (bg) and glutamine dehydrogenase (gdh) genes strongly supported the existence of different phylogenetic subgroups of G. microti that are preferentially harbored by distinct host species. CONCLUSIONS The present study highlights the preference of G. muris for Apodemus, and G. microti for Microtus and Myodes hosts and argues for a very low prevalence of zoonotic G. duodenalis assemblages in wild rodents in Germany. It also provides evidence that G. muris and G. microti subdivide into several phylogenetically distinguishable subgroups, each of which appears to be preferentially harbored by species of a particular rodent host genus. Finally, the study expands the database of sequences relevant for sequence typing of G. muris and G. microti isolates which will greatly help future analyses of these parasites' population structure.
Collapse
Affiliation(s)
- Yosra A Helmy
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Department of Infectious Diseases, Robert Koch-Institute, 13353, Berlin, Germany.,Department Panel Veterinary Public Health, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany.,Department of Animal Hygiene, Zoonoses and Animal Ethology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41511, Egypt
| | - Nastasja G Spierling
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493, Greifswald - Insel Riems, Germany
| | - Sabrina Schmidt
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493, Greifswald - Insel Riems, Germany.,German Society of Tissue Transplantation, Kruppstraße 98, 45145, Essen, Germany
| | - Ulrike M Rosenfeld
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493, Greifswald - Insel Riems, Germany
| | - Daniela Reil
- Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, 48161, Münster, Germany
| | - Christian Imholt
- Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, 48161, Münster, Germany
| | - Jens Jacob
- Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, 48161, Münster, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493, Greifswald - Insel Riems, Germany
| | - Toni Aebischer
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Department of Infectious Diseases, Robert Koch-Institute, 13353, Berlin, Germany
| | - Christian Klotz
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Department of Infectious Diseases, Robert Koch-Institute, 13353, Berlin, Germany.
| |
Collapse
|
11
|
Stulberg MJ, Huang Q. A computer program for fast and easy typing of a partial endoglucanase gene sequence into genospecies and sequevars 1&2 of the Ralstonia solanacearum species complex. J Microbiol Methods 2016; 123:101-7. [PMID: 26876453 DOI: 10.1016/j.mimet.2016.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 11/19/2015] [Revised: 02/08/2016] [Accepted: 02/08/2016] [Indexed: 01/24/2023]
Abstract
The phytopathogen Ralstonia solanacearum is a species complex that contains race 3 biovar 2 strains belonging to phylotype IIB sequevars 1 and 2 that are quarantined or select agent pathogens. Recently, the R. solanacearum species complex strains have been reclassified into three genospecies: R. solanacearum, Ralstonia pseudosolanacearum and Ralstonia syzygii. An unidentified R. solanacearum strain is considered a select agent in the US until proven to be a non-race 3 biovar 2 (non-phylotype IIB sequevars 1&2). Currently, sequevars of R. solanacearum species complex strains can only be determined by phylogenetic analysis of a partial endoglucanase (egl) sequence of approximately 700-bp in length. Such analysis, however, requires expert knowledge to properly trim the sequence, to include the correct reference strains, and to interpret the results. By comparing GenBank egl sequences of representative R. solanacearum species-complex strains, we identified genospecies- and sequevar 1 and 2-specific single nucleotide polymorphisms (SNPs). We also designed primers to amplify a shorter, 526-bp, egl fragment from R. solanacearum species complex strains for easy sequencing of the amplicon, and to facilitate direct and specific amplification of egl from R. solanacearum-infected plant samples without the need of bacterial isolation. We wrote a computer program (Ralstonia solanacearum typing program) that analyzes a minimum 400-bp user-input egl sequence from a R. solanacearum strain for egl homology and SNP content to determine 1) whether it belongs to the R. solanacearum species complex, 2) if so, to which genospecies, and 3) whether it is of the sequevar type (sequevars 1 and 2) associated with the select agent/quarantined R. solanacearum strain. The program correctly typed all 371 tested egl sequences with known sequevars, obtained either from GenBank or through personal communication. Additionally, the program successfully typed 25 R. solanacearum strains in our collection with no prior sequevar information, as well as 4 strains in infected plant samples, using their partial egl sequences amplified and sequenced with primers designed in this study. The Ralstonia solanacearum typing program does not require expertise or specific knowledge to use, gives results in seconds, and provides data interpretation for the user. The program and primers can help expert or non-expert users to quickly type an unknown R. solanacearum species-complex strain and determine whether it is a highly regulated R. solanacearum strain. The program can also serve as a confirmation method, since it is the only method that can easily and directly determine whether the strain in question is a sequevar 1 or 2 strain of R. solanacearum.
Collapse
Affiliation(s)
- Michael J Stulberg
- Floral and Nursery Plants Research Unit, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA; Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Qi Huang
- Floral and Nursery Plants Research Unit, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
| |
Collapse
|
12
|
Tan L, Wu S, Abdullahi AY, Yu X, Hu W, Song M, Shi X, Li G. PCR-RFLP method to detect zoonotic and host-specific Giardia duodenalis assemblages in dog fecal samples. Parasitol Res 2016; 115:2045-50. [PMID: 26852125 DOI: 10.1007/s00436-016-4948-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 01/11/2016] [Accepted: 01/29/2016] [Indexed: 11/26/2022]
Abstract
Giardia duodenalis is a zoonotic protozoan that parasitizes the upper small intestine of human and many mammals including dogs. To develop a restriction fragment length polymorphism (RFLP) method for typing zoonotic (A, B) and host-specific (C, D) assemblages of G. duodenalis from dog, β-giardin gene was amplified with design primer pairs B3 and B4. The PCR products were digested with restriction enzyme Afa I and Msp I; then, PCR-RFLP method was compared with HRM genotyping and sequencing method for G. duodenalis from dog. The results showed that each of assemblages A-D had unique restriction pattern, which was consistent with the predictive results. Among 21 samples tested by PCR-RFLP, 1 human-derived and 8 dog-derived G. duodenalis were identified as assemblage A; 5 dog-derived G. duodenalis as assemblage C; 7 dog-derived G. duodenalis as assemblage D, which were coincided with the HRM genotyping and sequencing results. It is concluded that the PCR-RFLP is quick, easy, and accurate method for the sequence typing of G. duodenalis zoonotic and specific assemblages from dogs.
Collapse
Affiliation(s)
- Liping Tan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, 510642, People's Republic of China
| | - Sheng Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, 510642, People's Republic of China
| | - Auwalu Yusuf Abdullahi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, 510642, People's Republic of China
| | - Xinggang Yu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, 510642, People's Republic of China
| | - Wei Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, 510642, People's Republic of China
| | - Meiran Song
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, 510642, People's Republic of China
| | - Xianli Shi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, 510642, People's Republic of China
| | - Guoqing Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, 510642, People's Republic of China.
| |
Collapse
|
13
|
Das K, Chowdhury P, Ganguly S. Internal Transcribed Spacer 1 (ITS1) based sequence typing reveals phylogenetically distinct Ascaris population. Comput Struct Biotechnol J 2015; 13:478-83. [PMID: 26504510 PMCID: PMC4579273 DOI: 10.1016/j.csbj.2015.08.006] [Citation(s) in RCA: 3] [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: 01/12/2015] [Revised: 08/22/2015] [Accepted: 08/25/2015] [Indexed: 12/02/2022] Open
Abstract
Taxonomic differentiation among morphologically identical Ascaris species is a debatable scientific issue in the context of Ascariasis epidemiology. To explain the disease epidemiology and also the taxonomic position of different Ascaris species, genome information of infecting strains from endemic areas throughout the world is certainly crucial. Ascaris population from human has been genetically characterized based on the widely used genetic marker, internal transcribed spacer1 (ITS1). Along with previously reported and prevalent genotype G1, 8 new sequence variants of ITS1 have been identified. Genotype G1 was significantly present among female patients aged between 10 to 15 years. Intragenic linkage disequilibrium (LD) analysis at target locus within our study population has identified an incomplete LD value with potential recombination events. A separate cluster of Indian isolates with high bootstrap value indicate their distinct phylogenetic position in comparison to the global Ascaris population. Genetic shuffling through recombination could be a possible reason for high population diversity and frequent emergence of new sequence variants, identified in present and other previous studies. This study explores the genetic organization of Indian Ascaris population for the first time which certainly includes some fundamental information on the molecular epidemiology of Ascariasis.
Collapse
Affiliation(s)
- Koushik Das
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Beliaghata, Kolkata 700010, India
| | - Punam Chowdhury
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Beliaghata, Kolkata 700010, India
| | - Sandipan Ganguly
- Division of Parasitology, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Beliaghata, Kolkata 700010, India
| |
Collapse
|