1
|
Khan A, Saraf VS, Siddiqui F, Batool T, Noreen Z, Javed S, Ahmad A, Alonazi WB, Ibrahim M, Pucciarelli S, Bokhari H. Multidrug resistance among uropathogenic clonal group A E. Coli isolates from Pakistani women with uncomplicated urinary tract infections. BMC Microbiol 2024; 24:74. [PMID: 38454332 PMCID: PMC10919050 DOI: 10.1186/s12866-024-03221-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/09/2024] [Indexed: 03/09/2024] Open
Abstract
OBJECTIVE Multi-drug resistance (MDR) has notably increased in community acquired uropathogens causing urinary tract infections (UTIs), predominantly Escherichia coli. Uropathogenic E. coli causes 80% of uncomplicated community acquired UTIs, particularly in pre-menopausal women. Considering this high prevalence and the potential to spread antimicrobial resistant genes, the current study was conducted to investigate the presence of clinically important strains of E. coli in Pakistani women having uncomplicated cystitis and pyelonephritis. Women belonging to low-income groups were exclusively included in the study. Seventy-four isolates from urine samples were processed, phylotyped, and screened for the presence of two Single Nucleotide Polymorphisms (SNPs) particularly associated with a clinically important clonal group A of E. coli (CgA) followed by antibiotic susceptibility testing and genome sequence analysis. RESULTS Phylogroup B2 was most prevalent in patients and 44% of isolates were positive for the presence of CgA specific SNPs in Fumarate hydratase and DNA gyrase subunit B genes. Antibiotic susceptibility testing showed widespread resistance to trimethoprim-sulfamethoxazole and extended-spectrum beta-lactamase production. The infection analysis revealed the phylogroup B2 to be more pathogenic as compared to the other groups. The genome sequence of E. coli strain U17 revealed genes encoding virulence, multidrug resistance, and host colonization mechanisms. CONCLUSIONS Our research findings not only validate the significant occurrence of multidrug-resistant clonal group A E. coli (CgA) in premenopausal Pakistani women suffering from cystitis and pyelonephritis but also reveal the presence of genes associated withvirulence, and drug efflux pumps. The detection of highly pathogenic, antimicrobial-resistant phylogroup B2 and CgA E. coli strains is likely to help in understanding the epidemiology of the pathogen and may ultimately help to reduce the impact of these strains on human health. Furthermore, the findings of this study will particularly help to reduce the prevalence of uncomplicated UTIs and the cost associated with their treatment in women belonging to low-income groups.
Collapse
Affiliation(s)
- Ayesha Khan
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
- Health Services Academy, Opposite NIH, Islamabad, Pakistan
| | - Viqar Sayeed Saraf
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Fariha Siddiqui
- Department of Biosciences, Shifa Tameer e Millat University, Islamabad, Pakistan
| | - Tahira Batool
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Zobia Noreen
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sundus Javed
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Aftab Ahmad
- Department of Microbiology, Kohsar University Murree, Rawalpindi, Punjab, Pakistan
| | - Wadi B Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Ibrahim
- Department of Microbiology, Kohsar University Murree, Rawalpindi, Punjab, Pakistan.
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan.
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, via Gentile III da Varano, Camerino, 62032, Italy
| | - Habib Bokhari
- Department of Microbiology, Kohsar University Murree, Rawalpindi, Punjab, Pakistan.
| |
Collapse
|
2
|
Aziz I, Noreen Z, Ijaz UZ, Gundogdu O, Hamid MH, Muhammad N, Khan A, Bokhari H. A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome. Sci Rep 2023; 13:6802. [PMID: 37185286 PMCID: PMC10133260 DOI: 10.1038/s41598-023-32491-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/28/2023] [Indexed: 05/17/2023] Open
Abstract
Stunted growth is an emerging global challenge affecting children under the age of 5 years in low- and middle-income countries. Despite such a high global prevalence of stunting, the mechanism of pathogenesis and the role of associated gut microbiota is poorly understood. The present study was designed to investigate the association of pathogenic strains of E. coli with the residential gut microbiota of stunted growth children. A total of 64 stool sample were collected from children aged ≤ 5 years, and were processed for isolation and molecular characterization of diarrheagenic E. coli. Selected stool samples (n = 39 including three normal controls) were then analysed for microbial community profiling using 16S ribosomal RNA (rRNA) gene sequencing. Furthermore, associations between changes in the microbiota in the presence of different E. coli strains was explored. Pathotyping of the isolated E. coli (n = 64) has shown that 39.68% belonged to one of the five pathotypes of E. coli whilst the remaining ones were non-typeable. Amongst the different pathotypes, EPEC was found to be the most prevalent (52%; n = 13), followed by EAEC (20%; n = 5), EIEC (12%; n = 3), EHEC (8%; n = 2) and ETEC 2 (8%; n = 2). Phylogrouping analysis has shown that majority of the strains belonged to B2 (28.12%). Microbial diversity is shown to be significant and varied when the samples are organized under the recovered phylogroups. Moreover, based on predictive metabolism, the colonization of these strains were found to be significantly associated with energy utilization pathways such as Denovoprine-2 and glyoxylate-by. Differential analysis has shown that Escherichia-Shigella and Enterococcus were altered for the children with stunted growth.
Collapse
Affiliation(s)
- Israr Aziz
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Zobia Noreen
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | | | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Muhammad Haroon Hamid
- Department of Pediatrics/Department of Preventive Pediatrics, Mayo Hospital, King Edward Medical University, Lahore, Pakistan
| | - Nazir Muhammad
- Department of Pediatrics/Department of Preventive Pediatrics, Mayo Hospital, King Edward Medical University, Lahore, Pakistan
| | - Abdullah Khan
- Paediatric Unit, Saidu Teaching Hospitals, Swat, Saidu Sharif, Pakistan
| | - Habib Bokhari
- Department of Biosciences, COMSATS University, Islamabad, Pakistan.
- Department of Biosciences, Kohsar University, Murree, Pakistan.
| |
Collapse
|
3
|
Saraf VS, Bhatti T, Javed S, Bokhari H. Antimicrobial Resistance Pattern in E. coli Isolated from Placental Tissues of Pregnant Women in Low-Socioeconomic Setting of Pakistan. Curr Microbiol 2022; 79:83. [PMID: 35122538 DOI: 10.1007/s00284-022-02769-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/14/2022] [Indexed: 11/27/2022]
Abstract
Infections during pregnancy can culminate in adverse pregnancy outcomes, including preterm birth (PTB). Pakistan is among the top ten nations with high PTB-associated neonatal mortality rates, where access to prenatal as well as neonatal care is only afforded by the privileged few. Societal stigma further discourages women seeking healthcare for minor infections. Microbial pathogens associated with genitourinary infections can lead to gestational complications culminating in earlier onset of labor. In this study, association of Escherichia coli (E. coli) with PTB in Pakistani women of low-socioeconomic status is examined. 57 paired vaginal swabs and placenta samples from mothers with full term and preterm deliveries were collected and processed for isolation and molecular characterization of extraintestinal pathogenic E. coli (ExPEC). ExPEC isolated from vaginal swabs and placenta showed phylotype B2 being most prevalent (Vagina n = 3 (9), 33%) (Placenta n = 4 (12), 33%) in preterm cases followed by phylotype B1 (Vagina n = 2 (9), 22%) (Placenta n = 3 (12), 25%) and untypeable strains. Antibiotic susceptibility profiling showed a large percentage of resistant isolates to multiple antibiotics, including carbapenem and included extended-spectrum beta-lactamase (ESBL) producers. Our study is the first to report different phylotypes of E. coli from placental tissues in preterm deliveries which may be a cause for concern for maternal and neonatal health. ExPEC from vaginal swabs and placental of females delivering preterm shows the pathogenic phylotype B2 dominance with a large percentage of isolates resistant to multiple antibiotics, including carbapenem and included ESBL producers. The placental isolates may indicate ascending infection from vagina or urinary tract which may lead to preterm birth.
Collapse
Affiliation(s)
- Viqar Sayeed Saraf
- Public Health and Microbiology Lab, Department of Biosciences, COMSATS University Islamabad, Park road, Tarlai Kalan, Islamabad, Pakistan
| | - Theophilus Bhatti
- Public Health and Microbiology Lab, Department of Biosciences, COMSATS University Islamabad, Park road, Tarlai Kalan, Islamabad, Pakistan
| | - Sundus Javed
- Public Health and Microbiology Lab, Department of Biosciences, COMSATS University Islamabad, Park road, Tarlai Kalan, Islamabad, Pakistan.
| | - Habib Bokhari
- Public Health and Microbiology Lab, Department of Biosciences, COMSATS University Islamabad, Park road, Tarlai Kalan, Islamabad, Pakistan.
- Kohsar University Murree, Kashmir point, Murree, Punjab, Pakistan.
| |
Collapse
|
4
|
Antibiotic resistance in Pakistan: a systematic review of past decade. BMC Infect Dis 2021; 21:244. [PMID: 33676421 PMCID: PMC7937258 DOI: 10.1186/s12879-021-05906-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Background During the last six decades, extensive use of antibiotics has selected resistant strains, increasing the rate of fatal infectious diseases, and exerting an economic burden on society. This situation is widely accepted as a global problem, yet its degree is not well elucidated in many regions of the world. Up till now, no systemic analysis of Antimicrobial resistance (AMR) in Pakistan has been published. The current study aims to describe the antibiotic-resistance scenario of Pakistan from human samples of the last 10 y, to find the gaps in surveillances and methodology and recommendations for researchers and prescribers founded on these outcomes. Methods Original research articles analyzed the pattern of Antibiotic resistance of any World Health Organization (WHO) enlisted priority pathogens in Pakistan (published onward 2009 till March 2020), were collected from PubMed, Google scholar, and PakMedi Net search engines. These articles were selected based on predefined inclusion and exclusion criteria. Data about the study characteristics and antibiotic-resistance for a given bacterium were excluded from literature. Antibiotic resistance to a particular bacterium was calculated as a median resistance with 95% Confidence Interval (CI). Results Studies published in the last 10 y showed that Urinary Tract Infection (UTI) is the most reported clinical diagnosis (16.1%) in Pakistan. E. coli were reported in 28 (30.11%) studies showing high resistance to antibiotics’ first line. Methicillin-resistant Staphylococcus aureus (MRSA) was found in 49% of S. aureus’ total reported cases. Phenotypic resistance pattern has mostly been evaluated by Disk Diffusion Method (DDM) (82.8%), taken Clinical Laboratory Standards Institute (CLSI) as a breakpoint reference guideline (in 79.6% studies). Only 28 (30.11%) studies have made molecular identification of the resistance gene. blaTEM (78.94% in Shigella spp) and blaNDM-1 (32.75% in Klebsiella spp) are the prominent reported resistant genes followed by VanA (45.53% in Enterococcus spp), mcr-1 (1.61% in Acinetobacter spp), and blaKPC-2 (31.67% in E. coli). Most of the studies were from Sindh (40.86%), followed by Punjab (35.48%), while Baluchistan’s AMR data was not available. Conclusion Outcomes of our study emphasize that most of the pathogens show high resistance to commonly used antibiotics; also, we find gaps in surveillances and breaches in methodological data. Based on these findings, we recommend the regularization of surveillance practice and precise actions to combat the region’s AMR.
Collapse
|
5
|
Foessleitner P, Gasser J, Kiss H, Flunt A, Presterl E, Petricevic L, Farr A. Vaginal colonization of extended-spectrum beta-lactamase-producing bacteria during pregnancy: An observational study. Eur J Obstet Gynecol Reprod Biol 2020; 246:86-89. [DOI: 10.1016/j.ejogrb.2020.01.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 02/04/2023]
|
6
|
Singh T, Das S, Ramachandran VG, Wani S, Shah D, Maroof KA, Sharma A. Distribution of Integrons and Phylogenetic Groups among Enteropathogenic Escherichia coli Isolates from Children <5 Years of Age in Delhi, India. Front Microbiol 2017; 8:561. [PMID: 28443072 PMCID: PMC5385330 DOI: 10.3389/fmicb.2017.00561] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/20/2017] [Indexed: 01/29/2023] Open
Abstract
Integrons by means of horizontal gene transfer carry multidrug resistance genes (MDR) among bacteria, including E. coli. The aim of this study was to determine the antibiotic resistance profiles and the genes associated with them, to gain insights in the distribution of phylogroups, prevalence, and characterization of class 1, 2 and 3 integrons among Enteropathogenic E. coli (EPEC) isolates, from children upto 5 years of age from Delhi and National Capital Region (NCR), India. A total of 120 E. coli isolates, including 80 from diarrheagenic E. coli (cases) and 40 from healthy isolates (controls) were recruited in this study. After isolation of E. coli, screening for EPEC was done by conventional multiplex PCR. Antibiotic suseptibility test was performed using disk diffusion method and further confirmed by minimum inhibitory concentration (MICs) by E-test. The presence and characterization of integrons and antimicrobial resistance genes were performed by PCR and DNA sequencing. Phylogeny determination was carried out by quadruplex PCR. EPEC strains were found in 64 of the 80 diarrheagenic cases, out of which 38 were MDR. In the 40 healthy controls, 23 were found to be EPEC strain, out of which only 2 were MDR. Amongst 80 diarrheagenic cases, class 1 integron were observed in 43 isolates, class 2 integron in 12 isolates and 9 isolates were found with co-existence of both. Similarly, in healthy controls; class 1 integron in 9 and class 2 integron in 7 isolates were observed with co-existence in 3 isolates. None of the isolates included class 3 integron. The dfr was the most commonly identified gene cassette within the integron-positive isolates. Phylogenetic studies showed considerable representation of phylogroup B2 in both diarrheagenic cases and healthy controls. This study reiterates the importance of class 1 integron predominantly for acquisition of antibiotic resistance genes among EPEC isolates. Furthermore, it also ascertains the possible association between multidrug resistance and presence of integrons. Approximately 91% of isolates were easily assigned to their respective phylogroups. Assessment of the relationship between antibiotic resistance and dominant phylogroups detected was also attempted. This study also highlights the increased burden of antimicrobial resistance in healthy controls.
Collapse
Affiliation(s)
- Taru Singh
- Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalNew Delhi, India
| | - Shukla Das
- Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalNew Delhi, India
| | - V G Ramachandran
- Dermatology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Dilshad GardenNew Delhi, India.,Department of Minimal Access and Bariatric Surgery, Fortis Flt. Rajan Dhall HospitalNew Delhi, India
| | - Sayim Wani
- Dermatology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Dilshad GardenNew Delhi, India.,Department of Minimal Access and Bariatric Surgery, Fortis Flt. Rajan Dhall HospitalNew Delhi, India
| | - Dheeraj Shah
- Pediatrics, University College of Medical Sciences and Guru Teg Bahadur HospitalNew Delhi, India
| | - Khan A Maroof
- Community Medicine, University College of Medical Sciences, and Guru Teg Bahadur Hospital, Dilshad GardenNew Delhi, India
| | - Aditi Sharma
- Vardhman Mahavir Medical College and Sardarjung HospitalNew Delhi, India
| |
Collapse
|