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Johar AA, Salih MA, Abdelrahman HA, Al Mana H, Hadi HA, Eltai NO. Wastewater-based epidemiology for tracking bacterial diversity and antibiotic resistance in COVID-19 isolation hospitals in Qatar. J Hosp Infect 2023; 141:209-220. [PMID: 37634602 DOI: 10.1016/j.jhin.2023.08.011] [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: 07/13/2023] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Hospitals are hotspots for antimicrobial resistance genes (ARGs), and play a significant role in their emergence and spread. Large numbers of ARGs will be ejected from hospitals via wastewater systems. Wastewater-based epidemiology has been consolidated as a tool to provide real-time information, and represents a promising approach to understanding the prevalence of bacteria and ARGs at community level. AIMS To determine bacterial diversity and identify ARG profiles in hospital wastewater pathogens obtained from coronavirus disease 2019 (COVID-19) isolation hospitals compared with non-COVID-19 facilities during the pandemic. METHODS Wastewater samples were obtained from four hospitals: three assigned to patients with COVID-19 patients and one assigned to non-COVID-19 patients. A microbial DNA quantitative polymerase chain reaction was used to determine bacterial diversity and ARGs. FINDINGS The assay recorded 27 different bacterial species in the samples, belonging to the following phyla: Firmicutes (44.4%), Proteobacteria (33.3%), Actinobacteria (11%), Bacteroidetes (7.4%) and Verrucomicrobiota (3.7%). In addition, 61 ARGs were detected in total. The highest number of ARGs was observed for the Hazem Mebaireek General Hospital (HMGH) COVID-19 patient site (88.5%), and the lowest number of ARGs was found for the HMGH non-patient site (24.1%). CONCLUSION The emergence of contaminants in sewage water, such as ARGs and high pathogen levels, poses a potential risk to public health and the aquatic ecosystem.
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Affiliation(s)
- A A Johar
- Research and Development Department, Barzan Holdings, Doha, Qatar
| | - M A Salih
- Biomedical Research Centre, Qatar University, Doha, Qatar
| | | | - H Al Mana
- Biomedical Research Centre, Qatar University, Doha, Qatar
| | - H A Hadi
- Communicable Diseases Centre, Infectious Disease Division, Hamad Medical Corporation, Doha, Qatar
| | - N O Eltai
- Biomedical Research Centre, Qatar University, Doha, Qatar.
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2
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Abdelrahman HA, Akawi N, Al-Shamsi AM, Al-Gazali L, Ali BR. Pontocerebellar Hypoplasia Type 9: A New Case with a Novel Mutation and Review of Literature. J Pediatr Genet 2022. [DOI: 10.1055/s-0042-1748018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractPontocerebellar hypoplasia type 9 (PCH-9) is a very rare autosomal recessive neurodegenerative disorder. Affected infants present early with severe developmental delay, spasticity, with the unique magnetic resonance imaging picture of thin corpus callosum, atrophied pons, and cerebellum. It is caused by loss of function mutations in the AMPD2 gene, encoding for the adenosine monophosphate deaminase enzyme-paralog 2. This gene is expressed in different somatic tissues with high level of expression in cerebellum and its encoded enzyme catalyzes a critical step in de novo biosynthesis of purines and its deficiency in the developing neurons severely affects neuronal differentiation and cell viability. We clinically evaluated an Emirati patient presented with severe developmental and growth delay, as well as corpus callosum agenesis and atrophy of brainstem and cerebellum. We performed exome sequencing, Sanger sequencing, and segregation analysis to identify the genetic cause of the phenotype, followed by in silico and in vitro analysis. We identified the novel variant (NM_004037.9:c.1471G > A) in AMPD2 gene leading to a single amino acid substitution (p.Gly491Arg) in adenosine monophosphate deaminase-2 enzyme. This variant is predicted to be pathogenic using several in silico tools, and resulted in a decrease in the enzyme function in the patient's polymorphonuclear cells by 82% (95% confidence interval: 73.3–91.7%, p = 0.029) compared with the control. This data establishes that the affected child is affected by PCH-9. Furthermore, we review all reported cases in literature to summarize the main clinical features of this rare disease.
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Affiliation(s)
- Hanadi A. Abdelrahman
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
| | - Nadia Akawi
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
| | | | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R. Ali
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
- Zayed Center for Health sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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3
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Abdelrahman HA, Akawi N, Al-Shamsi AM, Ali A, Al-Jasmi F, John A, Hertecant J, Al-Gazali L, Ali BR. Bi-allelic null variant in matrix metalloproteinase-15, causes congenital cardiac defect, cholestasis jaundice, and failure to thrive. Clin Genet 2022; 101:403-410. [PMID: 34988996 DOI: 10.1111/cge.14107] [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: 03/24/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023]
Abstract
Here, we delineate the phenotype of two siblings with a bi-allelic frameshift variant in MMP15 gene with congenital cardiac defects, cholestasis, and dysmorphism. Genome sequencing analysis revealed a recently reported homozygous frameshift variant (c.1058delC, p.Pro353Glnfs*102) in MMP15 gene that co-segregates with the phenotype in the family in a recessive mode of inheritance. Relative quantification of MMP15 mRNA showed evidence of degradation of the mutated transcript, presumably by nonsense mediated decay. Likewise, MMP15: p.Gly231Arg, a concurrently reported homozygous missense variant in another patient exhibiting a similar phenotype, was predicted to disrupt zinc ion binding to the MMP-15 enzyme catalytic domain, which is essential for substrate proteolysis, by structural modeling. Previous animal models and cellular findings suggested that MMP15 plays a crucial role in the formation of endocardial cushions. These findings confirm that MMP15 is an important gene in human development, particularly cardiac, and that its loss of function is likely to cause a severe disorder phenotype.
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Affiliation(s)
- Hanadi A Abdelrahman
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Nadia Akawi
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Aisha M Al-Shamsi
- Paediatrics Department, Tawam hospital, Al-Ain, United Arab Emirates
| | - Amanat Ali
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Fatma Al-Jasmi
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Department of Paediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Anne John
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Jozef Hertecant
- Paediatrics Department, Tawam hospital, Al-Ain, United Arab Emirates
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Zayed Center for Health sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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Abdelrahman HA, Al-Shamsi A, John A, Ali BR, Al-Gazali L. A Novel SLC1A4 Mutation (p.Y191*) Causes Spastic Tetraplegia, Thin Corpus Callosum, and Progressive Microcephaly (SPATCCM) With Seizure Disorder. Child Neurol Open 2019; 6:2329048X19880647. [PMID: 31763347 PMCID: PMC6852354 DOI: 10.1177/2329048x19880647] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 12/24/2018] [Accepted: 01/19/2019] [Indexed: 02/05/2023] Open
Abstract
Spastic tetraplegia, thin corpus callosum, and progressive microcephaly is a recently
described very rare autosomal recessive neurodevelopmental disorder. This disease was
first described in 2015 in several families from the Ashkenazi Jewish ancestry with a
founder mutation in SLC1A4 (p.E256K) as the underlying genetic cause.
SLC1A4 gene encodes for the amino acid transporter ASCT1 that is
necessary for serine cellular transport to neurons. We clinically evaluated 2 Pakistani
siblings with severe global developmental delay, progressive microcephaly, and seizure
disorder. We performed exome sequencing, Sanger sequencing, and segregation analysis to
identify the genetic cause of the phenotype followed by in silico analysis to evaluate the
pathogenicity of the identified mutation. We identified a novel homozygous variant
(c.573T>G) in both patients. The mutation is predicted to cause nonsense mutation
(p.Y191*) in the ASCT1 protein. Here, we report the fifth disease causing mutation in
SLC1A4 gene and review all previously reported cases.
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Affiliation(s)
- Hanadi A Abdelrahman
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Aisha Al-Shamsi
- Department of Paediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Anne John
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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Baldi C, Bertoli-Avella AM, Al-Sannaa N, Alfadhel M, Al-Thihli K, Alameer S, Elmonairy AA, Al Shamsi AM, Abdelrahman HA, Al-Gazali L, Shawli A, Al-Hakami F, Yavuz H, Kandaswamy KK, Rolfs A, Brandau O, Bauer P. Expanding the clinical and genetic spectra of NKX6-2-related disorder. Clin Genet 2019; 93:1087-1092. [PMID: 29388673 DOI: 10.1111/cge.13221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 12/23/2017] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 11/29/2022]
Abstract
Hypomyelinating leukodystrophies (HLDs) affect the white matter of the central nervous system and manifest as neurological disorders. They are genetically heterogeneous. Very recently, biallelic variants in NKX6-2 have been suggested to cause a novel form of autosomal recessive HLD. Using whole-exome or whole-genome sequencing, we identified the previously reported c.196delC and c.487C>G variants in NKX6-2 in 3 and 2 unrelated index cases, respectively; the novel c.608G>A variant was identified in a sixth patient. All variants were homozygous in affected family members only. Our patients share a primary diagnosis of psychomotor delay, and they show spastic quadriparesis, nystagmus and hypotonia. Seizures and dysmorphic features (observed in 2 families each) represent an addition to the phenotype, while developmental regression (observed in 3 families) appears to be a notable and previously underestimated clinical feature. Our findings extend the clinical and mutational spectra associated with this novel form of HLD. Comparative analysis of our 10 patients and the 15 reported previously did, however, not reveal clear evidence for a genotype-phenotype correlation.
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Affiliation(s)
- C Baldi
- Centogene AG, Rostock, Germany
| | | | - N Al-Sannaa
- John Hopkins Aramco Health Care, Pediatric Services, Dhahran, Saudi Arabia
| | - M Alfadhel
- King Abdullah International Medical Research Centre, King Saud Bin Abdulaziz University for Health Sciences, Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - K Al-Thihli
- Department of Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - S Alameer
- King Saud Bin Abdulaziz University for Health Sciences, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (NGHA), Jeddah, Saudi Arabia
| | | | - A M Al Shamsi
- Department of Paediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - H A Abdelrahman
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University Al Ain, Al-Ain, United Arab Emirates
| | - L Al-Gazali
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University Al Ain, United Arab Emirates
| | - A Shawli
- King Saud Bin Abdulaziz University for Health Sciences, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (NGHA), Jeddah, Saudi Arabia.,Molecular Medicine Section, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - F Al-Hakami
- Molecular Medicine Section, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia.,Molecular Medicine Section, King Abdulaziz Medical City-WR, Jeddah, Saudi Arabia
| | - H Yavuz
- Centogene AG, Rostock, Germany
| | | | - A Rolfs
- Centogene AG, Rostock, Germany.,Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Rostock, Germany
| | | | - P Bauer
- Centogene AG, Rostock, Germany
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Abdelrahman HA, John A, Ali BR, Al-Gazali L. Further Delineation of the Microcephaly-Micromelia Syndrome Associated with Loss-of-Function Variants in DONSON. Mol Syndromol 2019; 10:171-176. [PMID: 31191207 DOI: 10.1159/000497337] [Citation(s) in RCA: 5] [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] [Accepted: 01/10/2019] [Indexed: 02/05/2023] Open
Abstract
The DONSON gene encodes the downstream neighbor of SON, a replisome component that stabilizes the replication fork during replication. A severe form of microcephalic dwarfism, microcephaly-micromelia syndrome (MIMIS), has been recently associated with DONSON biallelic loss of function. Affected fetuses suffer severe growth restriction, microcephaly, and variable limb malformations which result in intrauterine or perinatal death. All described fetuses carried a homozygous founder mutation (c.1047-9A>G), a splice-altering variant that leads to transcript degradation. We evaluated 2 newborns from a consanguineous Emirati family with severe microcephaly, micromelia, craniofacial dysmorphism, and skeletal abnormalities; both died shortly after birth. Here, we report the second homozygous loss-of-function variant (c.763C>T) in DONSON causing MIMIS, and we provide detailed clinical description of this very rare disorder. In addition, we review all MIMIS cases in the literature and summarize the striking features of this phenotype. This manuscript is aimed to increase the clinical understanding of this rare, extremely severe disorder and encourage clinical and molecular geneticists to consider screening for DONSON loss-of-function variants in families with recurrent pregnancy loss and/or perinatal deaths.
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Affiliation(s)
| | - Anne John
- Department of Pathology, United Arab Emirates University, Al Ain, UAE
| | - Bassam R Ali
- Department of Pathology, United Arab Emirates University, Al Ain, UAE.,Department of Zayed Center for Health Sciences, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE
| | - Lihadh Al-Gazali
- Department of Pediatrics, United Arab Emirates University, Al Ain, UAE
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7
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Abdelrahman HA, Al-Shamsi AM, Ali BR, Al-Gazali L. A null variant in PUS3 confirms its involvement in intellectual disability and further delineates the associated neurodevelopmental disease. Clin Genet 2018; 94:586-587. [PMID: 30308082 DOI: 10.1111/cge.13443] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Hanadi A Abdelrahman
- College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Aisha M Al-Shamsi
- Paediatrics Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Zayed Center for Health sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Lihadh Al-Gazali
- College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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8
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Abdelrahman HA, Al-Shamsi A, John A, Hertecant J, Lootah A, Ali BR, Al-Gazali L. A recessive truncating variant in thrombospondin-1 domain containing protein 1 gene THSD1 is the underlying cause of nonimmune hydrops fetalis, congenital cardiac defects, and haemangiomas in four patients from a consanguineous family. Am J Med Genet A 2018; 176:1996-2003. [PMID: 30055085 DOI: 10.1002/ajmg.a.40424] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/15/2018] [Accepted: 06/10/2018] [Indexed: 02/05/2023]
Abstract
Non-immune hydrops fetalis (NIHF) is the abnormal accumulation of serous fluid in more than two fetal or neonatal interstitial spaces due to nonimmune causes. It is a serious condition that requires extensive medical care as it indicates severe fetal compromise. We clinically evaluated four patients from two branches of a highly consanguineous family from the UAE with NIHF using whole exome sequencing and in silico analysis. Fetal onset pleural and peritoneal effusions were detected in all four patients and were born with moderate to severe hydrops fetalis that resolved with age. Follow up showed relatively normal growth and development apart from mild ascites and haemangiomas in all affected children, recurrent hydrocele in all affected males, intestinal malabsorption in two patients, dysmorphic features in two patients, and congenital cardiac defects in three out of four patients. Molecular testing identified a homozygous eight nucleotide deletion in THSD1 gene (NM_199263:c.1163_1170delGGCCAGCC, p.Arg388Glnfs*66) as the underlying cause of this phenotype in the affected children. The novel variant cosegregates with the described phenotype in an autosomal recessive mode of inheritance and is predicted to be pathogenic as it leads to a truncated protein that lost important structural and functional domains. Thrombospondin-1 domain containing protein 1 gene THSD1 has been recently associated with of NIHF and embryonic lethality. Here, we report the novel truncating THSD1 variant, and describe new clinical features that have not been reported previously thus expanding the phenotype associate with loss-of-function mutations in THSD1 causing NIHF.
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Affiliation(s)
- Hanadi A Abdelrahman
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
| | - Aisha Al-Shamsi
- Department of Paediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Anne John
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
| | - Jozef Hertecant
- Department of Paediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Ali Lootah
- Department of Paediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates.,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Lihadh Al-Gazali
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
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