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1. Antibiotic resistance genes prevalence prediction and interpretation in beaches affected by urban wastewater discharge

Author

Qandeel Zahra, Jawaria Gul, Ali Raza Shah, Muhammad Yasir, and Asad Mustafa Karim

Subjects
Antibiotic resistance genes, Environment, Beach waters, Machine learning, Explainable artificial intelligence, Medicine (General), R5-920
Abstract

Background: The annual death toll of over 1.2 million worldwide is attributed to infections caused by resistant bacteria, driven by the significant impact of antibiotic misuse and overuse in spreading these bacteria and their associated antibiotic resistance genes (ARGs). While limited data suggest the presence of ARGs in beach environments, efficient prediction tools are needed for monitoring and detecting ARGs to ensure public health safety. This study aims to develop interpretable machine learning methods for predicting ARGs in beach waters, addressing the challenge of black-box models and enhancing our understanding of their internal mechanisms. Methods: In this study, we systematically collected beach water samples and subsequently isolated bacteria from these samples using various differential and selective media supplemented with different antibiotics. Resistance profiles of bacteria were determined by using Kirby-Bauer disk diffusion method. Further, ARGs were enumerated by using the quantitative polymerase chain reaction (qPCR) to detect and quantify ARGs. The obtained qPCR data and hydro-meteorological were used to create an ML model with high prediction performance and we further used two explainable artificial intelligence (xAI) model-agnostic interpretation methods to describe the internal behavior of ML model. Results: Using qPCR, we detected blaCTX−M, blaNDM, blaCMY, blaOXA, blatetX, blasul1, and blaaac(6′-Ib-cr) in the beach waters. Further, we developed ML prediction models for blaaac(6′-Ib-cr), blasul1, and blatetX using the hydro-metrological and qPCR-derived data and the models demonstrated strong performance, with R2 values of 0.957, 0.997, and 0.976, respectively. Conclusions: Our findings show that environmental factors, such as water temperature, precipitation, and tide, are among the important predictors of the abundance of resistance genes at beaches.

Published
2023
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2. Biallelic ZNF407 mutations in a neurodevelopmental disorder with ID, short stature and variable microcephaly, hypotonia, ocular anomalies and facial dysmorphism

Author

Maria J. Guillen Sacoto, Joselito Sobreira, Muhammad Shuaib, Qandeel Zahra, Louisa Kalsner, Çağla Çakmak, Aslıhan Tolun, Sajid Malik, Mine Koprulu, and Nara Sobreira

Subjects
0301 basic medicine, Microcephaly, Pediatrics, medicine.medical_specialty, business.industry, 030105 genetics & heredity, medicine.disease, Compound heterozygosity, Short stature, Hypotonia, 03 medical and health sciences, Camptodactyly, 030104 developmental biology, Neurodevelopmental disorder, Intellectual disability, Genetics, medicine, medicine.symptom, business, Genetics (clinical), Exome sequencing
Abstract

We describe five members of a consanguineous Pakistani family (Family I) plus two affected children from families of different ethnic origins presenting with neurodevelopmental disorders with overlapping features. All affected individuals from families have intellectual disability (ID), ranging from mild to profound, and reduced motor and cognitive skills plus variable features including short stature, microcephaly, developmental delay, hypotonia, dysarthria, deafness, visual problems, enuresis, encopresis, behavioural anomalies, delayed pubertal onset and facial dysmorphism. We first mapped the disease locus in the large family (Family I), and by exome sequencing identified homozygous ZNF407 c.2814_2816dup (p.Val939dup) in four affected members where DNA samples were available. By exome sequencing we detected homozygous c.2405G>T (p.Gly802Val) in the affected member of Family II and compound heterozygous variants c.2884C>G (p.Arg962Gly) and c.3642G>C (p.Lys1214Asn) in the affected member of Family III. Homozygous c.5054C>G (p.Ser1685Trp) has been reported in two brothers with an ID syndrome. Affected individuals we present did not exhibit synophrys, midface hypoplasia, kyphosis, 5th finger camptodactyly, short 4th metatarsals or limited knee mobility observed in the reported family.

Published
2020
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3. Biallelic ZNF407 mutations in a neurodevelopmental disorder with ID, short stature and variable microcephaly, hypotonia, ocular anomalies and facial dysmorphism

Author

Qandeel, Zahra, Çağla, Çakmak, Mine, Koprulu, Muhammad, Shuaib, Nara, Sobreira, Louisa, Kalsner, Joselito, Sobreira, Maria J, Guillen Sacoto, Sajid, Malik, and Aslıhan, Tolun

Subjects
Male, Heterozygote, Homozygote, Dwarfism, Motor Activity, Pedigree, DNA-Binding Proteins, Phenotype, Neurodevelopmental Disorders, Child, Preschool, Intellectual Disability, Exome Sequencing, Microcephaly, Humans, Muscle Hypotonia, Exome, Female, Child, Transcription Factors
Abstract

We describe five members of a consanguineous Pakistani family (Family I) plus two affected children from families of different ethnic origins presenting with neurodevelopmental disorders with overlapping features. All affected individuals from families have intellectual disability (ID), ranging from mild to profound, and reduced motor and cognitive skills plus variable features including short stature, microcephaly, developmental delay, hypotonia, dysarthria, deafness, visual problems, enuresis, encopresis, behavioural anomalies, delayed pubertal onset and facial dysmorphism. We first mapped the disease locus in the large family (Family I), and by exome sequencing identified homozygous ZNF407 c.2814_2816dup (p.Val939dup) in four affected members where DNA samples were available. By exome sequencing we detected homozygous c.2405GT (p.Gly802Val) in the affected member of Family II and compound heterozygous variants c.2884CG (p.Arg962Gly) and c.3642GC (p.Lys1214Asn) in the affected member of Family III. Homozygous c.5054CG (p.Ser1685Trp) has been reported in two brothers with an ID syndrome. Affected individuals we present did not exhibit synophrys, midface hypoplasia, kyphosis, 5th finger camptodactyly, short 4th metatarsals or limited knee mobility observed in the reported family.

Published
2020

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