Isolation and Characterization of NDM-Positive Escherichia coli from Municipal Wastewater in Jeddah, Saudi Arabia

ABSTRACTThe emergence of resistance to last-resort antibiotics is a public health concern of global scale. Besides direct person-to-person propagation, environmental pathways might contribute to the dissemination of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). Here, we describe the incidence ofblaNDM-1, a gene conferring resistance to carbapenems, in the wastewater of the city of Jeddah, Saudi Arabia, over a 1-year period.blaNDM-1was detected at concentrations ranging from 104to 105copies/m3of untreated wastewater during the entire monitoring period. These results indicate the ubiquity and high incidence ofblaNDM-1in the local wastewater. To track the bacteria carryingblaNDM-1, we isolatedEscherichia coliPI7, a strain of sequence type 101 (ST101), from wastewater around the Hajj event in October 2013. Genome sequencing of this strain revealed an extensive repertoire of ARGs as well as virulence and invasive traits. These traits were further confirmed by antibiotic resistance profiling andin vitrocell internalization in HeLa cell cultures. Given that this strain remains viable even after a certain duration in the sewerage, and that Jeddah lacks a robust sanitary infrastructure to fully capture all generated sewage, the presence of this bacterium in the untreated wastewater represents a potential hazard to the local public health. To the best of our knowledge, this is the first report of ablaNDM-1-positiveE. colistrain isolated from a nonnosocomial environment in Saudi Arabia and may set a priority concern for the need to establish improved surveillance for carbapenem-resistantE. coliin the country and nearby regions.

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Wastewater as a Probable Environmental Reservoir of Extended-Spectrum-β-Lactamase Genes: Detection of Chimeric β-Lactamases CTX-M-64 and CTX-M-123

Applied and Environmental Microbiology ◽

10.1128/aem.01740-19 ◽

2019 ◽

Vol 85 (22) ◽

Cited By ~ 1

Author(s):

Hayato Tanaka ◽

Wataru Hayashi ◽

Masaki Iimura ◽

Yui Taniguchi ◽

Eiji Soga ◽

...

Keyword(s):

Escherichia Coli ◽

Resistance Genes ◽

Health Concern ◽

Resistant Bacteria ◽

Content Type ◽

E Coli ◽

Chimeric Genes ◽

Untreated Wastewater ◽

Extended Spectrum ◽

Antimicrobial Resistance Genes

ABSTRACT The presence of antimicrobial-resistant bacteria and resistance genes in aquatic environments is a serious public health concern. This study focused on Escherichia coli possessing blaCTX-M genes in wastewater inflows. Twelve crude inflow water samples from wastewater treatment plant (WWTP) A and two samples each from three other WWTPs were collected in 2017 and 2018. A total of 73 E. coli isolates with 31 different sequence types (STs) harboring distinctive blaCTX-M gene repertoires were detected. In WWTP A influents, blaCTX-M-14 (14 isolates) was dominant, followed by blaCTX-M-15 (12 isolates) and blaCTX-M-27 (10 isolates). The chimeric blaCTX-M-64 and blaCTX-M-123 genes were each identified in one of the E. coli isolates from the same WWTP A inflow port. The blaCTX-M-27 gene was associated with five of seven B2-ST131 isolates, including three isolates of the B2-O25b-ST131-H30R/non-Rx lineage. One of the remaining two isolates belonged to the B2-O25b-ST131-H30R/Rx lineage harboring the blaCTX-M-15 gene. As for the B2-O25b-ST131-H30R/non-Rx lineage, two isolates with blaCTX-M-27 were recovered from each of the WWTP B and D influents, and one isolate with blaCTX-M-174 was also recovered from WWTP B influent. Whole-genome sequencing of chimeric blaCTX-M-harboring E. coli isolates revealed that the blaCTX-M-64 gene was integrated into the chromosome of ST10 E. coli B22 via ISEcp1-mediated transposition of a 9,467-bp sequence. The blaCTX-M-123-carrying IncI1 plasmid pB64 was 109,169 bp in length with pST108. The overall findings suggest that wastewater may act as a probable reservoir of clinically significant clonal lineages mediating antimicrobial resistance genes and chimeric genes that have not yet been identified from human isolates of domestic origin in Japan. IMPORTANCE Global spread of CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is a critical concern in both clinical and community settings. This dominance of CTX-M-type ESBL producers may be largely due to the successful international spread of epidemic clones, as represented by the extraintestinal pathogenic Escherichia coli (ExPEC) ST131. Our findings highlight the worrisome presence of diverse E. coli clones associated with humans, including ExPEC lineages harboring the most common blaCTX-M variants in untreated wastewater samples. Moreover, the chimeric genes blaCTX-M-64 and blaCTX-M-123, which have not yet been identified from human isolates of domestic origin in Japan, were identified. Exposure to untreated wastewater through combined sewer overflow caused by heavy rains derived from abnormal weather change could pose a risk for human health due to ingesting those antimicrobial-resistant bacteria.

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Antibiotic Resistance of Escherichia Coli Isolated from Lake Nainital, Uttarakhand State, India

Journal of Mountain Research ◽

10.51220/jmr.v16i1.12 ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Neha Giri ◽

Anchal Lodhi ◽

Devendra Singh Bisht ◽

Suvarna Bhoj ◽

Deepak Kumar Arya

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Multiple Drug Resistance ◽

Health Concern ◽

Penicillin G ◽

Resistant Bacteria ◽

Sample Collection ◽

E Coli ◽

Mar Index ◽

Collection Sites

Researchers have encountered new challenges with the discovery of multiple drug resistance in microbes. Currently, multidrug resistant bacteria are considered a major public health concern and an emerging global epidemic. Presence of Escherichia coli in water is used as a faecal pollution measure. In this study E. coli isolates were collected from 20 sample collection sites at Lake Nainital. 20 E. coli isolates, 1 from each sample collection sites, were examined for their antibiotic response patterns against a panel of widely used 15 antibiotics. The result of this study showed 100% resistance to Penicillin G followed by Erythromycin (80%). All isolates (100%) were found susceptible for Gentamycin. The susceptibilities for Chloramphenicol and Co-trimoxazaole were found next to Gentamycin as 90 and 85% respectively. Multiple antibiotic resistance (MAR) index was also determined. 0.73 MAR index was observed as highest in 1 isolate. 13 out of 20 isolates had more than 0.2 MAR indices. The result reveals the origin of E. coli isolates from an area of high antibiotics use.

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Antibiotic Resistance Patterns of Diverse Escherichia coli Phylogenetic Groups Isolated from the Al-Hillah River in Babylon Province, Iraq

The Scientific World JOURNAL ◽

10.1155/2019/5927059 ◽

2019 ◽

Vol 2019 ◽

pp. 1-8 ◽

Cited By ~ 2

Author(s):

Mourouge Saadi Alwash ◽

Hawraa Mohammed Al-Rafyai

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Anthropogenic Activities ◽

Health Concern ◽

Resistant Bacteria ◽

Anthropogenic Pressures ◽

Phylogenetic Groups ◽

E Coli ◽

Resistance Patterns ◽

Antibiotic Resistance Patterns

Surface water contamination remains a major worldwide public health concern and may contribute to the dissemination of antibiotic-resistant bacteria. The Al-Hillah River in the city of Babylon Province, Iraq, diverts flows from the Euphrates River. Because of its importance in irrigation and population density, it faces several forced and unforced changes due to anthropogenic activities. To evaluate water quality, water samples were collected from three sites with different anthropogenic pressures along the Al-Hillah River. These samples were subjected to bacteriological analyses, i.e., total coliforms, Escherichia coli, and faecal enterococci. The phylogenetic groups of the E. coli isolates (n = 61) were typed by rapid PCR-based analyses. Representatives of each isolate were tested phenotypically for resistance to six classes of antibiotics and characterized according to their phylogenetic groups. The results demonstrated the highest resistance levels were to β-lactam antibiotics, followed by fosfomycin and aminoglycosides. Escherichia coli isolates belonging to phylogenetic groups A and B2 were the most common and were characterized by a higher prevalence of antibiotic resistance. This study is important for understanding the current conditions of the Al-Hillah River, as the data reveal a high prevalence of multiresistance among E. coli isolates circulating at the three sampling sites.

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Extended-spectrum beta-lactamase and ampicillin Class C beta lactamase-producing Escherichia coli from food animals: A review

International Journal of One Health ◽

10.14202/ijoh.2019.65-75 ◽

2019 ◽

pp. 65-75 ◽

Cited By ~ 1

Author(s):

Asinamai Athliamai Bitrus ◽

Peter Anjili Mshelia ◽

Iliya Dauda Kwoji ◽

Mohammed Dauda Goni ◽

Saleh Mohammed Jajere

Keyword(s):

Public Health ◽

Escherichia Coli ◽

Health Concern ◽

Resistant Bacteria ◽

Beta Lactamase ◽

Care Providers ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Extended Spectrum ◽

Class C

Antimicrobial resistance has gained global notoriety due to its public health concern, the emergence of multiple drug-resistant bacteria, and lack of new antimicrobials. Extended-spectrum beta-lactamase (ESBL)/ampicillin Class C (AmpC)- producing Escherichia coli and other zoonotic pathogens can be transmitted to humans from animals either through the food chain, direct contact or contamination of shared environments. There is a surge in the rate of resistance to medically important antibiotics such as carbapenem, ESBL, aminoglycosides, and fluoroquinolones among bacteria of zoonotic importance. Factors that may facilitate the occurrence, persistence and dissemination of ESBL/AmpC-Producing E. coli in humans and animal includes; 1). o ral administration of antimicrobials to humans primarily (by physician and health care providers) and secondarily to animals, 2). importation of parent stock and day-old chickens, 3). farm management practice and lack of water acidification in poultry, 4). contamination of feed, water and environment, 5). contamination of plants with feces of animals. Understanding these key factors will help reduce the level of resistance, thereby boosting the therapeutic effectiveness of antimicrobial agents in the treatment of animal and human infections. This review highlights the occurrence, risk factors, and public health importance of ESBL/AmpC-beta-lactamase producing E. coli isolated from livestock.

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Multidrug Resistance among Gram Negative E. coli in Chicken Meat (Rafha-Saudi Arabia)

Journal of Pharmaceutical Research International ◽

10.9734/jpri/2021/v33i58a34087 ◽

2021 ◽

pp. 38-48

Author(s):

Akbar Ali ◽

Vijay R. Chidrawar

Keyword(s):

Public Health ◽

Saudi Arabia ◽

Antibiotic Resistance ◽

Multidrug Resistant ◽

Chicken Meat ◽

Penicillin G ◽

Diffusion Method ◽

Resistant Bacteria ◽

E Coli ◽

Northern Border

Aims: Multidrug resistant (MDR) bacteria pose a major public health issuer globally. The genes for antibiotic resistance are transferred vertically in the form of genomic DNA and horizontally in the form of plasmids or transposons. Antibiotic are extensively used in animal farming to treat and prevent animal diseases, and at sub-therapeutic doses, they are used to promote animal growth. This extensive use of antibiotics is causing an increase in resistance among bacteria. More frequent, chicken meat available at retail shops is reported to be contaminated with a variety of drug resistant bacteria including E. Coli. The aim of the present study was to investigate antibiotic resistance in Escherichia coli strains isolated from chicken meat available in the local shops of Rafha, Saudi Arabia. Place and Duration of Study: Department of basic health sciences, College of Pharmacy, Northern Border University, Rafha, Saudi Arabia, between February and October, 2019 Methodology: Eighty-six E. coli strains, isolated from chicken meat, were tested for their antibiotic resistance profile, using the disc diffusion method. Results: All the isolated E. coli strains were tested against 14 antibiotics. The maximum resistance was found against penicillin G (95%) followed by amoxicillin (85%), Cephalothin (81%), Erythromycin (72%), and Tetracycline (50%). Imipenem was the most effective agent of all with only 1% resistance followed by Cefepime with almost 6% resistance. A high percentage of the isolates (57%,) were multidrug resistant as they were non—susceptible to at least one antimicrobial in ≥3 antimicrobial classes including amoxicillin, erythromycin and tetracycline. Conclusion: The prevalence of MDR E. coli in retail chicken meat is very high and could pose a serious threat to public health.

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Complete Assembly ofEscherichia coliSequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts

mSphere ◽

10.1128/msphere.00130-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 10

Author(s):

Arun Gonzales Decano ◽

Catherine Ludden ◽

Theresa Feltwell ◽

Kim Judge ◽

Julian Parkhill ◽

...

Keyword(s):

Escherichia Coli ◽

Dna Sequencing ◽

Health Concern ◽

Resistant Bacteria ◽

Content Type ◽

Clonal Group ◽

E Coli ◽

Two Samples ◽

Long Read ◽

M 14

ABSTRACTThe incidence of infections caused by extraintestinalEscherichia coli(ExPEC) is rising globally, which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been associated with excess mortality, prolonged hospital stays, and higher health care costs.E. colisequence type 131 (ST131) is a major ExPEC clonal group worldwide, with variable plasmid composition, and has an array of genes enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genesblaCTX-M-14,blaCTX-M-15, andblaCTX-M-27, which are often rearranged, amplified, and translocated by mobile genetic elements (MGEs). Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow MGE structures encodingblaCTX-Mgenes to be fully determined. Here, we performed long-read sequencing to decipher the genome structures of sixE. coliST131 isolates from six patients. Most long-read assemblies generated entire chromosomes and plasmids as single contigs, in contrast to more fragmented assemblies created with short reads alone. The long-read assemblies highlighted diverse accessory genomes withblaCTX-M-15,blaCTX-M-14, andblaCTX-M-27genes identified in three, one, and one isolates, respectively. One sample had noblaCTX-Mgene. Two samples had chromosomalblaCTX-M-14andblaCTX-M-15genes, and the latter was at three distinct locations, likely transposed by the adjacent MGEs: ISEcp1, IS903B,and Tn2. This study showed that AMR genes exist in multiple different chromosomal and plasmid contexts, even between closely related isolates within a clonal group such asE. coliST131.IMPORTANCEDrug-resistant bacteria are a major cause of illness worldwide, and a specific subtype calledEscherichia coliST131 causes a significant number of these infections. ST131 bacteria become resistant to treatments by modifying their DNA and by transferring genes among one another via large packages of genes called plasmids, like a game of pass-the-parcel. Tackling infections more effectively requires a better understanding of what plasmids are being exchanged and their exact contents. To achieve this, we applied new high-resolution DNA sequencing technology to six ST131 samples from infected patients and compared the output to that of an existing approach. A combination of methods shows that drug resistance genes on plasmids are highly mobile because they can jump into ST131’s chromosomes. We found that the plasmids are very elastic and undergo extensive rearrangements even in closely related samples. This application of DNA sequencing technologies illustrates at a new level the highly dynamic nature of ST131 genomes.

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Genomic Analysis of Factors Associated with Low Prevalence of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Sequence Type 95 Strains

mSphere ◽

10.1128/msphere.00390-16 ◽

2017 ◽

Vol 2 (2) ◽

Cited By ~ 11

Author(s):

Craig M. Stephens ◽

Sheila Adams-Sapper ◽

Manraj Sekhon ◽

James R. Johnson ◽

Lee W. Riley

Keyword(s):

Public Health ◽

Antibiotic Resistance ◽

Genetic Factors ◽

Health Concern ◽

Public Health Concern ◽

Antibiotic Resistant ◽

Content Type ◽

E Coli ◽

Bacterial Genetic ◽

Public Health Strategies

ABSTRACT Antibiotic resistance in bacterial pathogens is a major public health concern. This work was motivated by the observation that only a small proportion of ST95 isolates, a major pandemic lineage of extraintestinal pathogenic E. coli, have acquired antibiotic resistance, in contrast to many other pandemic lineages. Understanding bacterial genetic factors that may prevent acquisition of resistance could contribute to the development of new biological, medical, or public health strategies to reduce antibiotic-resistant infections. Extraintestinal pathogenic Escherichia coli (ExPEC) strains belonging to multilocus sequence type 95 (ST95) are globally distributed and a common cause of infections in humans and domestic fowl. ST95 isolates generally show a lower prevalence of acquired antimicrobial resistance than other pandemic ExPEC lineages. We took a genomic approach to identify factors that may underlie reduced resistance. We fully assembled genomes for four ST95 isolates representing the four major fimH-based lineages within ST95 and also analyzed draft-level genomes from another 82 ST95 isolates, largely from the western United States. The fully assembled genomes of antibiotic-resistant isolates carried resistance genes exclusively on large (>90-kb) IncFIB/IncFII plasmids. These replicons were common in the draft genomes as well, particularly in antibiotic-resistant isolates, but we also observed multiple instances of a smaller (8.3-kb) ampicillin resistance plasmid that had been previously identified in Salmonella enterica. Among ST95 isolates, pansusceptibility to antibiotics was significantly associated with the fimH6 lineage and the presence of homologs of the previously identified 114-kb IncFIB/IncFII plasmid pUTI89, both of which were also associated with reduced carriage of other plasmids. Potential mechanistic explanations for lineage- and plasmid-specific effects on the prevalence of antibiotic resistance within the ST95 group are discussed. IMPORTANCE Antibiotic resistance in bacterial pathogens is a major public health concern. This work was motivated by the observation that only a small proportion of ST95 isolates, a major pandemic lineage of extraintestinal pathogenic E. coli, have acquired antibiotic resistance, in contrast to many other pandemic lineages. Understanding bacterial genetic factors that may prevent acquisition of resistance could contribute to the development of new biological, medical, or public health strategies to reduce antibiotic-resistant infections.

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Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms

mSystems ◽

10.1128/msystems.00913-20 ◽

2021 ◽

Author(s):

Nicole Pearcy ◽

Yue Hu ◽

Michelle Baker ◽

Alexandre Maciel-Guerra ◽

Ning Xue ◽

...

Keyword(s):

Machine Learning ◽

Escherichia Coli ◽

Antibiotic Resistance ◽

Health Concern ◽

Metabolic Adaptation ◽

Genetic Determinants ◽

Content Type ◽

E Coli ◽

Adaptation Mechanisms ◽

Genome Scale

Escherichia coli is a major public health concern given its increasing level of antibiotic resistance worldwide and extraordinary capacity to acquire and spread resistance via horizontal gene transfer with surrounding species and via mutations in its existing genome. E. coli also exhibits a large amount of metabolic pathway redundancy, which promotes resistance via metabolic adaptability. In this study, we developed a computational approach that integrates machine learning with metabolic modeling to understand the correlation between AMR and metabolic adaptation mechanisms in this model bacterium.

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Repeated Isolation of Extended-Spectrum-β-Lactamase-Positive Escherichia coli Sequence Types 648 and 131 from Community Wastewater Indicates that Sewage Systems Are Important Sources of Emerging Clones of Antibiotic-Resistant Bacteria

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00823-19 ◽

2019 ◽

Vol 63 (9) ◽

Cited By ~ 6

Author(s):

Erik Paulshus ◽

Kaisa Thorell ◽

Jessica Guzman-Otazo ◽

Enrique Joffre ◽

Patricia Colque ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Resistant Bacteria ◽

Antibiotic Resistant Bacteria ◽

Antibiotic Resistant ◽

Content Type ◽

E Coli ◽

Extended Spectrum ◽

Pump Station ◽

Sequence Types

ABSTRACT Antibiotic resistance in bacteria is an emerging problem globally. Resistant bacteria are found in human and animal microbiota, as well as in the environment. Wastewater receives bacteria from all these sources and thus can provide a measurement of abundance and diversity of antibiotic-resistant bacteria circulating in communities. In this study, water samples were collected from a wastewater pump station in a Norwegian suburban community over a period of 15 months. A total of 45 daily samples were cultured and analyzed for the presence of Escherichia coli. Eighty E. coli-like colonies were collected from each daily sample and then phenotyped and analyzed for antibiotic resistance using the PhenePlate-AREB system. During the sampling period, two unique E. coli phenotypes with resistance to cefotaxime and cefpodoxime indicating carriage of extended-spectrum β-lactamases (ESBL) were observed repeatedly. Whole-genome sequencing of 15 representative isolates from the two phenotypes identified these as two distinct clones belonging to the two globally spread E. coli multilocus sequence types (STs) ST131 and ST648 and carrying blaCTX-M-15. The number of ESBL-positive E. coli strains in the community wastewater pump station was 314 of 3,123 (10%) analyzed E. coli strains. Of the ESBL-positive isolates, 37% belonged to ST648, and 7% belonged to ST131. Repeated findings of CTX-M-15-positive ST648 and ST131 over time indicate that these STs are resident in the analyzed wastewater systems and/or circulate abundantly in the community.

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ESBL Activity, MDR, and Carbapenem Resistance among Predominant Enterobacterales Isolated in 2019

Antibiotics ◽

10.3390/antibiotics10060744 ◽

2021 ◽

Vol 10 (6) ◽

pp. 744

Author(s):

Altaf Bandy ◽

Bilal Tantry

Keyword(s):

Escherichia Coli ◽

Saudi Arabia ◽

Antimicrobial Resistance ◽

Carbapenem Resistance ◽

Resistant Bacteria ◽

Sociodemographic Characteristics ◽

Chi Square ◽

E Coli ◽

Chi Square Test ◽

Resistance Rates

Antimicrobial-resistance in Enterobacterales is a serious concern in Saudi Arabia. The present study retrospectively analyzed the antibiograms of Enterobacterales identified from 1 January 2019 to 31 December 2019 from a referral hospital in the Aljouf region of Saudi Arabia. The revised document of the Centers for Disease Control (CDC) CR-2015 and Magiorakos et al.’s document were used to define carbapenem resistance and classify resistant bacteria, respectively. The association of carbapenem resistance, MDR, and ESBL with various sociodemographic characteristics was assessed by the chi-square test and odds ratios. In total, 617 Enterobacterales were identified. The predominant (n = 533 (86.4%)) isolates consisted of 232 (37.6%), 200 (32.4%), and 101 (16.4%) Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis, respectively. In general, 432 (81.0%) and 128 (24.0%) isolates were of MDR and ESBL, respectively. The MDR strains were recovered in higher frequency from intensive care units (OR = 3.24 (1.78–5.91); p < 0.01). E. coli and K. pneumoniae resistance rates to imipenem (2.55 (1.21–5.37); p < 0.01) and meropenem (2.18 (1.01–4.67); p < 0.04), respectively, were significantly higher in winter. The data emphasize that MDR isolates among Enterobacterales are highly prevalent. The studied Enterobacterales exhibited seasonal variation in antimicrobial resistance rates towards carbapenems and ESBL activity.

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