Genotypic and phenotypic profiles of Escherichia coli isolates belonging to clinical sequence type 131 (ST131), clinical non-ST131, and fecal non-ST131 lineages from India

Epidemiology, Virulence and Antimicrobial Resistance of Escherichia coli Isolated from Small Brazilian Farms Producers of Raw Milk Fresh Cheese

This study aimed to identify contamination sources in raw milk and cheese on small farms in Brazil by isolating Escherichia coli at various stages of milk production and cheese manufacturing. The study targeted EAEC, EIEC, ETEC, EPEC, STEC, and ExPEC pathotypes, characterizing isolates for the presence of virulence genes, phylogroups, antimicrobial susceptibility, and phylogenetic relationships using PFGE and MLST. The presence of antimicrobial resistance genes and serogroups was also determined. Three categories of E. coli were identified: pathogenic, commensal, and ceftriaxone-resistant (ESBL) strains. Pathogenic EPEC, STEC, and ExPEC isolates were detected in milk and cheese samples. Most isolates belonged to phylogroups A and B1 and were resistant to antimicrobials such as nalidixic acid, ampicillin, kanamycin, streptomycin, sulfisoxazole, and tetracycline. Genetic analysis revealed that E. coli with identical virulence genes were present at different stages within the same farm. The most frequently identified serogroup was O18, and MLST identified ST131 associated with pathogenic isolates. The study concluded that E. coli was present at multiple points in milk collection and cheese production, with significant phylogroups and high antimicrobial resistance. These findings highlight the public health risk posed by contamination in raw milk and fresh cheese, emphasizing the need to adopt hygienic practices to control these microorganisms.

Multi-drug resistant (MDR) Gram-negative pathogenic bacteria isolated from poultry in the Noakhali region of Bangladesh

Rapidly increasing antibiotic-resistant bacterial strains in Bangladesh's food and farm animals stem from the excessive and inappropriate use of antibiotics. To assess the prevalence of multi-drug resistant (MDR) Gram-negative bacteria in poultry chicks, we sought to isolate and identify strains carrying antimicrobial resistance genes. Isolation and identification involved biochemical tests, 16S rRNA sequencing, and PCR screening of species-specific genes. MDR patterns were evaluated using CLSI guidelines with seventeen antibiotics across twelve classes. Targeted gene sequences were amplified for the detection of Extended-spectrum β-Lactamase (ESBL), carbapenem, tetracycline, sulfonamide, and colistin resistance genes. Common isolates, such as Escherichia coli, Klebsiella pneumoniae, Proteus penneri, and Enterobacter hormaechei, exhibited average Multiple Antimicrobial Resistance (MAR) indices of 0.66, 0.76, 0.8, 0.84, and 0.81, 0.76, 0.84, 0.41 for broiler and layer chicken, respectively. Providencia stuartii and Salmonella enterica, exclusive to broiler samples, had MAR indices of 0.82 and 0.84, respectively. Additional isolates Morganella morganii, Aeromonas spp., and Wohlfahrtiimonas chitiniclastica were found in layers (Average MAR indices: 0.73, 0.71, and 0.91). Notably, M. morganii, E. hormaechei and W. chitiniclastica were identified for the first time in Bangladeshi poultry chicken, although their evolution is yet to be understood. In this study, Pan-drug resistance was observed in one P. stuartii (broiler) and one Aeromonas spp. (layer) with a MAR index 1, while all isolates exhibited MAR indices >0.2, indicating MDR. Antimicrobial resistance (AMR) gene screening identified blaTEM, blaSHV, tetA, and sul1 in a majority of the MDR strains. Interestingly, E. coli (lactose positive and negative) and E. hormaechei were exclusively found to possess the tetB gene. In addition, E. coli (lactose negative), Klebsiella pneumoniae, Enterobacter hormaechei, M. morganii, and P. stuartii were observed to carry the colistin-resistant mcr-1 gene, whereas sul2 was detected in E. coli (lactose positive and negative), E. hormaechei, P. stuartii, and P. penneri. These findings emphasize the health risk of our consumers of both broiler and layer chickens as they have turned into a potent reservoir of various AMR gene carrying MDR and Pan-drug resistant bacteria.

E. coli Common pili promote the fitness and virulence of a hybrid aEPEC/ExPEC strain within diverse host environments

Pathogenic subsets of Escherichia coli include diarrheagenic (DEC) strains that cause disease within the gut and extraintestinal pathogenic E. coli (ExPEC) strains that are linked with urinary tract infections, bacteremia, and other infections outside of intestinal tract. Among DEC strains is an emergent pathotype known as atypical enteropathogenic E. coli (aEPEC), which can cause severe diarrhea. Recent sequencing efforts revealed that some E. coli strains possess genetic features that are characteristic of both DEC and ExPEC isolates. BA1250 is a newly reclassified hybrid strain with characteristics of aEPEC and ExPEC. This strain was isolated from a child with diarrhea, but its genetic features indicate that it might have the capacity to cause disease at extraintestinal sites. The spectrum of adhesins encoded by hybrid strains like BA1250 are expected to be especially important in facilitating colonization of diverse niches. E. coli common pilus (ECP) is an adhesin expressed by many E. coli pathogens, but how it impacts hybrid strains has not been ascertained. Here, using zebrafish larvae as surrogate hosts to model both gut colonization and extraintestinal infections, we found that ECP can act as a multi-niche colonization and virulence factor for BA1250. Furthermore, our results indicate that ECP-related changes in activation of envelope stress response pathways may alter the fitness of BA1250. Using an in silico approach, we also delineated the broader repertoire of adhesins that are encoded by BA1250, and provide evidence that the expression of at least a few of these varies in the absence of functional ECP.

Multidrug-Resistant Bacteria on Critically Ill Patients with Sepsis at Hospital Admission: Risk Factors and Effects on Hospital Mortality

Purpose

To evaluate the effect of MDRO infection on hospital mortality and the risk factors among critically ill patients with sepsis at hospital admission.

Patients and Methods

A cross-sectional study was performed between April 2019 and May 2020, followed by a cohort to evaluate hospital mortality that prospectively included all consecutive patients 18 years or older with sepsis admitted within 48 hours of hospital admission to an adult ICU in Brazil. Patients' characteristics, blood samples within one hour of ICU admission, and microbiological results within 48h of hospital admission were collected. In addition, descriptive statistics, binary logistic regression, and propensity score matching were performed.

Results

At least one MDRO was isolated in 85 patients (9.8%). The extended-spectrum beta-lactamase-producing Enterobacterales are the most frequent organism (56.1%). Hypoxemic acute respiratory failure (OR 1.87, 95% CI 1.02-3.40, p = 0.04), Glasgow Coma Score below 15 (OR 2.57, 95% CI 1.38-4.80, p < 0.01), neoplasm (OR 2.66, 95% CI 1.04-6.82, p = 0.04) and hemoglobin below 10.0 g/dL (OR 1.82, 95% CI 1.05-3.16, p = 0.03) were associated with increased MDRO. Admission from the Emergency Department (OR 0.25, 95% CI 0.14-0.43, p < 0.01) was associated with decreased MDRO. In the multivariate analysis, MDRO at hospital admission increased hospital mortality (OR 2.80, 95% CI 1.05-7.42, p = 0.04). After propensity score-matching adjusted to age, APACHE II, SOFA, and dementia, MDRO at hospital admission was associated with significantly high hospital mortality (OR 2.80, 95% CI 1.05-7.42, p = 0.04). The E-value of adjusted OR for the effect of MDRO infection on hospital mortality was 3.41, with a 95% CI of 1.31, suggesting that unmeasured confounders were unlikely to explain the entirety of the effect.

Conclusion

MDRO infection increased hospital mortality, and MDRO risk factors should be accessed even in patients admitted to ICU within 48 hours of hospital admission.

Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones

Multi-resistant pathogenic strains of non-lactose fermenting Escherichia coli (NLF E. coli) are responsible for various intestinal and extraintestinal infections. Although several studies have characterised such strains using conventional methods, they have not been comprehensively studied at the genomic level. To address this gap, we used whole-genome sequencing (WGS) coupled with detailed microbiological and biochemical testing to investigate 17 NLF E. coli from a diagnostic centre (icddr,b) in Dhaka, Bangladesh. The prevalence of NLF E. coli was 10%, of which 47% (8/17) exhibited multi-drug resistant (MDR) phenotypes. All isolates (17/17) were confirmed as E. coli and could not ferment lactose sugar. WGS data analysis revealed international high-risk clonal lineages. The most prevalent sequence types (STs) were ST131 (23%), ST1193 (18%), ST12 (18%), ST501 (12%), ST167 (6%), ST73 (6%) and ST12 (6%). Phylogenetic analysis corroborated a striking clonal population amongst the studied NLF E. coli isolates. The predominant phylogroup detected was B2 (65%). The bla CTX-M-15 extended-spectrum beta-lactamase gene was present in 53% of isolates (9/17), whilst 64.7% (11/17) isolates were affiliated with pathogenic pathotypes. All extraintestinal pathogenic E. coli pathotypes demonstrated β-hemolysis. Our study underscores the presence of critical pathogens and MDR clones amongst non-lactose fermenting E. coli. We suggest that non-lactose fermenting E. coli be considered equally capable as lactose fermenting forms in causing intestinal and extraintestinal infections. Further, there is a need to undertake systematic, unbiased monitoring of predominant lineages amongst non-lactose fermenting E. coli that would help in better treatment and prevention strategies.

Multidrug-Resistant Bacteria: Their Mechanism of Action and Prophylaxis

In the present scenario, resistance to antibiotics is one of the crucial issues related to public health. Earlier, such resistance to antibiotics was limited to nosocomial infections, but it has now become a common phenomenon. Several factors, like extensive development, overexploitation of antibiotics, excessive application of broad-spectrum drugs, and a shortage of target-oriented antimicrobial drugs, could be attributed to this condition. Nowadays, there is a rise in the occurrence of these drug-resistant pathogens due to the availability of a small number of effective antimicrobial agents. It has been estimated that if new novel drugs are not discovered or formulated, there would be no effective antibiotic available to treat these deadly resistant pathogens by 2050. For this reason, we have to look for the formulation of some new novel drugs or other options or substitutes to treat such multidrug-resistant microorganisms (MDR). The current review focuses on the evolution of the most common multidrug-resistant bacteria and discusses how these bacteria escape the effects of targeted antibiotics and become multidrug resistant. In addition, we also discuss some alternative mechanisms to prevent their infection as well.

High burden of ESBL- producing Klebsiella spp., Proteus mirabilis, Enterobacter cloacae and Pseudomonas aeruginosa in diagnosed cases of urinary tract infection in a Nigerian Teaching Hospital

Infections of the urinary tract have been on the rise globally and these are also worsened by the increasing rate of antibiotic resistance in uropathogens. This study aimed to determine the susceptibility profile of extended spectrum β-lactamase (ESBL)- producing uropathogens to selected antibiotics and their carriage of ESBL genes. Bacterial uropathogens were obtained from the urine bench of a Microbiology laboratory in a Teaching Hospital in South-West Nigeria. Susceptibility to antibiotics was tested using the disc diffusion method, while detection of ESBL production was done using the double disc synergy test (DDST). Detection of ESBL genes was performed by PCR. A total of 21 ESBL- producing uropathogens were obtained namely: Klebsiella pneumoniae (11), Klebsiella oxytoca (6), Proteus mirabilis (2), Enterobacter cloacae (1) and Pseudomonas aeruginosa (1). The resistance to antibiotics in the uropathogens was: imipenem (0%), gentamicin (38.1%), sulfamethoxazole-trimethoprim (52.4%), amoxicillin-clavulanate (61.9%), aztreonam (66.7%), ceftazidime (66.7%), tetracycline (90.5%), cefpodoxime (100%) and cefotaxime (100%). Altogether, 90.5% (19/21) of the isolates were multidrug resistant (MDR). Of the 21 uropathogens, 61.9% (13/21) carried bla CTX-M, 52.4% (11/21) carried bla TEM while bla SHV was detected in 47.6% (10/21) of the isolates. There was co-carriage of ESBL genes in 12 uropathogens. This study showed a high prevalence of multidrug resistance and a high carriage of ESBL genes in the ESBL- producing isolates obtained over the study period. There is a need for a review of antibiotic options in the treatment of UTI to clamp down on the ever-increasing tide of antibiotic resistance in uropathogens.

Genome Dynamics and Evolution of Multiple-Drug-Resistant Bacteria: Implications for Global Infection Control Priorities

Genomics-driven molecular epidemiology of pathogenic bacteria has largely been carried out through functionally neutral/inert sequences, mostly entailing polymorphic gene loci or repetitive tracts. However, it is very important to harness phenotypically relevant markers to assign a valid functional epidemiological context to tracking of pathogens. These should include microbial acumen to acquire multiple drug resistance (MDR), their physiological coordinates with reference to clinical or community-level dynamics of incidence/transmission, and their response or refractoriness to the activated immune system. We propose that multidimensional and multicentric approaches, based on diverse data integration coupled with comparative genomics and functional molecular infection epidemiology, would likely be successful in tracking the emergence and spread of MDR pathogens and thereby guiding the global infection control strategies in a highly informed manner.

International High-Risk Clones Among Extended-Spectrum β-Lactamase-Producing Escherichia coli in Dhaka, Bangladesh

Background:Escherichia coli is a major extended-spectrum β-lactamase (ESBL)–producing organism responsible for the rapid spread of antimicrobial resistance (AMR) that has compromised our ability to treat infections. Baseline data on population structure, virulence, and resistance mechanisms in E. coli lineages from developing countries such as Bangladesh are lacking.

Methods: Whole-genome sequencing was performed for 46 ESBL–E. coli isolates cultured from patient samples at the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b)-Dhaka. Sequence data were analyzed to glean details of AMR, virulence, and phylogenetic and molecular markers of E. coli lineages.

Results: Genome comparison revealed presence of all major high-risk clones including sequence type 131 (ST131) (46%), ST405 (13%), ST648 (7%), ST410 (4.3%), ST38 (2%), ST73 (2%), and ST1193 (2%). The predominant ESBL gene and plasmid combination were bla_CTX–M–15 and FII-FIA-FIB detected in diverse E. coli phylogroups and STs. The bla_NDM–5 (9%) gene was present in prominent E. coli STs. One (2%) mcr-1–positive ST1011 E. coli, coharboring bla_CTXM–55 gene, was detected. The extraintestinal pathogenic E. coli genotype was associated with specific E. coli lineages. The single nucleotide polymorphism (SNP)-based genome phylogeny largely showed correlation with phylogroups, serogroups, and fimH types. Majority of these isolates were susceptible to amikacin (93%), imipenem (93%), and nitrofurantoin (83%).

Conclusion: Our study reveals a high diversity of E. coli lineages among ESBL-producing E. coli from Dhaka. This study suggests ongoing circulation of ST131 and all major non-ST131 high-risk clones that are strongly associated with cephalosporin resistance and virulence genes. These findings warrant prospective monitoring of high-risk clones, which would otherwise worsen the AMR crises.

Virulence, Antimicrobial Resistance and Biofilm Production of Escherichia coli Isolates from Healthy Broiler Chickens in Western Algeria

The aim of this study was to assess the virulence, antimicrobial resistance and biofilm production of Escherichia coli strains isolated from healthy broiler chickens in Western Algeria. E. coli strains (n = 18) were identified by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry. Susceptibility to 10 antibiotics was determined by standard methods. Virulence and extended-spectrum β-lactamase (ESBL) genes were detected by PCR. The biofilm production was evaluated by microplate assay. All the isolates were negative for the major virulence/toxin genes tested (rfbE, fliC, eaeA, stx1), except one was stx2-positive. However, all were resistant to at least three antibiotics. Ten strains were ESBL-positive. Seven carried the β-lactamase bla_TEM gene only and two co-harbored bla_TEM and bla_CTX-M-1 genes. One carried the bla_SHV gene. Among the seven strains harboring bla_TEM only, six had putative enteroaggregative genes. Two contained irp2, two contained both irp2 and astA, one contained astA and another contained aggR, astA and irp2 genes. All isolates carrying ESBL genes were non-biofilm producers, except one weak producer. The ESBL-negative isolates were moderate biofilm producers and, among them, two harbored astA, two irp2, and one aggR, astA and irp2 genes. This study highlights the spread of antimicrobial-resistant E. coli strains from healthy broiler chickens in Western Algeria.

Molecular characterization of ESBL- producing uropathogenic Escherichia coli recovered from urine samples of patients attending a University Teaching hospital in Nigeria

Infection of the urinary tract ranks as one of the most common infections affecting people worldwide and its treatment is made complicated by the rising incidence of antibiotic resistance. This study aimed to detect extended spectrum beta-lactamase (ESBL) genes and antibiotic resistance profile of uropathogenic Escherichia coli (E. coli) recovered from patients attending a University Teaching hospital in Nigeria. Uropathogenic E. coli isolates were obtained from the culture collection of Department of Microbiology and Parasitology of the University Teaching hospital for a period of four months (October 2019-January, 2020). Antibiotic susceptibility testing was done using the disc diffusion method while phenotypic ESBL production was detected using double disc synergy test (DDST). Detection of β-lactamase genes was done using Real-Time PCR. Forty-nine E. coli isolates were recovered from 120 urine samples, with 24 (49%) being ESBL positive. The resistance to antibiotics in the ESBL producers was: ciprofloxacin (100%), cefotaxime (100%), cefpodoxime (100%), tetracycline (95.7%), ceftazidime (56.7%), amoxicillin-clavulanate (50%), gentamicin (33.3%), and imipenem (0%). All the ESBL producers carried blaTEM, blaCTX-M-1 and blaCTX-M-9, 75% (18/24) carried blaSHV, while blaCTX-M-2, blaCTX-M-8 and blaCTX-M-25 groups were detected in 20.8% (5/24) of the isolates. There was co-occurrence of CTX-M, SHV and TEM β-lactamases in 79.2% (19/24) isolates, while five isolates (20.8%) co-harbored blaCTX-M and blaTEM. This study showed a high level of multidrug resistance and ESBL gene carriage in uropathogenic E. coli obtained in this study, suggesting a likely review of therapeutic options in the treatment of UTI to clamp down on the rising cases of antibiotic resistance.

Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island

The genotoxin colibactin is a secondary metabolite produced by the polyketide synthase (pks) island harbored by extraintestinal pathogenic E. coli (ExPEC) and other members of the Enterobacteriaceae that has been increasingly reported to have critical implications in human health. The present study entails a high-throughput whole-genome comparison and phylogenetic analysis of such pathogenic E. coli isolates to gain insights into the patterns of distribution, horizontal transmission, and evolution of the island. For the current study, 23 pks-positive ExPEC genomes were newly sequenced, and their virulome and resistome profiles indicated a preponderance of virulence encoding genes and a reduced number of genes for antimicrobial resistance. In addition, 4,090 E. coli genomes from the public domain were also analyzed for large-scale screening for pks-positive genomes, out of which a total of 530 pks-positive genomes were studied to understand the subtype-based distribution pattern(s). The pks island showed a significant association with the B2 phylogroup (82.2%) and a high prevalence in sequence type 73 (ST73; n = 179) and ST95 (n = 110) and the O6:H1 (n = 110) serotype. Maximum-likelihood (ML) phylogeny of the core genome and intergenic regions (IGRs) of the ST95 model data set, which was selected because it had both pks-positive and pks-negative genomes, displayed clustering in relation to their carriage of the pks island. Prevalence patterns of genes encoding RM systems in the pks-positive and pks-negative genomes were also analyzed to determine their potential role in pks island acquisition and the maintenance capability of the genomes. Further, the maximum-likelihood phylogeny based on the core genome and pks island sequences from 247 genomes with an intact pks island demonstrated horizontal gene transfer of the island across sequence types and serotypes, with few exceptions. This study vitally contributes to understanding of the lineages and subtypes that have a higher propensity to harbor the pks island-encoded genotoxin with possible clinical implications.

Genome Informatics and Machine Learning-Based Identification of Antimicrobial Resistance-Encoding Features and Virulence Attributes in Escherichia coli Genomes Representing Globally Prevalent Lineages, Including High-Risk Clonal Complexes

Escherichia coli, a ubiquitous commensal/pathogenic member from the Enterobacteriaceae family, accounts for high infection burden, morbidity, and mortality throughout the world. With emerging multidrug resistance (MDR) on a massive scale, E. coli has been listed as one of the Global Antimicrobial Resistance and Use Surveillance System (GLASS) priority pathogens. Understanding the resistance mechanisms and underlying genomic features appears to be of utmost importance to tackle further spread of these multidrug-resistant superbugs. While a few of the globally prevalent sequence types (STs) of E. coli, such as ST131, ST69, ST405, and ST648, have been previously reported to be highly virulent and harboring MDR, there is no clarity if certain ST lineages have a greater propensity to acquire MDR. In this study, large-scale comparative genomics of a total of 5,653 E. coli genomes from 19 ST lineages revealed ST-wide prevalence patterns of genomic features, such as antimicrobial resistance (AMR)-encoding genes/mutations, virulence genes, integrons, and transposons. Interpretation of the importance of these features using a Random Forest Classifier trained with 11,988 genomic features from whole-genome sequence data identified ST-specific or phylogroup-specific signature proteins mostly belonging to different protein superfamilies, including the toxin-antitoxin systems. Our study provides a comprehensive understanding of a myriad of genomic features, ST-specific proteins, and resistance mechanisms entailing different lineages of E. coli at the level of genomes; this could be of significant downstream importance in understanding the mechanisms of AMR, in clinical discovery, in epidemiology, and in devising control strategies. IMPORTANCE With the leap in whole-genome data being generated, the application of relevant methods to mine biologically significant information from microbial genomes is of utmost importance to public health genomics. Machine-learning methods have been used not only to mine, curate, or classify the data but also to identify the relevant features that could be linked to a particular class/target. This is perhaps one of the pioneering studies that has attempted to classify a large repertoire of E. coli genome data sets (5,653 genomes) belonging to 19 different STs (including well-studied as well as understudied STs) using machine learning approaches. Important features identified by these approaches have revealed ST-specific signature proteins, which could be further studied to predict possible associations with the phenotypic profiles, thereby providing a better understanding of virulence and the resistance mechanisms among different clonal lineages of E. coli.

High Prevalence of blaCTX-M-15 Gene among Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Causing Extraintestinal Infections in Bangladesh

The emergence of multidrug-resistant (MDR) Escherichia coli (E. coli) clonal lineages with high virulence potential is alarming. Lack of sufficient data on molecular epidemiology of such pathogens from countries with high infection burden, such as Bangladesh, hinders management and infection control measures. In this study, we assessed the population structure, virulence potential and antimicrobial susceptibility of clinical E. coli isolates from Dhaka, Bangladesh. A high prevalence of MDR (69%) and extended-spectrum β-lactamase production (ESBL) (51%) was found. Most E. coli isolates were susceptible to amikacin (95%), meropenem (94%) and nitrofurantoin (89%) antibiotics. A high prevalence of ST131 (22%) and ST95 (9%) followed by ST69 (4%) and ST73 (3%) was observed. Phylogroups B2 (46%), B1 (16%), D (10%) and F (9%) were prominent. bla_CTX-M-15 (52%) and bla_NDM-1 (5%) were the most prevalent ESBL and carbapenem resistance genes, respectively. Moreover, the predominant pathotype identified was extraintestinal pathogenic E. coli (ExPEC) (41%) followed by enteric pathogens (11%). In conclusion, our results suggest the transmission of clonal E. coli groups amidst diverse E. coli population that are associated with high virulence potential and MDR phenotype. This is of high concern and mandates more efforts towards molecular surveillance of antimicrobial resistance (AMR) in clinically significant pathogens.

Multidrug-Resistant Bacteria in the Community: An Update

Multidrug-resistant bacteria are among the most important current threats to public health. Typically, they are associated with nosocomial infections. However, some have become prevalent causes of community-acquired infections, such as Neisseria gonorrhoeae, Shigella, Salmonella, and Streptococcus pneumoniae. The community spread of multidrug-resistant bacteria is also a crucial development. An important global threat on the horizon is represented by production of carbapenemases by community-acquired hypervirulent Klebsiella pneumoniae. Such strains have already been found in Asia, Europe, and North America. Prevention of further community spread of multidrug-resistant bacteria is of the utmost importance, and will require a multidisciplinary approach involving all stakeholders.

In-vitro Investigation of Antibiotics Efficacy Against Uropathogenic Escherichia coli Biofilms and Antibiotic Induced Biofilm Formation at Sub-Minimum Inhibitory Concentration of Ciprofloxacin

BACKGROUND

Community-acquired urinary tract infections are associated with significant morbidity, and uropathogenic Escherichia coli (UPEC) alone causes 90% of urinary tract infections. This bacterium retains a diverse armament of virulence factors including fimbria, hemolysins, and siderophores production. In a post invasion scenario, formation of intracellular communities mimic biofilm-like characteristics and are linked to recurrent urinary tract infections. We investigated the effects of different frontline antibiotics on the formation, inhibition, and eradication of biofilms of virulent UPEC strains.

MATERIALS AND METHODS

A total of 155 UPEC strains were scrutinized for various virulence factors including gelatinase, cell surface hydrophobicity, hemagglutination, and serum bactericidal activity. Biofilm formation was confirmed by three different methods: Congo red agar, test tube, and tissue culture plate method. Biofilm inhibition and eradication assays were performed according to the standard protocols. Topographical analysis of biofilms was done by scanning electronic microscopy (SEM).

RESULTS

Out of 155 strains, 113 (73%) were strong biofilm formesr, while 37 (24%) produced biofilms at moderate level. Significant differences were observed between MICs of planktonic cells (MIC-p) and MICs of UPEC biofilms (MIC-b). Among tested frontline antibiotics, levofloxacin successfully inhibited biofilms at a concentration of 32 µg/mL, while trimethoprim eradicated biofilms at higher concentrations (512-1024 µg/mL). Ciprofloxacin treatment at sub-MIC level significantly enhanced biofilm formation (P<0.05).

CONCLUSION

The majority of UPEC strains are strong biofilm formers and show higher tolerance towards frontline antibiotics in biofilm form. We observed significant inhibitory effects of levofloxacin (32 µg/mL) on UPEC biofilms, while treatment with sub-minimal concentrations of ciprofloxacin significantly enhanced biofilm formation. Out of all tested antibiotics, trimethoprim (512-1024 µg/mL) eradicated UPEC biofilms.

Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli

The rising rates of antibiotic resistance increasingly compromise empirical treatment. Knowing the antibiotic susceptibility of a pathogen's close genetic relative(s) may improve empirical antibiotic selection. Using genomic and phenotypic data for Escherichia coli isolates from three separate clinically derived databases, we evaluated multiple genomic methods and statistical models for predicting antibiotic susceptibility, focusing on potentially rapidly available information, such as lineage or genetic distance from archived isolates. We applied these methods to derive and validate the prediction of antibiotic susceptibility to common antibiotics. We evaluated 968 separate episodes of suspected and confirmed infection with Escherichia coli from three geographically and temporally separated databases in Ontario, Canada, from 2010 to 2018. Across all approaches, model performance (area under the curve [AUC]) ranges for predicting antibiotic susceptibility were the greatest for ciprofloxacin (AUC, 0.76 to 0.97) and the lowest for trimethoprim-sulfamethoxazole (AUC, 0.51 to 0.80). When a model predicted that an isolate was susceptible, the resulting (posttest) probabilities of susceptibility were sufficient to warrant empirical therapy for most antibiotics (mean, 92%). An approach combining multiple models could permit the use of narrower-spectrum oral agents in 2 out of every 3 patients while maintaining high treatment adequacy (∼90%). Methods based on genetic relatedness to archived samples of E. coli could be used to predict antibiotic resistance and improve antibiotic selection.

Genome-Based Analysis of Extended-Spectrum β-Lactamase-Producing Escherichia coli in the Aquatic Environment and Nile Perch (Lates niloticus) of Lake Victoria, Tanzania

Extended-spectrum β-lactamase (ESBL)-producing bacteria constitute an emerging global health issue with food products being vehicles of transmission and the aquatic environments serving as potential reservoirs. This study aimed to characterize ESBL-producing Escherichia coli in Nile perch and water from Lake Victoria in Tanzania. A total of 180 samples of Nile perch and 60 water samples were screened for ESBL-producing E. coli on MacConkey agar supplemented with 2 μg/ml of cefotaxime and confirmed by bla_CTX–M and bla_TEM PCR. Antimicrobial resistance was determined by the disk diffusion method, and the ESBL-producing isolates were whole genome sequencing (WGS). ESBL-producing E. coli were detected in eight of the 180 analyzed Nile perch samples, and only one water sample was positive (1.7%, n = 60). Isolates were resistant to sulfamethoxazole–trimethoprim (100%), ampicillin/cloxacillin (100%), erythromycin 72.7% (8/11), tetracycline 90.9% (10/11), and nalidixic acid 63.6% (7/11). This mostly corroborates the resistance genes that they carried for sulfonamides (sul1 and sul2), trimethoprim (dfrA and dfrB), aminoglycosides [aac(3)-IId, strA, and strB], tetracycline [tet(B) and tet(D)], and fluoroquinolones (qepA4). They harbored plasmid replicon types IncF, IncX, IncQ, and Col and carried bla_CTX–M–15 and bla_TEM–1B genes generally found on the same contigs as the IncF plasmid replicon. Although epidemiologically unrelated, the strains formed three separate sequence type–phylogroup–serotype-specific clusters: C1, C2, and C3. Cluster C1 included five strains (3 to 13 SNPs) belonging to ST167, phylogroup A, and serotype O9:H21; the two C2 strains (11 SNPs) belong to ST156, phylogroup B1, and serotype ONT:H28; and C3 was made up of four strains (SNPs ranged from 4 to 17) of ST636, phylogroup B2, and serotype O45:H7. The common virulence gene gad was reported in all strains. In addition, strains in C2 and C3 possessed iss, lpfA, and nfaE virulence genes, and the vat gene was found only in C3. The present study reports the occurrence of multidrug-resistant ESBL-producing E. coli carrying plasmid-mediated ESBL genes in offshore water and Nile perch in Lake Victoria. Strains formed three clonal clusters of unknown origin. This study reveals that the Lake may serve as reservoir for ESBL-producing bacteria that can be transmitted by fish as a food chain hazard of One-Health concern.

Genomic and Functional Characterization of Poultry Escherichia coli From India Revealed Diverse Extended-Spectrum β-Lactamase-Producing Lineages With Shared Virulence Profiles

Extended-spectrum β-lactamases (ESBLs) form the most important resistance determinants prevalent worldwide. Data on ESBL-producing Escherichia coli from poultry and livestock are scarce in India. We present data on the functional and genomic characterization of ESBL-producing E. coli obtained from poultry in India. The whole genome sequences of 28 ESBL-producing E. coli were analyzed comprising of 12 broiler chicken E. coli isolates, 11 free-range chicken E. coli isolates, and 5 human extraintestinal pathogenic E. coli. All of the 28 ESBL-producing E. coli isolates were tested for antibiotic susceptibilities, in vitro conjugation, and virulence-associated phenotypic characteristics. A total of 13 sequence types were identified from the poultry E. coli, which included globally successful sequence types such as ST117 (9%), ST131 (4.3%), and ST10 (4.3%). The most common ESBL gene detected in poultry E. coli genomes was bla_CTX-M-15 (17%). Also, FIB (73%) and FII (73%) were the most common plasmid replicons identified. Conjugation experiments demonstrated 54 (7/13), 30 (3/10), and 40% (2/5) of broiler, free-range, and human ExPEC E. coli to be able to transfer their ESBL genes, respectively. The in vitro virulence-associated phenotypic tests revealed the broiler, free-range, and human ExPEC isolates to be comparable in biofilm formation, resistance to serum bactericidal activity, adherence, and invasion capabilities. Our overall results showed prevalence of virulence phenotypes among the diverse ESBL-producing E. coli from poultry; while certain E. coli clones from broiler-poultry may indeed have the potential to cause infection in humans.

Characterization of a NDM-1- Encoding Plasmid pHFK418-NDM From a Clinical Proteus mirabilis Isolate Harboring Two Novel Transposons, Tn6624 and Tn6625

Acquisition of the bla_NDM–1 gene by Proteus mirabilis is a concern because it already has intrinsic resistance to polymyxin E and tigecycline antibiotics. Here, we describe a P. mirabilis isolate that carries a pPrY2001-like plasmid (pHFK418-NDM) containing a bla_NDM–1 gene. The pPrY2001-like plasmid, pHFK418-NDM, was first reported in China. The pHFK418-NDM plasmid was sequenced using a hybrid approach based on Illumina and MinION platforms. The sequence of pHFK418-NDM was compared with those of the six other pPrY2001-like plasmids deposited in GenBank. We found that the multidrug-resistance encoding region of pHFK418-NDM contains ΔTn10 and a novel transposon Tn6625. Tn6625 consists of ΔTn1696, Tn6260, In251, ΔTn125 (carrying bla_NDM–1), ΔTn2670, and a novel mph(E)-harboring transposon Tn6624. In251 was first identified in a clinical isolate, suggesting that it has been transferred efficiently from environmental organisms to clinical isolates. Genomic comparisons of all these pPrY2001-like plasmids showed that their relatively conserved backbones could integrate the numerous and various accessory modules carrying multifarious antibiotic resistance genes. Our results provide a greater depth of insight into the horizontal transfer of resistance genes and add interpretive value to the genomic diversity and evolution of pPrY2001-like plasmids.

The increasing threat of silver-resistance in clinical isolates from wounds and burns

Purpose

The widespread use of silver-containing compounds has led to emergence of silver-resistant bacteria. Few studies are available on the detectability of plasmid-mediated silver-resistance in developing countries. Therefore, we aimed to detect silver-resistance in isolates from wounds and burns, and to genetically characterize plasmid-mediated silver-resistance genes (sil genes).

Methods

One hundred and fifty clinical isolates were obtained from burns and wounds. They were identified using the suitable Analytical Profile Index and MicroScan identification systems. Their antimicrobial susceptibility was tested by the disk diffusion and broth microdilution methods. Their silver nitrate (AgNO₃) minimum inhibitory concentration (MIC) was determined using the broth macrodilution method. The presence of different sil genes on plasmids extracted from silver-resistant isolates and the replicon types of the extracted plasmids were investigated using polymerase chain reaction (PCR). The ability of these plasmids to impart silver-resistance was tested by transformation.

Results

All except two isolates were multidrug-resistant. Nineteen silver-resistant bacterial isolates (12.6%) were detected; with AgNO₃ MIC ≥512 µg/mL. They were identified as Klebsiella pneumoniae (n=7), Staphylococcus aureus (n=4), Escherichia coli (n=2), Enterobacter cloacae (n=2), Pseudomonas aeruginosa (n=2) and Acinetobacter baumannii (n=2). PCR revealed the presence of different sil genes on the extracted plasmids. Plasmid transformation resulted in the transfer of silver-resistance to the resulting transformants. The extracted plasmids had different replicon types.

Conclusion

Plasmid-mediated silver-resistance was detected for the first time, in clinical P. aeruginosa, A. baumannii and S. aureus isolates; in addition to its detection in K. pneumoniae, E. coli and Enterobacter cloacae. Therefore, strict monitoring on the use of silver compounds in medical settings is required; with implementation of an approved standardized method for silver-resistance detection.

CTX-M ESBL-producing Enterobacteriaceae: estimated prevalence in adults in England in 2014

Background

ESBL-producing Enterobacteriaceae (ESBLPE) are increasing in prevalence worldwide and are more difficult to treat than non-ESBLPE. Their prevalence in the UK general population is unknown, as the only previous UK ESBLPE faecal colonization study involved patients with diarrhoea.

Objectives

To estimate the prevalence of CTX-M ESBLPE faecal colonization in the general adult population of England in 2014, and investigate risk factors.

Methods

A stratified random sample of 58 337 registered patients from 16 general practices within four areas of England were invited to participate by returning faeces specimens and self-completed questionnaires. Specimens were tested for ESBLPE and carbapenemase-producing Enterobacteriaceae (CPE).

Results

2430 individuals participated (4% of those invited). The estimated prevalence of colonization with CTX-M ESBLPE in England was 7.3% (95% CI 5.6%–9.4%) (Shropshire 774 participants, 4.9% colonization; Southampton City 740 participants, 9.2%; Newham 612 participants, 12.7%; Heart of Birmingham 234 individuals, 16.0%) and was particularly high in: those born in Afghanistan (10 participants, 60.0% colonization, 95% CI 29.7%–84.2%); those born on the Indian subcontinent (India, Pakistan, Bangladesh or Sri Lanka) (259 participants, 25.0% colonization, 95% CI 18.5%–32.9%); travellers to South Asia (India, Pakistan, Bangladesh, Sri Lanka or Nepal) in the last year (140 participants, 38.5% colonization, 95% CI 27.8%–50.5%); and healthcare domestics (8 participants, unweighted 37.5% colonization, 95% CI 8.5%–75.5%). Risk factors identified included: being born in the Indian subcontinent (aOR 5.4, 95% CI 3.0–9.7); travel to South Asia (aOR 2.9, 95% CI 1.8–4.8) or to Africa, China, South or Central America, South East or Pacific Asia or Afghanistan (aOR 2.6, 95% CI 1.7–4.1) in the last year; and working as a healthcare domestic (aOR 6.2, 95% CI 1.3–31). None of the 48 participants who took co-amoxiclav in the last year was colonized with CTX-M ESBLPE. bla_CTX-M-15 accounted for 66% of CTX-M ESBLPE positives. 0.1% (two participants) were colonized with CPE.

Conclusions

CTX-M ESBLPE are established in the general population in England and prevalence is particularly high in people from certain countries of birth or with recent travel. We recommend that these findings be taken into account in guidance on the empirical management of patients presenting with a likely Enterobacteriaceae infection.

Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages

Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a majority of human extraintestinal infections globally, resulting in enormous direct medical and social costs. ExPEC strains are comprised of many lineages, but only a subset is responsible for the vast majority of infections. Few systematic surveillance systems exist for ExPEC. To address this gap, we systematically reviewed and meta-analyzed 217 studies (1995 to 2018) that performed multilocus sequence typing or whole-genome sequencing to genotype E. coli recovered from extraintestinal infections or the gut. Twenty major ExPEC sequence types (STs) accounted for 85% of E. coli isolates from the included studies. ST131 was the most common ST from 2000 onwards, covering all geographic regions. Antimicrobial resistance-based isolate study inclusion criteria likely led to an overestimation and underestimation of some lineages. European and North American studies showed similar distributions of ExPEC STs, but Asian and African studies diverged. Epidemiology and population dynamics of ExPEC are complex; summary proportion for some STs varied over time (e.g., ST95), while other STs were constant (e.g., ST10). Persistence, adaptation, and predominance in the intestinal reservoir may drive ExPEC success. Systematic, unbiased tracking of predominant ExPEC lineages will direct research toward better treatment and prevention strategies for extraintestinal infections.

Association Between Kinetics of Early Biofilm Formation and Clonal Lineage in Escherichia coli

Background

Escherichia coli biofilm formation has mostly been assessed in specific pathogenic E. coli groups. Here, we assessed the early biofilm formation (EBF), i.e., adhesion stage, using the BioFilm Ring Test^® on 394 E. coli clinical isolates (EC) [196 consecutively isolated (CEC) in 2016 and 198 ESBL-producing E. coli (ESBLEC) isolated in 2015]. Then, biofilm-forming ability was contrasted with phylogroups, clonotypes (fumC-fimH), and sequence types (STs), all being used to define clones, virulence factors (VF), and FimB.

Result

According to both biofilm production levels at 2, 3, and 5 h, and EBF kinetics over 5 h, CEC and ESBLEC isolates segregated into three EBF groups: strong (G1), moderate (G2), and weak (G3) producers. At 2 h, strong producers were more frequent among CEC (n = 28; 14.3%) than among ESBLEC (n = 8; 4%) (P = 0.0004). As CEC and ESBLEC isolates showed similar individual EBF kinetics in each group, a comparison of isolate features between each group was applied to gathered CEC and ESBLEC isolates after 2 h of incubation, 2 h being the most representative time point of the CEC and ESBLEC isolate segregation into the three groups. Phylogroup B2 displayed by 51.3% of the 394 isolates was more frequent in G1 (77.8%) than in G3 (47.6%) (P = 0.0006). The 394 isolates displayed 153 clones, of which 31 included at least three isolates. B2-CH14-2-ST127, B2-CH40-22-ST131, B2-CH52-5/14-ST141, and E-CH100-96-ST362 clones were associated with G1 (P < 0.03) and accounted for 41.7% of G1 isolates. B2-CH40-30-ST131 clone was associated with G3 (P < 0.0001) and accounted for 25.5% of G3 isolates. VF mean was higher among G1 than among G3 isolates (P < 0.001). FimB-P2 variant was associated with G1 (P = 0.0011) and FimB-P1 variant was associated with G3 (P = 0.0023). Clone, some VF, and FimB were associated with EBF, with clonal lineage being able to explain 72% of the variability of EBF.

Conclusion

Among our 394 isolates, <10% are able to quickly and persistently produce high biofilm levels over 5 h. These isolates belong to a few clones previously described in various studies as dominant gut colonizers in mammalians and birds and comprised the B2-CH40-22-ST131 clone, i.e., the ancestor of the globally disseminated B2-CH40-30-ST131 clone that is the dominant clone among the weak biofilm producers.

Clonal diversity, virulence genes content and subclone status of Escherichia coli sequence type 131: comparative analysis of E. coli ST131 and non-ST131 isolates from Iran

BACKGROUND

The Escherichia coli sequence type 131 (ST131) is a well established clone causing significant extraintestinal infections worldwide. However, no studies have been reported the phenotypic and molecular traits of ST131 isolates in comparison to other clones of E. coli from Iran. So, we determined the differences between 69 ST131 strains collected during a one year surveillance study and 84 non-ST131 isolates, including 56 clinical fluoroquinolone resistant and 28 broiler colibacillosis isolates in terms of clonality and genetic background.

RESULTS

ST131 isolates were associated with phylogroup B2 (68 out of 69 isolates, 98.4%), while clinical non-ST131 and fluoroquinolone resistant broiler isolates mainly belonged to phylogroup A. The highest virulence score was observed in ST131 clone, while they showed less diversity in virulence profiles than other clinical isolates. Almost all of the ST131 isolates (95.6%) were ExPEC and had the highest virulence scores, but their resistance scores were less than clinical non-ST131 isolates. Broiler isolates showed higher prevalence of ExPEC-associated virulence genes and CTX-M-G1/G9 resistance determinants as compared to clinical non-ST131 isolates. While bla_OXA-48/NDM carbapenemases were mostly found in ST131 clone, resistance rate against ertapenem was higher among clinical non-ST131 strains. According to ERIC-based fingerprinting, the ST131 strains were more genetically similar, followed by non-ST131 and broiler isolates.

CONCLUSIONS

ST131 isolates possess the ability to make a balance between clonality and extent of resistance/virulence genes content, so this phenomenon gives a fitness advantage over other E. coli clones. The broilers E. coli population poses a potential zoonotic risk which could be transmitted to the community through the food chain. A number of factors are involved in the dissemination of and infections due to ST131 clone.

Bloodstream infection with extended-spectrum beta-lactamase-producing Escherichia coli: The role of virulence genes

BACKGROUND

Extraintestinal pathogenic Escherichia coli (ExPEC) strains hold the responsibility for the majority of E. coli infections. Numerous extraintestinal virulence factors (VFs) were possessed by ExPEC which are involved in the pathogenesis of infection. However, the effect of comorbidities or infection syndrome in the association of VFs and mortality remains inconclusive.

METHOD

This study addressed whether specific sequence type (ST) and VFs of extended-spectrum beta-lactamase-producing E. coli (ESBL-EC) are associated with different outcomes in patients with bloodstream infection. 121 adults from southern Taiwan with ESBL-EC bloodstream infections were enrolled during a 6-year period. Demographic data, including infection syndromes, underlying disease and outcomes, were collected. The virulence factors in isolates were analyzed by PCR and multilocus sequence typing analyses were also performed.

RESULT

Positivity for the virulence genes iha, hlyD, sat, iutA, fyuA, malX, ompT, and traT was associated with ST131 positivity (P < 0.05). Some ESBL-EC virulence genes associated with urinary tract infection (UTI) were revealed. Positivity for ST405 and the virulence genes iroN and iss were significantly associated with increased 30-day mortality (death within 30 days) on univariate analysis (P < 0.05). Independent risk factors of 30-day mortality in bacteremic patients with UTI included underlying chronic liver disease and malignancy. ST131 was borderline associated with 30-day mortality. Independent risk factors associated with 30-day mortality among bacteremic patients without UTI included comorbidities and iroN positivity.

CONCLUSION

In bacteremic patients with UTI, and the ST131 clone was borderline associated with mortality. Positivity for the virulence gene iroN may be linked to mortality in bacteremic patients without UTI.

The role of wildlife (wild birds) in the global transmission of antimicrobial resistance genes

Antimicrobial resistance is an urgent global health challenge in human and veterinary medicine. Wild animals are not directly exposed to clinically relevant antibiotics; however, antibacterial resistance in wild animals has been increasingly reported worldwide in parallel to the situation in human and veterinary medicine. This underlies the complexity of bacterial resistance in wild animals and the possible interspecies transmission between humans, domestic animals, the environment, and wildlife. This review summarizes the current data on expanded-spectrum β-lactamase (ESBL), AmpC β-lactamase, carbapenemase, and colistin resistance genes in Enterobacteriaceae isolates of wildlife origin. The aim of this review is to better understand the important role of wild animals as reservoirs and vectors in the global dissemination of crucial clinical antibacterial resistance. In this regard, continued surveillance is urgently needed worldwide.

Peptidyl-prolyl isomerase-B is involved in Mycobacterium tuberculosis biofilm formation and a generic target for drug repurposing-based intervention

Tuberculosis (TB), a disease caused by Mycobacterium tuberculosis (M.tb), takes one human life every 15 s globally. Disease relapse occurs due to incomplete clearance of the pathogen and reactivation of the antibiotic tolerant bacilli. M.tb, like other bacterial pathogens, creates an ecosystem of biofilm formed by several proteins including the cyclophilins. We show that the M.tb cyclophilin peptidyl-prolyl isomerase (PpiB), an essential gene, is involved in biofilm formation and tolerance to anti-mycobacterial drugs. We predicted interaction between PpiB and US FDA approved drugs (cyclosporine-A and acarbose) by in-silico docking studies and this was confirmed by surface plasmon resonance (SPR) spectroscopy. While all these drugs inhibited growth of Mycobacterium smegmatis (M.smegmatis) when cultured in vitro, acarbose and cyclosporine-A showed bacteriostatic effect while gallium nanoparticle (GaNP) exhibited bactericidal effect. Cyclosporine-A and GaNP additionally disrupted M.tb H₃₇Rv biofilm formation. Co-culturing M.tb in their presence resulted in significant (2–4 fold) decrease in dosage of anti-tubercular drugs- isoniazid and ethambutol. Comparison of the cyclosporine-A and acarbose binding sites in PpiB homologues of other biofilm forming infectious pathogens revealed that these have largely remained unaltered across bacterial species. Targeting bacterial biofilms could be a generic strategy for intervention against bacterial pathogens.

Tuberculosis, caused by Mycobacterium tuberculosis, is the leading cause of death due to a single infectious agent. New therapeutic options are needed, and repurposing clinically approved drugs to destroy biofilms is an attractive approach, as these microbial communities are often less susceptible to antibiotics. A team lead by Seyed Hasnain at the Indian Institute of Technology Delhi identified an enzyme, PpiB, from M. tuberculosis that promoted biofilm formation and showed that PpiB interacts with several drugs that are currently used to treat diabetes, immunological diseases and cancer. These drugs destabilise M. tuberculosis biofilms in culture and enhanced the potency of two current anti-tuberculosis antibiotics. Future work is needed to test these medications against tuberculosis in humans, but given PpiB is found in different bacteria, there may be broader promise of using these repurposed drugs to combat other infections.

Clinical Impact of Sequence Type 131 in Adults with Community-Onset Monomicrobial Escherichia Coli Bacteremia

Background: The clinical impact of ST (sequence type) 131 in adults with community-onset Escherichia coli bacteremia remains controversial. Methods: Clinical data of 843 adults presenting with community-onset monomicrobial E. coli bacteremia at a medical center between 2008 and 2013 were collected. E. coli isolates were genotyped by a multiplex polymerase chain reaction to detect ST131 and non-ST131 clones. Results: Of 843 isolates from 843 patients with a mean age of 69 years, there were 102 (12.1%) isolates of ST131. The ST131 clone was more likely to be found in the elderly (76.5% vs. 64.0%; p = 0.01) and in nursing-home residents (12.7% vs. 3.8%; p < 0.001) than non-ST131 clones. Furthermore, the ST131 clone was associated with a longer time to appropriate antibiotic therapy (2.6 vs. 0.8 days; p = 0.004) and a higher 28-day mortality rate (14.7% vs. 6.5%, p = 0.003). In the Cox regression analysis with an adjustment of independent predictors, the ST131 clone exhibited a significant adverse impact on 28-day mortality (adjusted odds ratio (aOR), 2.18; p = 0.02). The different impact of the ST131 clone on 28-day mortality was disclosed in the non-ESBL (aOR 1.27; p = 0.70) and ESBL (aOR 10.19; p = 0.048) subgroups. Conclusions: Among adults with community-onset E. coli bacteremia, the ST131 clone was associated with higher 28-day mortality, particularly in those infected by ESBL producers.

Molecular Genetic and Functional Analysis of pks-Harboring, Extra-Intestinal Pathogenic Escherichia coli From India

Colibactin, a genotoxin, encoded by the pks pathogenicity island of Escherichia coli belonging to the B2 phylogroup has been reported as a determinant of bacterial pathogenicity. The present study was carried out to detect the pks pathogenicity island in extraintestinal pathogenic E. coli (ExPEC) isolated from a tertiary hospital in Pune, India. Of 462 isolates analyzed, the pks genomic island was detected in 35 (7.6%) isolates, which predominantly belonged to pathogenic phylogroup B2 (97%), and harbored virulence genes such as fimH, sfaD/E, and usp. Biofilm formation assay revealed 21 of the 35 pks-carrying isolates to be strong (SBF > 1.0), 10 isolates to be moderate (SBF = 0.5–1.0), and 4 as weak (SBF < 0.5) biofilm formers. All of the pks-carrying isolates proved resistant against bactericidal activity of human serum. Assays carried out to detect antimicrobial susceptibility revealed 11% of these isolates to be multidrug resistant, 37% producing ESBL and 25% were positive for bla_CTX-M-15. The observed prevalence of multidrug resistance and colibactin producing characteristics among pathogenic E. coli belonging to phylogenetic group B2 advocate urgent need for broader surveillance in order to understand and prevent transmission of these ExPEC in community and hospital settings.

Antimicrobial resistance in Enterobacteriaceae from healthy broilers in Egypt: emergence of colistin-resistant and extended-spectrum β-lactamase-producing Escherichia coli

Background

Poultry remains one of the most important reservoir for zoonotic multidrug resistant pathogens. The global rise of antimicrobial resistance in Gram-negative bacteria is of reasonable concern and demands intensified surveillance.

Methods

In 2016, 576 cloacal swabs were collected from 48 broiler farms located in five governorates in northern Egypt. Isolates of Enterobacteriaceae could be cultivated on different media and were identified by MALDI-TOF MS and PCR. Escherichia coli isolates were genotyped by DNA-microarray-based assays. The antimicrobial susceptibility to 14 antibiotics was determined and resistance-associated genes were detected. The VITEK-2 system was applied for phenotypical confirmation of extended-spectrum β-lactamase-producing isolates. The determination of colistin resistance was carried out phenotypically using E-test and genotypically using PCR for detection of the mcr-1 gene.

Results

Out of 576 samples, 72 representatives of Enterobacteriaceae were isolated and identified as 63 E. coli (87.5%), 5 Enterobacter cloacae (6.9%), 2 Klebsiella pneumoniae (2.8%) and 2 Citrobacter spp. (2.8%). Seven out of 56 cultivated E. coli (12.5%) were confirmed as ESBL-producing E. coli and one isolate (1.8%) as ESBL/carbapenemase-producing E. coli. Five out of 63 E. coli isolates (7.9%) recovered from different poultry flocks were phenotypically resistant to colistin and harboured mcr-1 gene.

Conclusions

This is the first study reporting colistin resistance and emergence of multidrug resistance in Enterobacteriaceae isolated from healthy broilers in the Nile Delta region, Egypt. Colistin-resistant E. coli in poultry is of public health significance. The global rise of ESBL- and carbapenemase-producing Gram-negative bacteria demands intensified surveillance. ESBL-producing E. coli in poultry farms in Egypt are of major concern that emphasizes the possibility of spread of such strains to humans. The results also reinforce the need to develop strategies and to implement specific control procedures to reduce the use of antibiotics.

Risk of Transmission of Antimicrobial Resistant Escherichia coli from Commercial Broiler and Free-Range Retail Chicken in India

Multidrug-resistant Escherichia coli infections are a growing public health concern. This study analyzed the possibility of contamination of commercial poultry meat (broiler and free-range) with pathogenic and or multi-resistant E. coli in retail chain poultry meat markets in India. We analyzed 168 E. coli isolates from broiler and free-range retail poultry (meat/ceca) sampled over a wide geographical area, for their antimicrobial sensitivity, phylogenetic groupings, virulence determinants, extended-spectrum-β-lactamase (ESBL) genotypes, fingerprinting by Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR and genetic relatedness to human pathogenic E. coli using whole genome sequencing (WGS). The prevalence rates of ESBL producing E. coli among broiler chicken were: meat 46%; ceca 40%. Whereas, those for free range chicken were: meat 15%; ceca 30%. E. coli from broiler and free-range chicken exhibited varied prevalence rates for multi-drug resistance (meat 68%; ceca 64% and meat 8%; ceca 26%, respectively) and extraintestinal pathogenic E. coli (ExPEC) contamination (5 and 0%, respectively). WGS analysis confirmed two globally emergent human pathogenic lineages of E. coli, namely the ST131 (H30-Rx subclone) and ST117 among our poultry E. coli isolates. These results suggest that commercial poultry meat is not only an indirect public health risk by being a possible carrier of non-pathogenic multi-drug resistant (MDR)-E. coli, but could as well be the carrier of human E. coli pathotypes. Further, the free-range chicken appears to carry low risk of contamination with antimicrobial resistant and extraintestinal pathogenic E. coli (ExPEC). Overall, these observations reinforce the understanding that poultry meat in the retail chain could possibly be contaminated by MDR and/or pathogenic E. coli.

Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting

Objectives

Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi.

Methods

Ninety-four E. coli isolates from patients admitted to Queen's Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics.

Results

Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was bla CTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates].

Conclusions

This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance.

Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages

Escherichia coli sequence type 131 (ST131), a pandemic clone responsible for the high incidence of extraintestinal pathogenic E. coli (ExPEC) infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL)-producing E. coli clones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131 E. coli strains with 40 genomes from three other STs, including ST38 (n = 12), ST405 (n = 10), and ST648 (n = 18), and functional studies were performed on five in-house strains corresponding to the four STs. Phylogenomic analysis results from this study corroborated with the sequence type-specific clonality. Results from the genome-wide resistance profiling confirmed that all strains were inherently multidrug resistant. ST131 genomes showed unique virulence profiles, and analysis of mobile genetic elements and their associated methyltransferases (MTases) has revealed that several of them were missing from the majority of the non-ST131 strains. Despite the fact that non-ST131 strains lacked few essential genes belonging to the serum resistome, the in-house strains representing all four STs demonstrated similar resistance levels to serum antibactericidal activity. Core genome analysis data revealed that non-ST131 strains usually lacked several ST131-defined genomic coordinates, and a significant number of genes were missing from the core of the ST131 genomes. Data from this study reinforce adaptive diversification of E. coli strains belonging to the ST131 lineage and provide new insights into the molecular mechanisms underlying clonal diversification of the ST131 lineage.

E. coli, particularly the ST131 extraintestinal pathogenic E. coli (ExPEC) lineage, is an important cause of community- and hospital-acquired infections, such as urinary tract infections, surgical site infections, bloodstream infections, and sepsis. The treatment of infections caused by ExPEC has become very challenging due to the emergence of resistance to the first-line as well as the last-resort antibiotics. This study analyzes E. coli ST131 against three other important and globally distributed ExPEC lineages (ST38, ST405, and ST648) that also produced extended-spectrum β-lactamase (ESBL). This is perhaps the first study that employs the high-throughput whole-genome sequence-based approach to compare and study the genomic features of these four ExPEC lineages in relation to their functional properties. Findings from this study highlight the differences in the genomic coordinates of ST131 with respect to the other STs considered here. Results from this comparative genomics study can help in advancing the understanding of ST131 evolution and also offer a framework towards future developments in pathogen identification and targeted therapeutics to prevent diseases caused by this pandemic E. coli ST131 clone.

Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand

BACKGROUND

Tackling multidrug-resistant Escherichia coli requires evidence from One Health studies that capture numerous potential reservoirs in circumscribed geographic areas.

METHODS

We conducted a survey of extended β-lactamase (ESBL)-producing E. coli isolated from patients, canals and livestock wastewater in eastern Thailand between 2014 and 2015, and analyzed isolates using whole genome sequencing.

RESULTS

The bacterial collection of 149 isolates consisted of 84 isolates from a single hospital and 65 from the hospital sewer, canals and farm wastewater within a 20 km radius. E. coli ST131 predominated the clinical collection (28.6%), but was uncommon in the environment. Genome-based comparison of E. coli from infected patients and their immediate environment indicated low genetic similarity overall between the two, although three clinical-environmental isolate pairs differed by ≤ 5 single nucleotide polymorphisms. Thai E. coli isolates were dispersed throughout a phylogenetic tree containing a global E. coli collection. All Thai ESBL-positive E. coli isolates were multidrug resistant, including high rates of resistance to tobramycin (77.2%), gentamicin (77.2%), ciprofloxacin (67.8%) and trimethoprim (68.5%). ESBL was encoded by six different CTX-M elements and SHV-12. Three isolates from clinical samples (n = 2) or a hospital sewer (n = 1) were resistant to the carbapenem drugs (encoded by NDM-1, NDM-5 or GES-5), and three isolates (clinical (n = 1) and canal water (n = 2)) were resistant to colistin (encoded by mcr-1); no isolates were resistant to both carbapenems and colistin.

CONCLUSIONS

Tackling ESBL-producing E. coli in this setting will be challenging based on widespread distribution, but the low prevalence of resistance to carbapenems and colistin suggests that efforts are now required to prevent these from becoming ubiquitous.

Comparative Genomics of Escherichia coli Isolated from Skin and Soft Tissue and Other Extraintestinal Infections

Escherichia coli, an intestinal Gram-negative bacterium, has been shown to be associated with a variety of diseases in addition to intestinal infections, such as urinary tract infections (UTIs), meningitis in neonates, septicemia, skin and soft tissue infections (SSTIs), and colisepticemia. Thus, for nonintestinal infections, it is categorized as extraintestinal pathogenic E. coli (ExPEC). It is also an opportunistic pathogen, causing cross infections, notably as an agent of zoonotic diseases. However, comparative genomic data providing functional and genetic coordinates for ExPEC strains associated with these different types of infections have not proven conclusive. In the study reported here, ExPEC E. coli isolated from SSTIs was characterized, including virulence and drug resistance profiles, and compared with isolates from patients suffering either pyelonephritis or septicemia. Results revealed that the majority of the isolates belonged to two pathogenic phylogroups, B2 and D. Approximately 67% of the isolates were multidrug resistant (MDR), with 85% producing extended-spectrum beta-lactamase (ESBL) and 6% producing metallo-beta-lactamase (MBL). The bla_CTX-M-15 genotype was observed in at least 70% of the E. coli isolates in each category, conferring resistance to an extended range of beta-lactam antibiotics. Whole-genome sequencing and comparative genomics of the ExPEC isolates revealed that two of the four isolates from SSTIs, NA633 and NA643, belong to pandemic sequence type ST131, whereas functional characteristics of three of the ExPEC pathotypes revealed that they had equal capabilities to form biofilm and were resistant to human serum. Overall, the isolates from a variety of ExPEC infections demonstrated similar resistomes and virulomes and did not display any disease-specific functional or genetic coordinates.

Infections caused by extraintestinal pathogenic E. coli (ExPEC) are of global concern as they result in significant costs to health care facilities management. The recent emergence of a multidrug-resistant pandemic clone, Escherichia coli ST131, is of primary concern as a global threat. In developing countries, such as India, skin and soft tissue infections (SSTIs) associated with E. coli are marginally addressed. In this study, we employed both genomic analysis and phenotypic assays to determine relationships, if any, among the ExPEC pathotypes. Similarity between antibiotic resistance and virulence profiles was observed, ST131 isolates from SSTIs were reported, and genomic similarities among strains isolated from different disease conditions were detected. This study provides functional molecular infection epidemiology insight into SSTI-associated E. coli compared with ExPEC pathotypes.

Multidrug-Resistant Bacteria in the Community: Trends and Lessons Learned

Multidrug resistant (MDR) bacteria are one of the most important threats to public health. Typically, MDR bacteria are associated with nosocomial infections. However, some MDR bacteria have become prevalent causes of community-acquired infections. The spread of MDR bacteria into the community is a crucial development, and is associated with increased morbidity, mortality, health care costs, and antibiotic use. Factors associated with community dissemination of MDR bacteria overlap but are distinct from those associated with nosocomial spread. Prevention of further community spread of MDR bacteria is of the utmost importance, and requires a multidisciplinary approach involving all stakeholders.

Antibiotic resistance, serogroups, virulence genes, and phylogenetic groups of Escherichia coli isolated from yaks with diarrhea in Qinghai Plateau, China

Background

Ruminants serve as one of the most important reservoirs for pathogenic Escherichia coli. Infection with E. coli, a foodborne enteropathogen, can lead to asymptomatic infections that can cause life-threatening complications in humans. Therefore, from a clinical and human health perspective, it is important to know which virulence genes, phylogenetic groups, serogroups, and antibiotic resistance patterns are present in E. coli strains in yaks with diarrheic infections.

Methods

Two-hundred and ninety-two rectal swabs were collected from diarrheic yaks in Qinghai Plateau, China. The antimicrobial sensitivity of each resulting isolate was evaluated according to the disk diffusion method, and different PCR assays were performed for the detection of virulence genes and different phylogroups. Additionally, strains were allocated to different serogroups based on the presence of O antigen via the slide agglutination method.

Results

Among the E. coli isolates tested, most of the isolates were multidrug resistant (97%) and harbored at least one virulence gene (100%). We observed ten virulence genes (sfa, eaeA, cnf1, etrA, papC, hlyA, aer, faeG, rfc, and sepA), of which sfa was the most commonly found (96.9%). Significant positive associations between some resistance phenotypes and virulence genes were observed (P < 0.05, OR > 1). The majority of the E. coli isolates belonged to phylogroup A (79.5%), and the others belonged to phylogroups B1 (7.5%), D (4.1%), B2 (5.8%), and F (0.7%). Among all the E. coli strains tested, serogroups O₉₁ and O₁₄₅ were the most prevalent, accounting for 15.4 and 14.4%, respectively.

Conclusions

Our results suggest that yaks with diarrhea serve as a reservoir of pathogenic E. coli carrying various virulence genes and resistance phenotypes. Therefore, clinicians and relevant authorities must ensure the regulatory use of antimicrobial agents and prevent the spread of these organisms through manure to farm workers and food-processing plants.

Antibiotic Resistance in an Indian Rural Community: A 'One-Health' Observational Study on Commensal Coliform from Humans, Animals, and Water

Antibiotic-resistant bacteria are an escalating grim menace to global public health. Our aim is to phenotype and genotype antibiotic-resistant commensal Escherichia coli (E. coli) from humans, animals, and water from the same community with a ‘one-health’ approach. The samples were collected from a village belonging to demographic surveillance site of Ruxmaniben Deepchand (R.D.) Gardi Medical College Ujjain, Central India. Commensal coliforms from stool samples from children aged 1–3 years and their environment (animals, drinking water from children's households, common source- and waste-water) were studied for antibiotic susceptibility and plasmid-encoded resistance genes. E. coli isolates from human (n = 127), animal (n = 21), waste- (n = 12), source- (n = 10), and household drinking water (n = 122) carried 70%, 29%, 41%, 30%, and 30% multi-drug resistance, respectively. Extended spectrum beta-lactamase (ESBL) producers were 57% in human and 23% in environmental isolates. Co-resistance was frequent in penicillin, cephalosporin, and quinolone. Antibiotic-resistance genes bla_CTX-M-9 and qnrS were most frequent. Group D-type isolates with resistance genes were mainly from humans and wastewater. Colistin resistance, or the mcr-1 gene, was not detected. The frequency of resistance, co-resistance, and resistant genes are high and similar in coliforms from humans and their environment. This emphasizes the need to mitigate antibiotic resistance with a ‘one-health’ approach.

The ST131 Escherichia coli H22 subclone from human intestinal microbiota: Comparison of genomic and phenotypic traits with those of the globally successful H30 subclone

Background

In 2006, we found healthy subjects carrying ST131 Escherichia coli in their intestinal microbiota consisting of two populations: a subdominant population of fluoroquinolone-resistant E. coli belonging to subclone H30 (H30-R or subclade C1), the current worldwide dominant ST131 subclone, and a dominant E. coli population composed of antibiotic-susceptible E. coli belonging to subclone H22 (clade B), the precursor of subclone H30. We sequenced the whole genome of fecal H22 strain S250, compared it to the genomes of ExPEC ST131 H30-Rx strain JJ1886 and commensal ST131 H41 strain SE15, sought the H22-H30 genomic differences in our fecal strains and assessed their phenotypic consequences.

Results

We detected 173 genes found in the Virulence Factor Database, of which 148 were shared by the three ST131 genomes, whereas some were genome-specific, notably those allowing determination of virotype (D for S250 and C for JJ1886). We found three sequences of the FimH site involved in adhesion: two in S250 and SE15 close and identical, respectively, to that previously reported to confer strong intestinal adhesion, and one in JJ1886, corresponding to that commonly present in uropathogenic E. coli. Among the genes involved in sugar metabolism, one encoding a gluconate kinase lacked in S250 and JJ1886. Although this gene was also absent in both our fecal H22 and H30-R strains, H22 strains showed a higher capacity to grow in minimal medium with gluconate. Among the genes involved in gluconate metabolism, only the ghrB gene differed between S250/H22 and JJ1886/H30-R strains, resulting in different gluconate reductases. Of the genes involved in biofilm formation, two were absent in the three genomes and one, fimB, in the JJ1886 genome. Our fecal H30-R strains lacking intact fimB displayed delayed biofilm formation relative to our fecal H22 strains. The H22 strains differed by subclade B type and plasmid content, whereas the H30-R strains were identical.

Conclusions

Phenotypic analysis of our fecal strains based on observed genomic differences between S250 and JJ1886 strains suggests the presence of traits related to bacterial commensalism in our H22 strains and traits commonly found in uropathogenic E. coli in our H30-R strains.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-0984-8) contains supplementary material, which is available to authorized users.

Transcriptional analysis of blaNDM-1 and copy number alteration under carbapenem stress

BACKGROUND

New Delhi metallo beta-lactamase is known to compromise carbapenem therapy and leading to treatment failure. However, their response to carbapenem stress is not clearly known. Here, we have investigated the transcriptional response of blaNDM-1 and plasmid copy number alteration under carbapenem exposure.

METHODS

Three blaNDM-1 harboring plasmids representing three incompatibility types (IncFIC, IncA/C and IncK) were inoculated in LB broth with and without imipenem, meropenem and ertapenem. After each 1 h total RNA was isolated, immediately reverse transcribed into cDNA and quantitative real time PCR was used for transcriptional expression of blaNDM-1. Horizontal transferability and stability of the plasmids encoding blaNDM-1 were also determined. Changes in copy number of blaNDM-1 harboring plasmids under the exposure of different carbapenems were determined by real time PCR. Clonal relatedness among the isolates was determined by pulsed field gel electrophoresis.

RESULTS

Under carbapenem stress over an interval of time there was a sharp variation in the transcriptional expression of blaNDM-1 although it did not follow a specific pattern. All blaNDM-1 carrying plasmids were transferable by conjugation. These plasmids were highly stable and complete loss was observed between 92nd to 96th serial passages when antibiotic pressure was withdrawn. High copy number of blaNDM-1 was found for IncF type plasmids compared to the other replicon types.

CONCLUSION

This study suggests that the single dose of carbapenem pressure does not significantly influence the expression of blaNDM-1 and also focus on the stability of this gene as well as the change in copy number with respect to the incompatible type of plasmid harboring resistance determinant.

Genome Dynamics and Molecular Infection Epidemiology of Multidrug-Resistant Helicobacter pullorum Isolates Obtained from Broiler and Free-Range Chickens in India

Some life-threatening, foodborne, and zoonotic infections are transmitted through poultry birds. Inappropriate and indiscriminate use of antimicrobials in the livestock industry has led to an increased prevalence of multidrug-resistant bacteria with epidemic potential. Here, we present a functional molecular epidemiological analysis entailing the phenotypic and whole-genome sequence-based characterization of 11 H. pullorum isolates from broiler and free-range chickens sampled from retail wet markets in Hyderabad City, India. Antimicrobial susceptibility tests revealed all of the isolates to be resistant to multiple antibiotic classes such as fluoroquinolones, cephalosporins, sulfonamides, and macrolides. The isolates were also found to be extended-spectrum β-lactamase producers and were even resistant to clavulanic acid. Whole-genome sequencing and comparative genomic analysis of these isolates revealed the presence of five or six well-characterized antimicrobial resistance genes, including those encoding a resistance-nodulation-division efflux pump(s). Phylogenetic analysis combined with pan-genome analysis revealed a remarkable degree of genetic diversity among the isolates from free-range chickens; in contrast, a high degree of genetic similarity was observed among broiler chicken isolates. Comparative genomic analysis of all publicly available H. pullorum genomes, including our isolates (n = 16), together with the genomes of 17 other Helicobacter species, revealed a high number (8,560) of H. pullorum-specific protein-encoding genes, with an average of 535 such genes per isolate. In silico virulence screening identified 182 important virulence genes and also revealed high strain-specific gene content in isolates from free-range chickens (average, 34) compared to broiler chicken isolates. A significant prevalence of prophages (ranging from 1 to 9) and a significant presence of genomic islands (0 to 4) were observed in free-range and broiler chicken isolates. Taken together, these observations provide significant baseline data for functional molecular infection epidemiology of nonpyloric Helicobacter species such as H. pullorum by unraveling their evolution in chickens and their possible zoonotic transmission to humans.

IMPORTANCE

Globally, the poultry industry is expanding with an ever-growing consumer base for chicken meat. Given this, food-associated transmission of multidrug-resistant bacteria represents an important health care issue. Our study involves a critical baseline approach directed at genome sequence-based epidemiology and transmission dynamics of H. pullorum, a poultry pathogen having established zoonotic potential. We believe our studies would facilitate the development of surveillance systems that ensure the safety of food for humans and guide public health policies related to the use of antibiotics in animal feed in countries such as India. We sequenced 11 new genomes of H. pullorum as a part of this study. These genomes would provide much value in addition to the ongoing comparative genomic studies of helicobacters.

Community carriage of ESBL-producing Escherichia coli is associated with strains of low pathogenicity: a Swedish nationwide study

OBJECTIVES

Community carriage of ESBL-producing Escherichia coli (EPE) is common worldwide and there is a need to understand the connection between carriage and infection. We compared the molecular characteristics of EPE among Swedish community carriers with those of EPE causing invasive infections.

METHODS

We collected 2134 faecal samples from randomly selected Swedish inhabitants and examined them for the presence of EPE. All participating volunteers answered a questionnaire about putative risk factors for EPE carriage. Suspected EPE isolates (n = 418) from patients with bloodstream infection (BSI) were collected from Swedish laboratories. Isolates were genotypically and phenotypically characterized.

RESULTS

Our results show that the EPE population found in carriers generally had lower pathogenicity compared with the isolates from BSIs, since carriers had a lower proportion of E. coli belonging to phylogroup B2, ST131 and ST131 subclone H30-Rx. Isolates from carriers also had lower levels of multiresistance. The Swedish carriage rate of EPE was 4.7% (101/2134) among healthy volunteers. Risk factors associated with carriage were travel to countries in Asia (OR = 3.6, 95% CI = 1.4-9.2) and Africa (OR = 3.6, 95% CI = 1.7-7.7) and a diet without pork (OR = 0.5, 95% CI = 0.3-0.8 for pork eaters).

CONCLUSIONS

E. coli host factors previously associated with higher pathogenicity were all more common in BSIs compared with carriers. This indicates that the risk of invasive infection with EPE may be relatively modest in many community carriers and that EPE carriage of high-risk strains should be the focus of attention for prevention.

Molecular Epidemiology and Genome Dynamics of New Delhi Metallo-β-Lactamase-Producing Extraintestinal Pathogenic Escherichia coli Strains from India

The global dissemination and increasing incidence of carbapenem-resistant, Gram-negative organisms have resulted in acute public health concerns. Here, we present a retrospective multicenter study on molecular characterization of metallo-β-lactamase (MBL)-producing clinical Escherichia coli isolates recovered from extraintestinal infections in two hospitals in Pune, India. We screened a large sample size of 510 E. coli isolates for MBL production wherein we profiled their molecular determinants, antimicrobial resistance phenotypes, functional virulence properties, genomic features, and transmission dynamics. Approximately 8% of these isolates were MBL producers, the majority of which were of the NDM-1 (69%) type, followed by NDM-5 (19%), NDM-4 (5.5%), and NDM-7 (5.5%). MBL producers were resistant to all antibiotics tested except for colistin, fosfomycin, and chloramphenicol, which were effective to various extents. Plasmids were found to be an effective means of dissemination of NDM genes and other resistance traits. All MBL producers adhered to and invaded bladder epithelial (T24) cells and demonstrated significant serum resistance. Genomic analysis of MBL-producing E. coli isolates revealed higher resistance but a moderate virulence gene repertoire. A subset of NDM-1-positive E. coli isolates was identified as dominant sequence type 101 (ST101) while two strains belonging to ST167 and ST405 harbored NDM-5. A majority of MBL-producing E. coli strains revealed unique genotypes, suggesting that they were clonally unrelated. Overall, the coexistence of virulence and carbapenem resistance in clinical E. coli isolates is of serious concern. Moreover, the emergence of NDM-1 among the globally dominant E. coli ST101 isolates warrants stringent surveillance and control measures.

Prevalence of O25b-ST131 clone among Escherichia coli strains producing CTX-M-15, CTX-M-14 and CTX-M-92 β-lactamases

BACKGROUND

Dissemination of multidrug-resistant Escherichia coli is closely associated with the worldwide spread of a single clone ST131, which is the main cause of urinary tract and bloodstream infections in patients from nursing homes and immunocompromised patients. The aim of our study was to determine the prevalence of ST131 clone and the replicons involved in the spread of bla_CTX-M genes among O25b-ST131 CTX-M-producing E. coli isolates in Lithuania.

METHODS

The strains included in this study were screened for CTX-M β-lactamase-encoding genes, phylogenetic groups and ST131 clone by PCR. Bacterial conjugation was performed to identify plasmid replicon types responsible for bla_CTX-M genes dissemination.

RESULTS

A total of 158 E. coli clinical non-duplicate ESBL isolates were analyzed. Nearly half (n = 67, 42.4%) of the investigated E. coli isolates belonged to phylogenetic group B2. The isolates producing CTX-M-92 β-lactamases were identified to be the ST131 clone more frequently than the non-ST131 clone (11.5% vs. 3.1%, p = .035). The CTX-M-15 isolates were identified as ST131 isolates less frequently than non-ST131 isolates (50.8% vs. 71.1%; p = .015). The ST131 clone isolates contained type L/M and A/C replicons; a fused FII/FIB replicon was found in four isolates (23.5%). Type HI1 replicon was identified in ST131 E. coli isolates producing CTX-M-15 β-lactamases.

CONCLUSIONS

This study demonstrates the predominance of the ST131 clone among CTX-M β-lactamase-producing E. coli isolates. Dissemination of bla_CTX-M genes in ST131 strains can be linked not only to highly adapted IncF plasmids such as FII/FIB and FII, but also to plasmid replicon types A/C, L/M and HI1.

Epidemic potential of Escherichia coli ST131 and Klebsiella pneumoniae ST258: a systematic review and meta-analysis

OBJECTIVES

Observational studies have suggested that Escherichia coli sequence type (ST) 131 and Klebsiella pneumoniae ST258 have hyperendemic properties. This would be obvious from continuously high incidence and/or prevalence of carriage or infection with these bacteria in specific patient populations. Hyperendemicity could result from increased transmissibility, longer duration of infectiousness, and/or higher pathogenic potential as compared with other lineages of the same species. The aim of our research is to quantitatively estimate these critical parameters for E. coli ST131 and K. pneumoniae ST258, in order to investigate whether E. coli ST131 and K. pneumoniae ST258 are truly hyperendemic clones.

PRIMARY OUTCOME MEASURES

A systematic literature search was performed to assess the evidence of transmissibility, duration of infectiousness, and pathogenicity for E. coli ST131 and K. pneumoniae ST258. Meta-regression was performed to quantify these characteristics.

RESULTS

The systematic literature search yielded 639 articles, of which 19 data sources provided information on transmissibility (E. coli ST131 n=9; K. pneumoniae ST258 n=10)), 2 on duration of infectiousness (E. coli ST131 n=2), and 324 on pathogenicity (E. coli ST131 n=285; K. pneumoniae ST258 n=39). Available data on duration of carriage and on transmissibility were insufficient for quantitative assessment. In multivariable meta-regression E. coli isolates causing infection were associated with ST131, compared to isolates only causing colonisation, suggesting that E. coli ST131 can be considered more pathogenic than non-ST131 isolates. Date of isolation, location and resistance mechanism also influenced the prevalence of ST131. E. coli ST131 was 3.2 (95% CI 2.0 to 5.0) times more pathogenic than non-ST131. For K. pneumoniae ST258 there were not enough data for meta-regression assessing the influence of colonisation versus infection on ST258 prevalence.

CONCLUSIONS

With the currently available data, it cannot be confirmed nor rejected, that E. coli ST131 or K. pneumoniae ST258 are hyperendemic clones.