Molecular epidemiology of Escherichia coli producing CTX-M β-lactamases: the worldwide emergence of clone ST131 O25:H4

Prevalence of specific serogroups, antibiotic resistance and virulence factors of avian pathogenic Escherichia coli (APEC) isolated from clinical cases: A systematic review and meta-analysis

Pathogenic strains of Escherichia coli infecting poultry, commonly called avian pathogenic E. coli (APEC) present significant risks, to the health of both poultry and the general public. This systematic review aimed to examine the prevalence of APEC serotypes, sequence types (ST), phylogenetic groups, virulence factors and antibiotic resistance patterns based on 189 research papers sourced from PubMed, Web of Science, and ProQuest. Then, data were extracted from the selected studies and analyzed to assess the global distribution and characteristics of APEC strains. The metaprop codes in the Meta and Metafor packages of R as implemented in RStudio were then used to conduct meta-analysis. Among APEC strains identified from these different research reports serogroup O78 had the highest overall prevalence (16 %), followed by serogroups O2 (10 %), and O117 (8 %). The most common ST profiles were ST117 (20 %), ST140 (15 %), ST95 (12 %), and ST131 (9 %). ST117 and ST140 are known reservoirs for pathogenic E. coli in humans. Moreover, phylogenetic assessment highlighted the prevalence of phylogroups A, A1, F, D, and B2 among APEC strains indicating diversity in phylogenetic origin within poultry populations. The presence of antimicrobial resistance was notable among APEC strains against antibiotics such as tetracyclines, penicillins, and cephalosporins. This resistance may be linked to use of antimicrobials in poultry production in certain regions presenting challenges for both animal health management and human infection control. Analysis of sequences linked to adherence or virulence indicated that genes encoding adhesins (csg, fimC), iron/metal uptake (sitB, sitC, iroD) and cytotoxicity (estB, hlyF), and serum resistance (traT, iss) were highly prevalent. These factors have been reported to contribute to APEC host colonization and virulence in poultry. In summary, this overview of the characteristics of APEC highlights the pressing importance of monitoring and implementing management approaches to reduce antimicrobial resistance considering that a phylogenetic diversity of E. coli strains causes infections in both poultry and humans and represents a risk to both animal and public health. Further, determining the major conserved aspects and predominant mechanisms of virulence of APEC is critical for improving diagnostics and developing preventative measures to reduce the burden of infection caused by pathogenic E. coli in poultry and lower risks associated with foodborne transmission of E. coli to humans through poultry and poultry products.

Demographic, clinical and molecular epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli bloodstream infections in Central Australia

We describe the demographics, clinical and molecular epidemiology of extended-spectrum β-lactamase (ESBL) Escherichia coli bloodstream infections (BSI) in Central Australia. All ESBL-producing E. coli bloodstream isolates from January 2018 to December 2020 were retrospectively identified. Demographic and clinical information was extracted by chart review. Whole-genome sequencing was performed for multi-locus sequence typing, antibiotic-resistance genes, and phylogenetic relationships. We identified 41 non-duplicate episodes of ESBL E. coli BSI. Median age was 55 years (IQR 47-63), 78% were female, 93% were Aboriginal, and half came from a remote community. Infections were predominantly urinary (68%, 28/41). In the 12 months prior, 70% (26/37) of identified patients had been hospitalised and 81% (30/37) prescribed antibiotics. Meropenem and piperacillin-tazobactam susceptibility was maintained in 100% and 95% of isolates, respectively. Co-resistance to non-β-lactam antibiotics was 32% to gentamicin, 61% to trimethoprim/sulfamethoxazole, and 68% to ciprofloxacin. For sequenced isolates, 41% (16/35) were sequence type 131 (ST131). Mean acquired antibiotic-resistance genes for each isolate was 12.3 (SD 3.1). Four isolates carried an OXA-1 gene. Only non-ST131 isolates carried AmpC and acquired quinolone-resistance genes. There was some evidence of clustering of closely related strains, but no evidence of community or healthcare admission overlap. ESBL rates are rapidly rising in Central Australia, which is a conducive environment for antibiotic resistance development (e.g., overcrowding, socioeconomic disadvantages, high healthcare exposure and high antibiotic use). Future research is required to explore resistance-transmission dynamics in this unique setting.

Exploring the presence, genomic traits, and pathogenic potential of extended-spectrum β-lactamase Escherichia coli in freshwater, wastewater, and hospital effluents

AIMS

The purpose of this work was to study extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) in freshwaters, hospital effluents, and wastewaters during two sampling campaigns in 2021.

METHODS AND RESULTS

Water sampling was performed at 24 stations in the Ourthe watershed in Belgium. A total of 644 ESBL (n = 642) and AmpC (n = 2) E. coli strains were isolated. Disk-diffusion assays were performed following the EUCAST's recommendations. All strains were tested for the presence of blaCTX-M-1, blaCTX-M-2, and blaCTX-M-9 gene groups by PCR. Genes belonging to blaCTX-M-1 and blaCTX-M-9 groups were detected, respectively, in 73.6% and 14.9% of the strains. No blaCTX-M-2 group's gene was found. A subset of strains (n = 40) was selected for whole genome sequencing. Escherichia coli serotype O18: H7 ST 1463 was predominant (n = 14) in the sequenced strains and showed pathogenicity in the Galleria mellonella larvae model. β-lactamase genes identified were blaCTX-M (n = 21), with blaCTX-M-15 mostly represented (n = 15), as well as blaTEM (n = 11), blaOXA (n = 7), blaSHV (n = 9), and carbapenemase (CP) genes were observed in several strains-blaKPC-3 (n = 19), blaNDM-1 (n = 1), blaVIM-1 (n = 2), and blaOXA-244 (n = 2)-even from freshwaters.

CONCLUSIONS

ESBL-EC are widely distributed in the aquatic environment in Belgium and contain a variety of ESBL and CP genes.

Distribution and antimicrobial susceptibility pattern of CTX-M-type extended-spectrum β-lactamase-producing Escherichia coli isolated in Chubu region, Japan

The widespread prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli limits treatment options and is a worldwide problem. The aim of this study was to investigate the antimicrobial susceptibility and ESBL-type of 204 strains of CTX-M-type ESBLs-producing E. coli isolated from 2011 to 2017 in the Chubu region of Japan. Minimal inhibitory concentrations were determined in accordance with the guidelines of the Clinical and Laboratory Standards Institute. Genes encoding CTX-M group β-lactamases were detected by PCR amplification. The CTX-M subtypes were determined using sequence analysis. The CTX-M-9 group was the most frequently detected ESBL group, and CTX-M-27 was the most frequently detected ESBL gene. CTX-M-15-producing strains showed significantly lower rates of susceptibility to tazobactam/piperacillin (TAZ/PIPC) than those by CTX-M-14 and -27-producing strains. Additional analysis of secondary β-lactamases revealed that most of the OXA-1-positive strains were CTX-M-15-producing strains (94.7%). These strains displayed significantly lower susceptibility rates to TAZ/PIPC (47.4%), sulbactam/ampicillin (SBT/ABPC) (0.0%), and amikacin (AMK) (73.7%) than those by OXA-1-negative strains, suggesting that the high non-susceptibility rate of the CTX-M-15-producing strain was due to the co-carriage of OXA-1. The CTX-M-15-producing strains showed reduced susceptibility to TAZ/PIPC, SBT/ABPC, and AMK, presumably due to the co-carriage of OXA-1.

Genome Sequences of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Recovered from Mid-Stream Urine Samples in Accra, Ghana

Escherichia coli, a member of the commensal intestinal microbiota, is a significant aetiology of urinary tract infections (UTIs) and has a propensity for acquiring multidrug resistance characteristics, such as extended-spectrum beta-lactamases (ESBLs). Despite the increase in the incidence of ESBL-producing E. coli infections in sub-Saharan Africa, routine ESBL detection in Ghana is often absent, and molecular data on ESBL genotypes is scarce. Eleven ESBL-producing E. coli recovered from mid-stream urine samples were subjected to antimicrobial susceptibility testing and whole-genome sequence analyses. All isolates exhibited multidrug resistance, demonstrating phenotypic resistance to third-generation cephalosporins, such as cefotaxime, ceftazidime, and cefpodoxime. Three isolates demonstrated resistance to norfloxacin (a fluoroquinolone), and one isolate demonstrated intermediate resistance to ertapenem (a carbapenem). Analysis of the draft genomes identified multiple antimicrobial resistance genes including ESBL genotypes blaTEM-1B/TEM-190 (6/11 and 1/11, respectively), blaCTX-M-15/CTX-M-3 (7/11 and 1/11) and blaOXA-1/OXA-181 (3/11 and 1/11). The strains belong to 10 different serotypes and 10 different multilocus sequence types. This study provides information on phenotypic resistance in 11 ESBL E. coli from Ghana and AMR genotypes within their genomes.

Extended spectrum beta-lactamase carriage among elderly residents of a long-term care facility in Beirut

BACKGROUND

Antimicrobial resistance is an emerging problem worldwide, endangering antimicrobials efficacy and resulting in high rates of morbidity and mortality. It is one of the major concerns that health care facilities are facing nowadays. Mainly, extended-spectrum beta-lactamases (ESBL)-producing Enterobacterales play a role in hydrolyzing β-lactams, specifically the third-generation cephalosporins. This study aimed to investigate the prevalence of fecal carriage and molecular characterization of ESBL-producing Enterobacterales among Lebanese elderly residents in a long-term care facility (Dar Al-Ajaza Al Islamia Hospital).

METHODS

Rectal culture swab specimens were collected from 132 patients at Dar Al Ajaza Al Islamia hospital between January 2019 till June 2020. The phenotype of ESBL producers was confirmed by a modified double disc synergy test and antibiotic susceptibility was determined using the Kirby-Bauer disk diffusion method. Genotypically, multiplex polymerase chain reaction was used to detect the ESBL genes.

RESULTS

The main Enterobacterales strain observed was E coli (90.15%) followed by Klebsiella pneumoniae (4.54%) and Klebsiella oxytoca (3.80%). It has been found that the ESBL percentage rate has decreased when compared to a study conducted previously at the same hospital. Moreover, the predominant ESBL gene was CTX-M (cefotaximase).

CONCLUSIONS

This study is the first to demonstrate the improved current status of ESBL in one long-term care facility. In addition, the CTX-M is still the major type in ESBL-producing organisms.

A comparative study on antibiotic resistant Escherichia coli isolates from Austrian patients and wastewater-influenced Danube River water and biofilms

Antimicrobial resistance (AMR) poses a major threat to human health worldwide. AMR can be introduced into natural aquatic ecosystems, for example, from clinical facilities via wastewater emissions. Understanding AMR patterns in environmental populations of bacterial pathogens is important to elucidate propagation routes and develop mitigation strategies. In this study, AMR patterns of Escherichia coli isolates from urinary tract infections and colonised urinary catheters of inpatients and outpatients were compared to isolates from the Danube River within the same catchment in Austria to potentially link environmental with clinical resistance patterns. Susceptibility to 20 antibiotics was tested for 697 patient, 489 water and 440 biofilm isolates. The resistance ratios in patient isolates were significantly higher than in the environmental isolates and higher resistance ratios were found in biofilm in comparison to water isolates. The role of the biofilm as potential sink of resistances was reflected by two extended-spectrum beta-lactamase (ESBL) producing isolates in the biofilm while none were found in water, and by higher amoxicillin/clavulanic acid resistance ratios in biofilm compared to patient isolates. Although, resistances to last-line antibiotics such as carbapenems and tigecycline were found in the patient and in the environmental isolates, they still occurred at low frequency.

Cobalt complexes modulate plasmid conjugation in Escherichia coli and Klebsiella pneumoniae

Antimicrobial resistance genes (ARG), such as extended-spectrum β-lactamase (ESBL) and carbapenemase genes, are commonly carried on plasmids. Plasmids can transmit between bacteria, disseminate globally, and cause clinically important resistance. Therefore, targeting plasmids could reduce ARG prevalence, and restore the efficacy of existing antibiotics. Cobalt complexes possess diverse biological activities, including antimicrobial and anticancer properties. However, their effect on plasmid conjugation has not been explored yet. Here, we assessed the effect of four previously characterised bis(N-picolinamido)cobalt(II) complexes lacking antibacterial activity on plasmid conjugation in Escherichia coli and Klebsiella pneumoniae. Antimicrobial susceptibility testing of these cobalt complexes confirmed the lack of antibacterial activity in E. coli and K. pneumoniae. Liquid broth and solid agar conjugation assays were used to screen the activity of the complexes on four archetypical plasmids in E. coli J53. The cobalt complexes significantly reduced the conjugation of RP4, R6K, and R388 plasmids, but not pKM101, on solid agar in E. coli J53. Owing to their promising activity, the impact of cobalt complexes was tested on the conjugation of fluorescently tagged extended-spectrum β-lactamase encoding pCTgfp plasmid in E. coli and carbapenemase encoding pKpQILgfp plasmid in K. pneumoniae, using flow cytometry. The complexes significantly reduced the conjugation of pKpQILgfp in K. pneumoniae but had no impact on pCTgfp conjugation in E. coli. The cobalt complexes did not have plasmid-curing activity, suggesting that they target conjugation rather than plasmid stability. To our knowledge, this is the first study to report reduced conjugation of clinically relevant plasmids with cobalt complexes. These cobalt complexes are not cytotoxic towards mammalian cells and are not antibacterial, therefore they could be optimised and employed as inhibitors of plasmid conjugation.

Spatiotemporal distribution of community-acquired phenotypic extended-spectrum beta-lactamase Escherichia coli in United States counties, 2010-2019

Using data from the Veterans' Health Administration from 2010 to 2019, we examined the distribution and prevalence of community-acquired phenotypic extended-spectrum β-lactamase (ESBL) E. coli in the United States. ESBL prevalence slowly increased during the study period, and cluster analysis showed clustering in both urban and rural locations.

Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales

Antibiotic resistance is a significant global public health concern. Uropathogenic Escherichia coli sequence type (ST)131, a widely prevalent multidrug-resistant clone, is frequently associated with bacteraemia. This study investigates third-generation cephalosporin resistance in bloodstream infections caused by E. coli ST131. From 2013-2014 blood culture surveillance in Wales, 142 E. coli ST131 genomes were studied alongside global data. All three major ST131 clades were represented across Wales, with clade C/H30 predominant (n = 102/142, 71.8%). Consistent with global findings, Welsh strains of clade C/H30 contain β-lactamase genes from the blaCTX-M-1 group (n = 65/102, 63.7%), which confer resistance to third-generation cephalosporins. Most Welsh clade C/H30 genomes belonged to sub-clade C2/H30Rx (58.3%). A Wales-specific sub-lineage, named GB-WLS.C2, diverged around 1996-2000. An introduction to North Wales around 2002 led to a localised cluster by 2009, depicting limited genomic diversity within North Wales. This investigation emphasises the value of genomic epidemiology, allowing the detection of genetically similar strains in local areas, enabling targeted and timely public health interventions.

Escherichia coli sequence type 410 with carbapenemases: a paradigm shift within E. coli toward multidrug resistance

Escherichia coli sequence type ST410 is an emerging carbapenemase-producing multidrug-resistant (MDR) high-risk One-Health clone with the potential to significantly increase carbapenem resistance among E. coli. ST410 belongs to two clades (ST410-A and ST410-B) and three subclades (ST410-B1, ST410-B2, and ST410-B3). After a fimH switch between clades ST410-A and ST410-B1, ST410-B2 and ST410-B3 subclades showed a stepwise progression toward developing MDR. (i) ST410-B2 initially acquired fluoroquinolone resistance (via homologous recombination) in the 1980s. (ii) ST410-B2 then obtained CMY-2, CTX-M-15, and OXA-181 genes on different plasmid platforms during the 1990s. (iii) This was followed by the chromosomal integration of blaCMY-2, fstl YRIN insertion, and ompC/ompF mutations during the 2000s to create the ST410-B3 subclade. (iv) An IncF plasmid "replacement" scenario happened when ST410-B2 transformed into ST410-B3: F36:31:A4:B1 plasmids were replaced by F1:A1:B49 plasmids (both containing blaCTX-M-15) followed by blaNDM-5 incorporation during the 2010s. User-friendly cost-effective methods for the rapid identification of ST410 isolates and clades are needed because limited data are available about the frequencies and global distribution of ST410 clades. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST410 (including the ability to acquire successive MDR determinants). Such information will aid with management and prevention strategies to curb the spread of carbapenem-resistant E. coli. The medical community can ill afford to ignore the spread of a global E. coli clone with the potential to end the carbapenem era.

Epidemiology of Cefotaxime-Hydrolysing β-Lactamase-Producing Escherichia coli in Children with Diarrhoea Reported Globally between 2012 and 2022

The global spread of cefotaxime-hydrolysing β-lactamase (CTX-M)-producing Escherichia coli (E. coli) and its associated impact on paediatric diarrhoeal treatment and management has become a public health concern. This review assessed surveillance studies on CTX-M-producing E. coli associated with diarrhoea in children published between 2012 and 2022 globally. A total of thirty-eight studies were included for data analysis, categorised into continental regions, and tabulated. The majority (68%) of studies were conducted in Asian countries while few studies were conducted in Europe (11%) and Africa (18%), respectively. On the African continent, the majority (11%) of studies were conducted in Northern Africa while no studies were reported in East Africa. On the American continent, 3% of the studies were reported from South America. The studies included were classified into diarrheagenic E. coli (74%; 28/38) and faecal carriage (26%; 10/38). Of all the E. coli pathotypes associated with CTX-M production, EPEC was frequently reported. The prevalence of CTX-M-producing E. coli including the CTX-M-15-producing variants ranged between 1% and 94%. About 37% of the studies generalised the report as blaCTX-M-positive E. coli. The use of sequencing in characterising the CTX-M-producing E. coli was reported in only 32% of all the studies. This review provides information on the epidemiology of CTX-M-15-producing E. coli in paediatric diarrhoea and the extent to which surveillance is being performed. This is relevant in informing clinical practice for the management of diarrhoea as well as the design of future surveillance studies.

Efficacy and Safety of Cefmetazole for Bacteremia Caused by Extended-Spectrum β-Lactamase-Producing Enterobacterales vs Carbapenems: A Retrospective Study

Background

Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales have become a global concern owing to increased infections, high mortality, and limited antibiotic treatment options. Carbapenems (CPMs) are effective against ESBL-producing Enterobacterales, but their overuse leads to the emergence of multidrug-resistant bacteria. Cefmetazole (CMZ) is effective in vitro; however, its clinical efficacy remains unclear.

Methods

We retrospectively reviewed patients who were treated with CMZ or CPMs for bacteremia caused by ESBL-producing Enterobacterales between 1 April 2014 and 31 September 2022 at Tenri Hospital. The primary outcome measure was 90-day mortality. We also evaluated resistance genes and sequence types of ESBL-producing Enterobacterales.

Results

In total, 156 patients were enrolled in this study. Ninety patients (58%) received CMZ therapy. Patients in the CMZ group were significantly older than those in the CPM group (median [IQR], 79 years [71-86] vs 74 years [64-83]; P = .001). The severity of the Pitt bacteremia score of the CMZ group was lower than that in the CPM group (0 [0-2] vs 2 [0-2], P = .042). Six patients (7%) in the CMZ group and 10 (15%) in the CPM group died by day 90 (P = .110). Charlson Comorbidity Index and prevalence of sequence 131 between the groups were statistically insignificant.

Conclusions

Our findings suggest that CMZ is a well-tolerated alternative to CPM for treating bacteremia caused by ESBL-producing Enterobacterales.

The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom

Escherichia coli is a ubiquitous component of the human gut microbiome, but is also a common pathogen, causing around 40, 000 bloodstream infections (BSI) in the United Kingdom (UK) annually. The number of E. coli BSI has increased over the last decade in the UK, and emerging antimicrobial resistance (AMR) profiles threaten treatment options. Here, we combined clinical, epidemiological, and whole genome sequencing data with high content imaging to characterise over 300 E. coli isolates associated with BSI in a large teaching hospital in the East of England. Overall, only a limited number of sequence types (ST) were responsible for the majority of organisms causing invasive disease. The most abundant (20 % of all isolates) was ST131, of which around 90 % comprised the pandemic O25b:H4 group. ST131-O25b:H4 isolates were frequently multi-drug resistant (MDR), with a high prevalence of extended spectrum β-lactamases (ESBL) and fluoroquinolone resistance. There was no association between AMR phenotypes and the source of E. coli bacteraemia or whether the infection was healthcare-associated. Several clusters of ST131 were genetically similar, potentially suggesting a shared transmission network. However, there was no clear epidemiological associations between these cases, and they included organisms from both healthcare-associated and non-healthcare-associated origins. The majority of ST131 isolates exhibited strong binding with an anti-O25b antibody, raising the possibility of developing rapid diagnostics targeting this pathogen. In summary, our data suggest that a restricted set of MDR E. coli populations can be maintained and spread across both community and healthcare settings in this location, contributing disproportionately to invasive disease and AMR.

Antimicrobial Susceptibility of E. coli Isolates from Intra-Abdominal Infections in the Asia-Pacific Region: Trends in Ciprofloxacin, Ceftriaxone, Cefepime, and Piperacillin/Tazobactam Susceptibility

Purpose

To investigate the antibiotic susceptibility of Escherichia coli isolates in patients diagnosed with intra-abdominal infections (IAIs) in the Asia-Pacific region.

Patients and Methods

This study was conducted at 50 medical hospitals across 9 countries/regions as part of the Study for Monitoring Antimicrobial Resistance Trends (SMART) surveillance program from 2014 to 2018. Nonduplicate isolates of aerobic and facultative gram-negative bacilli were collected and processed for further antimicrobial susceptibility testing.

Results

A total of 10,709 isolates were collected, with E. coli (n=4737, 44.2%) being the leading pathogen causing IAIs, followed by Klebsiella pneumoniae (n=2429, 22.7%) and Pseudomonas aeruginosa (n=931, 8.7%). Community-associated (CA) E. coli isolates generally exhibited higher susceptibility rates for most antibiotics than hospital-associated (HA) isolates. In countries/regions other than Hong Kong, South Korea, and Singapore, HA isolates displayed lower susceptibility rates for multiple classes (≥4) of antibiotics. Among the commonly used antibiotics in IAIs, the overall susceptibility rate for ciprofloxacin was low, with an average of 41.3%. Ceftriaxone susceptibility rates in all selected countries were below 80% starting in 2018, ranging from 23.3% to 75.8%. The cefepime susceptibility rates varied across regions, with consistently reduced susceptibility ranging from 45.5% to 57.8% in India, Thailand, and Vietnam. Piperacillin/tazobactam demonstrated effectiveness against E. coli isolates in almost all countries except India, with a downward trend observed in the Philippines and Taiwan. Carbapenems remained effective against more than 90% of E. coli isolates, except in India.

Conclusion

Prudent use of fluoroquinolones and ceftriaxone is advised when treating both CA and HA IAIs in the Asia-Pacific region. The low susceptibility rate of cefepime in India, Thailand, and Vietnam needs careful consideration in its administration. Moreover, the increase in nonsusceptibility to piperacillin/tazobactam in the Philippines and Taiwan poses a potential risk that should be closely monitored.

Genomic Insights into Global blaCTX-M-55-Positive Escherichia coli Epidemiology and Transmission Characteristics

In recent years, blaCTX-M-55-positive Escherichia coli has been widely reported in multiple locations with an increasing trend in prevalence, yet few studies have comprehensively analyzed the transmission characteristics and epidemiological patterns of blaCTX-M-55-positive E. coli. Here, we constructed a blaCTX-M-55-positive E. coli global genomic data set as completely as possible and explored the epidemiology and potential impact of blaCTX-M-55-positive E. coli on a global scale by high-resolution bioinformatics methods. The results show that blaCTX-M-55-positive E. coli has spread widely worldwide, especially in Asia, with the rich sequence typing (ST) diversity and high proportion of auxiliary genome occupancy indicating a high degree of openness. The phylogenetic tree suggests that blaCTX-M-55-positive E. coli is frequently clonally transmitted between the three human-animal environments and often cotransmitted with fosA, mcr, blaNDM, and tet(X). The stable presence of InclI1 and InclI2 in different hosts from different sources suggests that this part of the plasmid drives the widespread transmission of blaCTX-M-55-positive E. coli. We inductively clustered all blaCTX-M-55 flanking environmental gene structures and obtained five types. Notably, "ISEcp1-blaCTX-M-55-orf477-(Tn2)" and "IS26(IS15DI)-hp-hp-blaCTX-M-55-orf477-hp-blaTEM-IS26-hp-IS26-Tn2" are dominant in "humans" and in "animals and related foods," respectively. Overall, our findings highlight the importance of whole-genome sequencing-based surveillance in exploring the transmission and evolution of blaCTX-M-55-positive E. coli in the context of "One Health," and they serve as a reminder to strengthen the surveillance of blaCTX-M-55-positive E. coli in order to address the potential risk of future large outbreaks. IMPORTANCE CTX-M-55 was first discovered in Thailand in 2004, and today, this enzyme is the most common CTX-M subtype in E. coli of animal origin in China. Thus, blaCTX-M-55-positive E. coli getting widely spread is a growing public health problem. Although prevalence surveys of blaCTX-M-55-positive E. coli in different hosts have been widely reported in recent years, they remain insufficient in "One Health" context and from a global comprehensive perspective. Here, we constructed a genomic database of 2144 blaCTX-M-55-positive E. coli and used bioinformatics methods to resolve the spread and evolution of blaCTX-M-55-positive E. coli. The results suggest a potential risk of rapid transmission of blaCTX-M-55-positive E. coli and that long-term continuous surveillance of blaCTX-M-55-positive E. coli should be emphasized.

Detection of Plasmid-Mediated Resistance against Colistin in Multi-Drug-Resistant Gram-Negative Bacilli Isolated from a Tertiary Hospital

The aim of this study was to determine the prevalence of plasmid-mediated colistin resistance mcr-1 to mcr-5 genes among colistin and multi-drug-resistant Gram-negative bacilli strains isolated from patients in a tertiary hospital in Toluca, Mexico. The presence of mcr genes among the 241 strains collected was assessed by PCR. In the case of mcr-carrying E. coli, further PCR tests were performed to determine the presence of blaCTX-M and whether the strains belonged to the O25b-ST131 clone. Conjugation experiments were also carried out to assess the horizontal transmission of colistin resistance. A total of twelve strains (5.0%), of which four were E. coli; four were P. aeruginosa; three were K. pneumoniae, and one E. cloacae, were found to be resistant to colistin. Of these strains, two E. coli isolates were found to carry mcr-1, and Southern blot hybridization demonstrated its presence on an approximately 60 kb plasmid. Both mcr-1-carrying E. coli strains were found to co-express blaCTX-M, belong to the O25b-ST131 clone, and horizontally transmit their colistin resistance. The results of this study confirm the presence of plasmid-mediated colistin resistance in hospitalized patients in Mexico and demonstrated that the multi-drug-resistant O25b-ST131 E. coli clone can acquire mcr genes and transmit such resistance traits to other bacteria.

Antimicrobial Resistance Patterns and Risk Factors Associated with ESBL-Producing and MDR Escherichia coli in Hospital and Environmental Settings in Lusaka, Zambia: Implications for One Health, Antimicrobial Stewardship and Surveillance Systems

Antimicrobial resistance (AMR) is a public health problem threatening human, animal, and environmental safety. This study assessed the AMR profiles and risk factors associated with Escherichia coli in hospital and environmental settings in Lusaka, Zambia. This cross-sectional study was conducted from April 2022 to August 2022 using 980 samples collected from clinical and environmental settings. Antimicrobial susceptibility testing was conducted using BD PhoenixTM 100. The data were analysed using SPSS version 26.0. Of the 980 samples, 51% were from environmental sources. Overall, 64.5% of the samples tested positive for E. coli, of which 52.5% were from clinical sources. Additionally, 31.8% were ESBL, of which 70.1% were clinical isolates. Of the 632 isolates, 48.3% were MDR. Most clinical isolates were resistant to ampicillin (83.4%), sulfamethoxazole/trimethoprim (73.8%), and ciprofloxacin (65.7%) while all environmental isolates were resistant to sulfamethoxazole/trimethoprim (100%) and some were resistant to levofloxacin (30.6%). The drivers of MDR in the tested isolates included pus (AOR = 4.6, CI: 1.9-11.3), male sex (AOR = 2.1, CI: 1.2-3.9), and water (AOR = 2.6, CI: 1.2-5.8). This study found that E. coli isolates were resistant to common antibiotics used in humans. The presence of MDR isolates is a public health concern and calls for vigorous infection prevention measures and surveillance to reduce AMR and its burdens.

Comparative Genomic Analysis of ST131 Subclade C2 of ESBL-Producing E. coli Isolates from Patients with Recurrent and Sporadic Urinary Tract Infections

The global emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli), mainly causing urinary tract infections (UTI), is a major threat to human health. ESBL-E. coli sequence type (ST) 131 is the dominating clone worldwide, especially its subclade C2. Patients developing recurrent UTI (RUTI) due to ST131 subclade C2 appear to have an increased risk of recurrent infections. We have thus compared the whole genome of ST131 subclade C2 isolates from 14 patients with RUTI to those from 14 patients with sporadic UTI (SUTI). We aimed to elucidate if isolates causing RUTI can be associated with specific genomic features. Paired isolates from patients with RUTI were identical, presenting 2-18 single nucleotide polymorphism (SNP) differences for all six patients investigated. Comparative genomic analyses, including virulence factors, antibiotic resistance, pangenome and SNP analyses did not find any pattern associated with isolates causing RUTI. Despite extensive whole genome analyses, an increased risk of recurrences seen in patients with UTI due to ST131 subclade C2 isolates could not be explained by bacterial genetic differences in the two groups of isolates. Hence, additional factors that could aid in identifying bacterial properties contributing to the increased risk of RUTI due to ESBL-E. coli ST131 subclade C2 remains to be explored.

Co-Harboring of Beta-Lactamases and mcr-1 Genes in Escherichia coli and Klebsiella pneumoniae from Healthy Carriers and Backyard Animals in Rural Communities in Ecuador

Few studies have addressed drug resistance of Enterobacterales in rural communities in developing countries. This study aimed to determine the coexistence of extended-spectrum β-lactamase (ESBL) and carbapenemase genes in Escherichia coli and Klebsiella pneumoniae strains carrying the mcr-1 gene in rural communities in Ecuador from healthy humans and their backyard animals. Sixty-two strains, thirty E. coli and thirty-two K. pneumoniae strains carrying the mcr-1 gene were selected from a previous study. PCR were performed for the presence of ESBLs and carbapenemase genes. The strains were further characterized, and the genetic relationship was studied with multi-locus sequencing typing (MLST) of seven housekeeping genes. Fifty-nine of the sixty-two mcr-1 isolates (95%) harbored at least on β-lactam resistance gene. The most prevalent ESBL genes were the bla_TEM genes (present in in 80% of the E. coli strains) and the bla_SHV gene (present in 84% of the K. pneumoniae strains). MSLT analysis revealed 28 different sequence types (ST); 15 for E. coli and 12 for K. pneumoniae, with most ST never described in humans and animals. The coexistence of mcr-1 and β-lactams resistant genes in E. coli and K. pneumoniae strains is alarming and threatens the efficacy of last-resort antibiotics. Our findings highlight backyard animals as a reservoir of mcr-1/β-lactams resistant genes.

Characterisation of OXA-48-like carbapenemases in Escherichia coli and Klebsiella pneumoniae from North India

The oxacillinase-48 (OXA-48)-like carbapenemases are class D β-lactamases and increasingly reported in Enterobacterial species. The detection of these carbapenemases is challenging and little information is available on the epidemiology and plasmid characteristics of OXA-48-like carbapenemase producers. We detected the presence of OXA-48-like carbapenemases in 500 clinical isolates of Escherichia coli and Klebsiella pneumoniae, followed by detection of other carbapenemases, extended spectrum β-lactamases (ESBLs) and 16S rRNA methyltransferases in OXA-48 producers. Clonal relatedness was studied using pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Finally, plasmid characterisation was performed through conjugation experiment, S1-PFGE and Southern hybridisation. Around 40% of E. coli and K. pneumoniae isolates harboured OXA-48-like β-lactamases. Two OXA-48 allele variants, OXA-232 and OXA-181 were detected in our study. OXA-48 producers co-harbored diverse drug-resistant genes belonging to other classes of carbapenemases, ESBLs and 16S rRNA methyltransferases. OXA-48-like carbapenemase producers exhibited high clonal diversity. Bla OXA-48 carrying plasmids were conjugative, untypable and their size was ~ 45 kb and ~ 104.5 kb in E. coli and K. pneumoniae respectively. In conclusion, OXA-48-like carbapenemases have emerged as major cause of carbapenem resistance in Enterobacteriaceae and probably still being under reported. Strict surveillance and adequate detection methods are needed to prevent the dissemination of OXA-48-like carbapenemases.

The contributions of multidrug resistant clones to the success of pandemic extra-intestinal Pathogenic Escherichia coli

INTRODUCTION

High-risk multidrug (MDR) clones have played essential roles in the global emergence and spread of antimicrobial resistance (AMR), especially among Extra-intestinal Escherichia coli (ExPEC).

AREAS COVERED

Successful global ExPEC MDR clones are linked with the acquisition of fluoroquinolone resistance, CTX-M enzymes, and with carbapenemases. This article described the underlying mechanisms of fluoroquinolone resistance, the acquisition of CTX-M and carbapenemase genes among three global ExPEC high-risk MDR clones, namely i) ST1193 as being an example of a fluoroquinolone resistant clone. ii) ST131 as an example of a fluoroquinolone resistant and CTX-M clone. iii) ST410 as an example of a fluoroquinolone resistant, CTX-M and carbapenemase clone. This article also highlighted the contributions of these MDR determinants in the evolution of these high-risk MDR clones.

EXPERT OPINION

There is an enormous public health burden due to E. coli MDR high-risk clones such as ST1193, ST131 and ST410. These clones have played pivotal roles in the global spread of AMR. Sparse information is available on which specific features of these high-risk MDR clones have enabled them to become such successful global pathogens in relative short time periods.

The Significance of Epidemic Plasmids in the Success of Multidrug-Resistant Drug Pandemic Extraintestinal Pathogenic Escherichia coli

Epidemic IncF plasmids have been pivotal in the selective advantage of multidrug-resistant (MDR) extraintestinal pathogenic Escherichia coli (ExPEC). These plasmids have offered several advantages to their hosts that allowed them to coevolve with the bacterial host genomes and played an integral role in the success of ExPEC. IncF plasmids are large, mosaic, and often contain various types of antimicrobial resistance (AMR) and virulence associated factor (VAF) genes. The presence of AMR, VAF genes, several addition/restriction systems combined with truncated transfer regions, led to the fixation of IncF plasmids in certain ExPEC MDR clones, such as ST131 and ST410. IncF plasmids entered the ST131 ancestral lineage in the mid 1900s and different ST131 clade/CTX-M plasmid combinations coevolved over time. The IncF_CTX-M-15/ST131-C2 subclade combination emerged during the early 2000s, spread rapidly across the globe, and is one of the greatest clone/plasmid successes of the millennium. The ST410-B3 subclade containing bla_CTX-M-15 incorporated the NDM-5 carbapenemase gene into existing IncF platforms, providing an additional positive selective advantage that included the carbapenems. A "plasmid-replacement" clade scenario occurred in the histories of ST131 and ST410 as different subclades gained different AMR genes on different IncF platforms. The use of antimicrobial agents will generate selection pressures that enhance the risks for the continuous emergence of MDR ExPEC clone/IncF plasmid combinations. The reasons for clade/IncF replacements and associations between certain clades and specific IncF plasmid types are unknown. Such information will aid in designing management and prevention strategies to combat AMR.

Incidence and molecular characterization of ESBL-producing and colistin-resistant Escherichia coli isolates recovered from healthy food-producing animals in Pakistan

OBJECTIVES

To investigate the occurrence and molecular features of ESBL-producing and colistin-resistant Escherichia coli isolates recovered from healthy food-producing animals in Pakistan.

METHODS

A total of 153 E. coli isolates were recovered from 250 faecal samples collected from livestock and poultry. The antibiotic susceptibility, resistant determinants and mobile genetic elements were determined for all the isolates. The clonal relatedness was analysed by MLST. Plasmids harbouring, localization and transferability of mcr-1 gene were carried out by Southern hybridization, S1-PFGE and transconjugation.

RESULTS

Out of 153 E. coli strains, 49.01% isolates were ESBLs producers, whereas 18.95% were resistant to colistin and 84.31% of the isolates. Multidrug resistance was found in 84% of the isolates. The ESBL-producing E. coli in buffaloes, cattle, sheep, goat and broilers faecal samples were 60%, 74%, 54%, 50% and 68%, respectively. Among the ESBLs genes, bla_CTX-M was the most prevalent group detected in 98.66%, while only mcr-1 of the colistin-resistant genes could be PCR amplified in 29 isolates. The common MGEs found were ISECP1 (35.13%), ISCR1 (33.78%), ISApl1 (20.27%) and Inti1 (58.10%). The most predominant Inc. types found were IncFIB 46.66%, followed by IncFIA 30.66%, IncFIC 26.66%, IncFrepB 26.66%, IncHI2 26.66%, IncP 22.66% and IncX4 21.33%. The most frequent sequence type detected was ST58. Southern blot and S1-PFGE confirmed the plasmid harbouring of mcr-1 gene.

CONCLUSION

The co-occurrence of mcr-1 and ESBLs-encoding genes, along with MGEs in E. coli from healthy food animals in Pakistan, is a major concern.

SIGNIFICANCE AND IMPACT OF STUDY

Antimicrobial resistance can be transferred from animals to humans by direct contact or via the food chain and environment. The prevalence and co-occurrence of ESBL and colistin resistance genes from food-producing animals is rare in Pakistan. To our knowledge, this is the first report to find ESBLs and mcr-1-harbouring E. coli from the faecal samples of the healthy food-producing animals in Pakistan. The presence of ARGs in association with MGEs, co-harbouring the virulence factors, as determined in the current study, is a severe threat to livestock and the human community as it has horizontally and food web transferability.

Prevalence of Escherichia coli ST1193 Causing Intracranial Infection in Changsha, China

ST1193 is an emerging new virulent and resistant clone among Escherichia coli with a tendency to spread rapidly across the globe. However, the prevalence of intracranial infection-causing E. coli ST1193 is rarely reported. This study aimed at determining the prevalence of E. coli ST1193 isolates, causing intracranial infections in Changsha, central China. A total of 28 E. coli isolates were collected from the cerebrospinal fluid of patients with intracranial infection over a four-year period. All isolates were differentiated using multilocus sequence typing (MLST), and phylogenetic grouping, and tested for antibiotic resistance. MLST analysis showed 11 sequence types (ST) among the 28 E. coli isolates. The most prevalent ST was B2-ST1193 (28.6%, 8/28), followed by B2-ST131 (21.4%, 6/28) and F-ST648 (10.7%, 3/28). Of the eight ST1193 isolates, three carried CTX-M-55, and one carried CTX-M-27. All eight ST1193 isolates were resistant to Ciprofloxacin, showing gyrA1AB/parC4A mutations. Two ST1193 isolates carried the aac(6′)-Ib-cr gene. All ST1193 isolates were recovered from infants with meningitis, with a fatal outcome for one three-month-old infant. ST1193 has emerged as the predominant type of E. coli strain causing intracranial infections in Changsha, China. This study highlights the importance of implementing appropriate surveillance measures to prevent the spread of this emerging public health threat.

Resistance mechanisms in Gram-negative bacteria

Enterobacterales resistant to carbapenems or producing extended-spectrum β-lactamases (ESBL) and non-fermenters resistant to carbapenems present resistance to many of the antimicrobials commonly used in clinical practice, and have been recognized by the World Health Organization as a critical priority for the development of new antimicrobials. In this review, the main mechanisms of resistance of Enterobacterales, Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia to β-lactams, quinolones, aminoglycosides and polymyxins will be addressed. Updated information will be presented on the importance in resistance of antimicrobial modification mechanisms (including class C or extended-spectrum β-lactamases, carbapenemases and aminoglycoside-modifying enzymes), permeability alterations due to porin or lipopolysaccharide expression disorders, production of active efflux pumps, target alterations or protection, and expression of two-component systems.

Changes in Fecal Carriage of Extended-Spectrum β-Lactamase Producing Enterobacterales in Dutch Veal Calves by Clonal Spread of Klebsiella pneumoniae

This study aimed to characterize the changes in fecal carriage of Extended-Spectrum β-Lactamase (ESBL) producing Enterobacterales (ESBL-PE) in a single Dutch veal calves. During the rearing period at the Dutch veal farm, a decrease in fecal carriage of cefotaxime-resistant Escherichia coli isolates was observed after 2 weeks at the veal farm, while an increase of cefotaxime-resistant Klebsiella pneumoniae isolates was demonstrated. E. coli and K. pneumoniae were isolated from rectal swabs collected from 110 veal calves in week 2, 6, 10, 18, and 24 after their arrival at the farm. ESBL-PE isolates were selectively cultured and identified by MALDI-TOF. ESBL genes were characterized by RT-PCR, PCRs, and amplicon sequencing. A total of 80 E. coli and 174 K. pneumoniae strains were isolated from 104 out of 110 veal calves. The prevalence of ESBL-E. coli decreased from week 2 (61%) to week 6 (7%), while an unexpected increase in ESBL-K. pneumoniae colonization was detected in week 6 (80%). The predominant ESBL genes detected in E. coli isolates were bla_CTX-M-15 and the non-ESBL gene bla_TEM-1a, while in K. pneumoniae bla_CTX-M-14 gene was detected in all isolates. Four cefotaxime-resistant K. pneumoniae isolates were randomly selected and characterized in deep by transformation, PCR-based replicon typing, and whole-genome sequencing (WGS). The clonal relatedness of a subgroup of nine animals carrying K. pneumoniae ESBL genes was investigated by Multi Locus sequence typing (MLST). In four ESBL-K. pneumoniae isolates, bla_CTX-M-14 was located on IncFII_K and IncFII_NK plasmid replicons and the isolates were multi-drug resistant (MDR). MLST demonstrated a clonal spread of ESBL-K. pneumoniae ST107. To the best of our knowledge, this is the first study to report a change in fecal carriage of ESBL-PE over time in the same veal calf during the rearing period.

Comparative Metabolic Characterization of Extraintestinal Pathogenic Escherichia coli Blood Isolates from Saudi Arabia

Background

The prevalence of bloodstream infections caused by extraintestinal pathogenic Escherichia coli (ExPEC) has increased substantially. E. coli ST131 is one of the dominant ExPEC clones among E. coli bacteremia population. Metabolism can trigger the pathogenesis of some bacterial isolates, and here we evaluated and compared the metabolic traits of E. coli bacteremia isolates including β-lactamase (BL)/extended-spectrum β-lactamase (ESBL)-positive and ESBL-negative isolates and ST131 and non-ST131 isolates.

Methods

The metabolic profiles of thirty E. coli isolates, obtained from blood samples for hospitalized individuals at a tertiary healthcare facility in Riyadh, were determined using HiMedia carbohydrate test strips. The difference in the utilization ability between isolate groups was then statistically assessed.

Results

Our data found that non-BL/ESBL producers were of low metabolic capacity compared with ESBL-positive isolates although the difference remained insignificant. Higher levels of utilization for some carbohydrates, such as fructose and trehalose, were detected among ST131 isolates when compared with non-ST131, and ST131 was also significantly associated with metabolizing rhamnose. The mean bio-score of both isolate groups was insignificant. We showed no link between metabolism and antimicrobial susceptibility profiles among tested blood isolates.

Conclusion

ST131 blood isolates were slightly higher in their carbohydrate utilization activity than non-ST131. More importantly, ST131 isolates were significantly capable of metabolizing rhamnose. Future research should focus on the factors that might drive the success of major ExPEC clones such as ST131.

High plasmidome diversity of extended-spectrum beta-lactam-resistant Escherichia coli isolates collected during one year in one community hospital

Plasmid-encoded antibiotic resistance encompasses many classes of currently used antibiotics. In globally distributed Escherichia coli lineages plasmids, which spread via horizontal gene transfer, are responsible for the dissemination of genes encoding extended-spectrum β-lactamases (ESBL). In this study, we combined 2nd and 3rd generation sequencing techniques to reconstruct the plasmidome of overall 97 clinical ESBL-E. coli isolates. Our results highlight the enormous plasmid diversity in respect to size, replicon-type and genetic content. Furthermore, we emphasize the diverse plasmid distribution patterns among the clinical isolates and the high intra- and extracellular mobility potential of resistance conferring genes. While the majority of resistance conferring genes were located on large plasmids of known replicon type, small cryptic plasmids seem to be underestimated resistance gene vectors. Our results contribute to a better understanding of the dissemination of resistance-conferring genes through horizontal gene transfer as well as clonal spread.

Draft Genome Sequences of Sixteen Fluoroquinolone-Resistant Extraintestinal Escherichia coli Isolates from Human Patients

We report here the draft genome sequences of 16 fluoroquinolone-resistant extraintestinal Escherichia coli isolates from human patients. These isolates had high MICs (32 to 256 μg/mL) for ciprofloxacin and contained point mutations in the quinolone resistance-determining region (QRDR) of both gyrA and parC that confer resistance to fluoroquinolone. The whole-genome sequence data provide a better understanding of the fluoroquinolone resistance mechanisms in these isolates and would be beneficial in source tracking these pathogens during pandemic outbreaks.

Beta-lactamase resistance genes in Enterobacteriaceae from Nigeria

Background

Beta-lactamase genes are one of the most important groups of antimicrobial resistance genes in human and animal health. Therefore, continuous surveillance of this group of resistance genes is needed for a better understanding of the local epidemiology within a country and global dissemination.

Aim

This review was carried out to identify different beta-lactamase resistance genes reported in published literature from Nigeria.

Methods

Systematic review and meta-analysis was carried out on eligible Nigerian articles retrieved from electronic literature searches of PubMed^®, African Journals Online, and Google Scholar published between January 1990 and December 2019. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses method was adopted to facilitate clarity and transparency in reporting review findings.

Results

Fifty-seven articles were included. All beta-lactamases reported were detected from Gram-negative bacteria, particularly from Enterobacteriaceae. Thirty-six different beta-lactamase genes were reported in Nigeria. These genes belong to the narrow-spectrum, AmpC, extended-spectrum and carbapenemase beta-lactamase resistance genes. The pooled proportion estimate of extended-spectrum beta-lactamase genes in Nigeria was 31% (95% confidence interval [CI]: 26% – 36%, p < 0.0001), while the estimate of the bla_CTX-M-15 gene in Nigeria was 46% (95% CI: 36% – 57%, p < 0.0001). The proportion estimate of AmpC genes was 32% (95% CI: 11% – 52%, p < 0.001), while the estimate for carbapenemases was 8% (95% CI: 5% – 12%, p < 0.001).

Conclusion

This study provides information on beta-lactamase distribution in Nigeria. This is necessary for a better understanding of molecular epidemiology of clinically important beta-lactamases, especially the extended-spectrum beta-lactamases and carbapenemases in Nigeria.

Plasmid Replicon Diversity of Clinical Uropathogenic Escherichia coli Isolates from Riyadh, Saudi Arabia

The aim of this study was to identify and compare the plasmid replicons of clinical uropathogenic Escherichia coli (UPEC) isolates, involving extended spectrum β-lactamase (ESBL)-positive and ESBL-negative, E. coli ST131 and non-ST131 and various ST131 subclones. Plasmid replicon typing on 24 clinical UPEC isolates was carried out using polymerase chain reaction-based replicon typing. A statistical analysis was performed to assess the associations between plasmid replicon types and ESBL carriage, and to evaluate the link between ST131 isolates and high replicon carriage. Eight replicons, I1α, N2, Iγ, X1, FIIS, K, FIA, and FII were detected. The FII was the most common replicon identified here. ESBL-positive E. coli isolates were highly associated with I1α, N2, Iγ, X1, and FIIS replicons, while FIA was present only in ESBL-negative group. ST131 isolates were highly associated with I1α and N2 replicons compared to non-ST131. No link was found between replicon carriage and the number or type of ESBLs in E. coli isolates. The diversity observed in replicon patterns of our clinical E. coli isolates indicates that they might be originated from different sources. The presence of replicons reported previously in animal sources suggests a possible transfer of antimicrobial resistance between animal and human bacterial isolates.

Overcoming the rising incidence and evolving mechanisms of antibiotic resistance by novel drug delivery approaches - An overview

Antimicrobial resistance is a normal evolutionary process for microorganisms. Antibiotics exerted accelerated selective pressure that hasten bacterial resistance through mutation, and acquisition external genes. These genes often carry multiple antibiotic resistant determinants allowing the recipient microbe an instant "super-bug" status. The extent of Antimicrobial Resistance (AMR) has reached a level of global crisis, existing antimicrobials are no long effective in treating infections caused by AMR pathogens. The great majority of clinically available antimicrobial agents are administered through oral and intra-venous routes. Overcoming antibacterial resistance by novel drug delivery approach offered new hopes, particularly in the treatment of AMR pathogens in sites less assessible through systemic circulation such as the lung and skin. In the current review, we will revisit the mechanism and incidence of important AMR pathogens. Finally, we will discuss novel drug delivery approaches including novel local antibiotic delivery systems, hybrid antibiotics, and nanoparticle-based antibiotic delivery systems.

Antibacterial activity of medicinal plants against uropathogenic Escherichia coli

Urinary tract infections (UTIs) are one of the most common bacterial infections with uropathogenic Escherichia coli (UPEC) being the most prevalent causative agent in both complicated and uncomplicated UTIs. Antibiotic resistance among UPEC has been already demonstrated against a wide variety of antibiotics and the situation is continuing to deteriorate increasing the rate of recurrence and the difficulty of treatment and prophylaxis. Recently, a big attention has been paid to non-antibiotic approaches as an alternative to conventional antibiotics. Among many strategies, phytotherapy has gained a special attention worldwide. Herbal remedies have been used in traditional medicine since ancient times and they are well known for their effectiveness in treating many health conditions including UTIs. Researches are conducted continuously to validate the use of many medicinal plants against UPEC, investigate their mechanisms of action, and determine their active constituents. Our extensive review of the recent literature revealed that many phytochemicals are shown to target and inhibit a wide variety of bioprocesses in UPEC, such as adhesion, motility, biofilm formation, and quorum sensing. Such natural approaches are very promising in confronting the antibiotic resistance of UPEC and can be further used to develop plant-based strategies and pharmaceutical products to treat and prevent UTIs caused by UPEC.

The cnf1 gene is associated with an expanding Escherichia coli ST131 H30Rx/C2 subclade and confers a competitive advantage for gut colonization

Epidemiological projections point to acquisition of ever-expanding multidrug resistance (MDR) by Escherichia coli, a commensal of the digestive tract and a source of urinary tract pathogens. Bioinformatics analyses of a large collection of E. coli genomes from EnteroBase, enriched in clinical isolates of worldwide origins, suggest the Cytotoxic Necrotizing Factor 1 (CNF1)-toxin encoding gene, cnf1, is preferentially distributed in four common sequence types (ST) encompassing the pandemic E. coli MDR lineage ST131. This lineage is responsible for a majority of extraintestinal infections that escape first-line antibiotic treatment, with known enhanced capacities to colonize the gastrointestinal tract. Statistical projections based on this dataset point to a global expansion of cnf1-positive multidrug-resistant ST131 strains from subclade H30Rx/C2, accounting for a rising prevalence of cnf1-positive strains in ST131. Despite the absence of phylogeographical signals, cnf1-positive isolates segregated into clusters in the ST131-H30Rx/C2 phylogeny, sharing a similar profile of virulence factors and the same cnf1 allele. The suggested dominant expansion of cnf1-positive strains in ST131-H30Rx/C2 led us to uncover the competitive advantage conferred by cnf1 for gut colonization to the clinical strain EC131GY ST131-H30Rx/C2 versus cnf1-deleted isogenic strain. Complementation experiments showed that colon tissue invasion was compromised in the absence of deamidase activity on Rho GTPases by CNF1. Hence, gut colonization factor function of cnf1 was confirmed for another clinical strain ST131-H30Rx/C2. In addition, functional analysis of the cnf1-positive clinical strain EC131GY ST131-H30Rx/C2 and a cnf1-deleted isogenic strain showed no detectable impact of the CNF1 gene on bacterial fitness and inflammation during the acute phase of bladder monoinfection. Together these data argue for an absence of role of CNF1 in virulence during UTI, while enhancing gut colonization capacities of ST131-H30Rx/C2 and suggested expansion of cnf1-positive MDR isolates in subclade ST131-H30Rx/C2.

Molecular epidemiology of extended-spectrum beta-lactamase-producing extra-intestinal pathogenic Escherichia coli strains over a 2-year period (2017-2019) from Zimbabwe

This study was designed to characterize extended-spectrum beta-lactamase (ESBL)-producing extra-intestinal pathogenic Escherichia coli (E.coli) (ExPEC) associated with urinary tract infections in nine different geographic regions of Zimbabwe over a 2-year period (2017-2019). A total of 48 ESBL-positive isolates from urine specimen were selected for whole-genome sequencing from 1246 Escherichia coli isolates biobanked at the National Microbiology Reference laboratory using phenotypic susceptibility testing results from the National Escherichia coli Surveillance Programme to provide representation of different geographical regions and year of isolation. The majority of ESBL E. coli isolates produced cefotaximase-Munich (CTX-M)-15, CTX-M-27, and CTX-M-14. In this study, sequence types (ST) 131 and ST410 were the most predominant antimicrobial-resistant clones and responsible for the increase in ESBL-producing E. coli strains since 2017. Novel ST131 complex strains were recorded during the period 2017 to 2018, thus showing the establishment and evolution of this antimicrobial-resistant ESBL clone in Zimbabwe posing an important public health threat. Incompatibility group F plasmids were predominant among ST131 and ST410 isolates with the following replicons recorded most frequently: F1:A2:B20 (9/19, 47%), F2:A1: B (5/19, 26%), and F1:A1:B49 (8/13, 62%). The results indicate the need for continuous tracking of different ESBL ExPEC clones on a global scale, while targeting specific STs (e.g. ST131 and ST410) through control programs will substantially decrease the spread of ESBLs among ExPEC.

Clinical Characteristics of Patients and Whole Genome Sequencing-Based Surveillance of Escherichia coli Community-Onset Bloodstream Infections at a Non-tertiary Hospital in CHINA

Background:Escherichia coli is the most common pathogens in patients with community-onset blood stream infections (COBSI). Knowledge of the epidemiology of this disease is crucial to improve allocation of health resources, formulate isolation strategies that prevent transmission, and guide empirical antibiotic therapy.

Methods: This retrospective observational study examined patients with E. coli COBSI (EC-COBSI) at a non-tertiary hospital in China. Whole-genome sequencing and analysis of the isolates was performed. The relationships of clinical variables with antimicrobial resistance and the genetic background of the isolates were examined.

Results: There were 148 isolates in patients with EC-COBSI. All isolates were susceptible to ceftazidime/avibactam, carbapenems, and tigecycline; 35.1% were positive for extended spectrum β-lactamase (ESBL+); and bla_CTX–M–14 was the most common ESBL gene. Patients with ESBL- isolates were more likely to receive appropriate empiric treatment than those with ESBL+ isolates (61.5% vs. 91.4%, p < 0.001), but these two groups had similar mortality rates. The overall 30-day mortality rate was 9.5%. Phylogenetic analysis showed that the isolates were diverse, and that the main sequence types (STs) were ST95, ST131, and ST69. Intra-abdominal infection was the primary source of disease, and isolates from these patients had lower frequencies of virulence genes.

Conclusion: The mortality rate of patients with EC-COBSI was unrelated to ESBL status of the isolates. Most isolates had low resistance to most of the tested antimicrobial agents. The isolates were diverse, and multiple strains were related. Prevention and control of EC-COBSI should target prevention of patient colonization and the living environment.

Mechanisms Involved in the Active Secretion of CTX-M-15 β-Lactamase by Pathogenic Escherichia coli ST131

Infections caused by antimicrobial-resistant bacterial pathogens are fast becoming an important global health issue. Strains of Escherichia coli are common causal agents of urinary tract infection and can carry multiple resistance genes. This includes the gene blaCTX-M-15, which encodes an extended-spectrum beta-lactamase (ESBL). While studying antimicrobial resistance (AMR) in the environment, we isolated several strains of E. coli ST131 downstream of a wastewater treatment plan (WWTP) in a local river. These isolates were surviving in the river sediment, and characterization proved that a multiresistant phenotype was evident. Here, we show that E. coli strain 48 (river isolate ST131) provided a protective effect against a third-generation cephalosporin (cefotaxime) for susceptible E. coli strain 33 (river isolate ST3576) through secretion of a functional ESBL into the growth medium. Furthermore, extracellular ESBL activity was stable for at least 24 h after secretion. Proteomic and molecular genetic analyses identified CTX-M-15 as the major secreted ESBL responsible for the observed protective effect. In contrast to previous studies, outer membrane vesicles (OMVs) were not the route for CTX-M-15 secretion. Indeed, mutation of the type I secretion system led to a significant reduction in the growth of the ESBL-producing strain as well as a significantly reduced ability to confer protective effect. We speculate that CTX-M-15 secretion, mediated through active secretion using molecular machinery, provides a public goods service by facilitating the survival of otherwise susceptible bacteria in the presence of cefotaxime.

Antimicrobial Resistance and Molecular Epidemiology of Uropathogenic Escherichia coli Isolated From Female Patients in Shanghai, China

Urinary tract infection (UTI) is one of the most common bacterial infections and UTI is the most common extraintestinal infectious disease entity in women worldwide. Uropathogenic Escherichia coli (UPEC) is the leading cause of UTI. While antimicrobial resistance has emerged as one of the principal problems of UTI, little is known about the epidemiology of UPEC isolated from female patients in Shanghai. This study aimed to describe the antimicrobial resistance and molecular epidemiology of UPEC isolated from female patients in Shanghai, China. UPEC isolates were collected from female patients from July 2019 to June 2020 in Shanghai and a total of 151 isolates were obtained randomly. Antimicrobial susceptibility testing was performed using the disk diffusion method. Multilocus sequencing type, phylogenetic groups, antimicrobial resistance genes, and virulence genes were detected by polymerase chain reaction. In our study, no carbapenem-resistant isolates were found, but fluoroquinolone-resistant and multi-drug resistant UPEC accounted for 62.25% and 42.38%, respectively. The phylogenetic group B2 (58.94%) predominated, followed by phylogenetic group D (26.49%). The most prevalent sequence type was ST1193 (25.83%), which was first reported in Shanghai. The rate of extended-spectrum β-lactamase (ESBL)-positive isolates was 39.74% and the dominant ESBL genotype was bla_CTX-M-14 (21/60), followed by bla_CTX-M-55 (12/60). Mutations in gyrA were detected in the majority of fluoroquinolone-resistant isolates (90/94), followed by parC (85/94) and parE (71/94). The aac (3) -IIa was also found in 85% of aminoglycoside resistance isolates. Among 151 UPEC isolates, the common virulence genes were csgA (97.35%), fimH (92.72%), sitA (82.12%), and malX (65.56%). In conclusion, the high antimicrobial resistance of UPEC isolated from female patients, harboring a series of virulence genes, are troublesome for medical practitioners in Shanghai. At present, the prevalent ST1193 and emerging bla_CTX-M-55 make UTI therapy more challenging.

Infective Endocarditis Caused by Extended-Spectrum Beta-Lactamase-Producing Escherichia coli: A Case Report

Introduction

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) reportedly accounts for >20% of E. coli infections and 2.0% of infective endocarditis cases. Nonetheless, there is a global paucity of reports on infective endocarditis caused by ESBL-EC.

Case

An 83-year-old Japanese man who underwent mitral annuloplasty for mitral valve prolapse 5 years ago developed a fever of 38.5°C. The patient was hospitalized the first time for pyelonephritis and bacteremia due to ESBL-EC and treated successfully with the antimicrobial meropenem for 14 days. Two days after discharge, however, the patient was re-admitted with bacteremia due to ESBL-EC. He was treated successfully with the antimicrobial cefmetazole for 14 days. The patient was admitted to our institution for a third time due to bacteremia again, a day after discharge following meropenem antibiotic therapy. Transesophageal echocardiography showed vegetation in the anterior mitral valve annulus. Magnetic resonance imaging of the head showed septic cerebral embolism. The patient was diagnosed with infective endocarditis due to ESBL-EC and underwent mitral valve replacement. After 6 weeks of antibiotic therapy with meropenem and tobramycin, the patient recovered completely. The causative E. coli strain MS6396 was identified as the E. coli clone ST131 by multilocus sequence typing and confirmed the presence of bla_CTX-M-27 ESBL gene.

Conclusion

Only six cases of infective endocarditis associated with ESBL-EC have been reported in the past. Moreover, this is the first report of a patient with infective endocarditis bacteriologically or genetically analyzed for ESBL-EC. In future, factors that may cause infective endocarditis in ESBL-EC infections may be clarified through more thorough bacteriological/genetic analyses of ESBL-EC.

Arrangements of Mobile Genetic Elements among Virotype E Subpopulation of Escherichia coli Sequence Type 131 Strains with High Antimicrobial Resistance and Virulence Gene Content

Escherichia coli sequence type 131 (ST131) is known for its contribution to multidrug resistance and the worldwide spread of this clone has become a global problem. Understanding the trends among ST131 clades will help design strategies to prevent its rapid dissemination. In this study, 72 ST131 strains were subjected to comparative genomic analysis and 64 clade C strains were compared with clade C strains reported from other regions using publicly available whole-genome sequencing data. C1 (n = 31 [48.4%]) and C2 (n = 33 [%51.5]) strains had the same prevalence in our collection, and C1-M27 (n = 22) strains were closely related, carried a unique plasmid type (F1:A2:B20), and exhibited virotype C. Removal of 11 C2 strains with varied virotype patterns and the heterogeneous IncF type identified 22 closely related virotype E/F strains with replicon type F31/F36:A4:B1, forming what we denote as the “C2-subset.” In a global context, the C2-subset constituted a distinct cluster with international virotype E strains and harbored a genomic island, GI-pheU. Association of cnf1/hlyCABD genes with 1 to 7 mobile genetic elements, mostly IS682/ISKpn37 combination within GI-pheU was identified. The C2-subset accounted for excess resistance/virulence of subclade C2 relative to C1 strains. In addition, a conserved chromosomal IS26-mediated composite transposon (IS15DIV-ISEcp1-bla_CTX-M-15-WbuC cupin fold metalloprotein-Tn2-IS15DIV) was observed in the C2-subset. The local spread of the C2-subset in the hospital studied, with the carriage of higher virulence/resistance markers and a peculiar F-type plasmid, demonstrates the potential for diversification of the ST131 lineage and the emergence of subpopulations with higher survival potential to cause health care-associated outbreaks.

IMPORTANCEEscherichia coli sequence type 131 (ST131) is a globally dominant multidrug-resistant clone that is commonly associated with extraintestinal infections. Specific sublineages have been shown to have emerged and spread within ST131, highlighting the complex nature of ST131 epidemiology. This study systematically compared the Iranian ST131 population to those reported from other countries and found a subpopulation harboring virotype E, a homogeneous profile of plasmid Inc-F type F31/F36:A4:B1 harboring cnf1/hemolysin genes on the genomic island GI-pheU, and up to seven mobile genetic elements (MGEs) flanking cnf1/hemolysin virulence markers. The results of this study highlight the importance of MGEs for virulence gene acquisition and the formation of new subpopulations among pandemic clones such as E. coli ST131.

Antibiotic resistance and detection of plasmid mediated colistin resistance mcr-1 gene among Escherichia coli and Klebsiella pneumoniae isolated from clinical samples

BACKGROUND

The prevalence of antimicrobial resistance (AMR) among Gram-negative bacteria is alarmingly high. Reintroduction of colistin as last resort treatment in the infections caused by drug-resistant Gram-negative bacteria has led to the emergence and spread of colistin resistance. This study was designed to determine the prevalence of drug-resistance among beta-lactamase-producing strains of Escherichia coli and Klebsiella pneumoniae, isolated from the clinical specimens received at a tertiary care centre of Kathmandu, Nepal during the period of March to August, 2019.

METHODS

A total of 3216 different clinical samples were processed in the Microbiology laboratory of Kathmandu Model Hospital. Gram-negative isolates (E. coli and K. pneumoniae) were processed for antimicrobial susceptibility test (AST) by using modified Kirby-Bauer disc diffusion method. Drug-resistant isolates were further screened for extended-spectrum beta-lactamase (ESBL), metallo-beta-lactamase (MBL), carbapenemase and K. pneumoniae carbapenemase (KPC) production tests. All the suspected enzyme producers were processed for phenotypic confirmatory tests. Colistin resistance was determined by minimum inhibitory concentration (MIC) using agar dilution method. Colistin resistant strains were further screened for plasmid-mediated mcr-1 gene using conventional polymerase chain reaction (PCR).

RESULTS

Among the total samples processed, 16.4% (529/3216) samples had bacterial growth. A total of 583 bacterial isolates were recovered from 529 clinical samples. Among the total isolates, 78.0% (455/583) isolates were Gram-negative bacteria. The most predominant isolate among Gram-negatives was E. coli (66.4%; 302/455) and K. pneumoniae isolates were 9% (41/455). In AST, colistin, polymyxin B and tigecycline were the most effective antibiotics. The overall prevalence of multidrug-resistance (MDR) among both of the isolates was 58.0% (199/343). In the ESBL testing, 41.1% (n = 141) isolates were confirmed as ESBL-producers. The prevalence of ESBL-producing E. coli was 43% (130/302) whereas that of K. pneumoniae was 26.8% (11/41). Similarly, 12.5% (43/343) of the total isolates, 10.9% (33/302) of E. coli and 24.3% of (10/41) K. pneumoniae were resistant to carbapenem. Among 43 carbapenem resistant isolates, 30.2% (13/43) and 60.5% (26/43) were KPC and MBL-producers respectively. KPC-producers isolates of E. coli and K. pneumoniae were 33.3% (11/33) and 20% (2/10) respectively. Similarly, 63.6% (21/33) of the E. coli and 50% (5/10) of the K. pneumoniae were MBL-producers. In MIC assay, 2.2% (4/179) of E. coli and 10% (2/20) of K. pneumoniae isolates were confirmed as colistin resistant (MIC ≥ 4 µg/ml). Overall, the prevalence of colistin resistance was 3.1% (6/199) and acquisition of mcr-1 was 16.6% (3/18) among the E. coli isolates.

CONCLUSION

High prevalence of drug-resistance in our study is indicative of a deteriorating situation of AMR. Moreover, significant prevalence of resistant enzymes in our study reinforces their roles in the emergence of drug resistance. Resistance to last resort drug (colistin) and the isolation of mcr-1 indicate further urgency in infection management. Therefore, extensive surveillance, formulation and implementation of effective policies, augmentation of diagnostic facilities and incorporation of antibiotic stewardship programs can be some remedies to cope with this global crisis.

Emergence and Spread of Cephalosporinases in Wildlife: A Review

Simple Summary

Antimicrobial resistance (AMR) is one of the global public health challenges nowadays. AMR threatens the effective prevention and treatment of an ever-increasing range of infections, being present in healthcare settings but also detected across the whole ecosystem, including wildlife. This work compiles the available information about an important resistance mechanism that gives bacteria the ability to inactivate cephalosporin antibiotics, the cephalosporinases (extended-spectrum beta-lactamase (ESBL) and AmpC beta-lactamase), in wildlife. Through a rigorous systematic literature review in the Web of Science database, the available publications on this topic in the wildlife sphere were analysed. The emergence and spread of cephalosporinases in wildlife has been reported in 46 countries from all continents (52% in Europe), with descriptions mainly in birds and mammals. The most widely disseminated cephalosporinases in human-related settings (e.g. CTX-M-1, CTX-M-14, CTX-M-15 and CMY-2) are also the most reported in wildlife, suggesting that anthropogenic pressure upon natural environments have a strong impact on antimicrobial resistance spread, including the dissemination of genes encoding these enzymes. Our work highlights the urgence and importance of public and ecosystem health policies, including improved surveillance and control strategies that breakdown AMR transmission chains across wildlife, as part of an integrated strategy of the One Health approach.

Abstract

In the last decade, detection of antibiotic resistant bacteria from wildlife has received increasing interest, due to the potential risk posed by those bacteria to wild animals, livestock or humans at the interface with wildlife, and due to the ensuing contamination of the environment. According to World Health Organization, cephalosporins are critically important antibiotics to human health. However, acquired resistance to β-lactams is widely distributed and is mainly mediated by extended-spectrum beta-lactamase and AmpC beta-lactamases, such as cephalosporinases. This work thus aimed to compile and analyse the information available on the emergence and dissemination of cephalosporinases in wildlife worldwide. Results suggest a serious scenario, with reporting of cephalosporinases in 46 countries from all continents (52% in Europe), across 188 host species, mainly birds and mammals, especially gulls and ungulates. The most widely reported cephalosporinases, CTX-M-1, CTX-M-14, CTX-M-15 and CMY-2, were also the most common in wild animals, in agreement with their ubiquity in human settings, including their association to high-risk clones of Escherichia coli (E. coli), such as the worldwide distributed CTX-M-15/ST131 E. coli. Altogether, our findings show that anthropogenic activities affect the whole ecosystem and that public policies promoting animal and environmental surveillance, as well as mitigation measures to avoid antimicrobial misuse and AMR spread, are urgently needed to be out in practise.

Trends in Population Dynamics of Escherichia coli Sequence Type 131, Calgary, Alberta, Canada, 2006-20161

Global expansion of antimicrobial drug–resistant Escherichia coli sequence type (ST) 131 is unrivaled among human bacteria. Understanding trends among ST131 clades will help with designing prevention strategies. We screened E. coli from blood samples (n = 1,784) obtained in Calgary, Alberta, Canada, during 2006, 2012, and 2016 by PCR for ST131 and positive samples (n = 344) underwent whole-genome sequencing. The incidence rate per 100,000 residents increased from 4.91 during 2006 to 12.35 during 2012 and 10.12 during 2016. ST131 belonged to clades A (10%), B (9%), and C (81%). Clades C1-nonM27 and B were common during 2006, and C2 containing bla_CTX-M-15, C1-M27 containing bla_CTX-M-27, and A were responsible for the increase of ST131 during 2012 and 2016. C2 was the most antimicrobial drug–resistant subclade and increased exponentially over time. Eradicating ST131, more specifically the C2 subclade, will lead to considerable public health benefits for persons in Calgary.

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.

Genetic Environments of Plasmid-Mediated blaCTXM-15 Beta-Lactamase Gene in Enterobacteriaceae from Africa

The most widely distributed blaCTX-M gene on a global scale is blaCTX-M-15. The dissemination has been associated with clonal spread and different types of mobile genetic elements. The objective of this review was to describe the genetic environments of the blaCTX-M-15 gene detected from Enterobacteriaceae in published literature from Africa. A literature search for relevant articles was performed through PubMed, AJOL, and Google Scholar electronic databases; 43 articles from 17 African countries were included in the review based on the eligibility criteria. Insertion sequences were reported as part of the genetic environment of blaCTX-M-15 gene in 32 studies, integrons in 13 studies, and plasmids in 23 studies. In this review, five insertion sequences including ISEcp1, IS26, orf447, IS903, and IS3 have been detected which are associated with the genetic environment of blaCTX-M-15 in Africa. Seven different genetic patterns were seen in the blaCTX-M-15 genetic environment. Insertion sequence ISEcp1 was commonly located upstream of the end of the blaCTX-M-15 gene, while the insertion sequence orf477 was located downstream. In some studies, ISEcp1 was truncated upstream of blaCTX-M-15 by insertion sequences IS26 and IS3. The class 1 integron (Intl1) was most commonly reported to be associated with blaCTX-M-15 (13 studies), with Intl1/dfrA17–aadA5 being the most common gene cassette array. IncFIA-FIB-FII multi-replicons and IncHI2 replicon types were the most common plasmid replicon types that horizontally transferred the blaCTX-M-15 gene. Aminoglycoside-modifying enzymes, and plasmid-mediated quinolone resistance genes were commonly collocated with the blaCTX-M-15 gene on plasmids. This review revealed the predominant role of ISEcp1, Intl1 and IncF plasmids in the mobilization and continental dissemination of the blaCTX-M-15 gene in Africa.

Multidrug Resistance Dissemination in Escherichia coli Isolated from Wild Animals: Bacterial Clones and Plasmid Complicity

Objectives. Epidemiological data concerning third-generation cephalosporin (3GC) resistance in wild fauna are scarce. The aim of this study was to characterize the resistance genes, their genetic context, and clonal relatedness in 17 Escherichia coli resistant to 3GC isolated from wild animals. Methods. The isolates were characterized by short-read whole genome sequencing, and long-read sequencing was used for the hybrid assembly of plasmid sequences. Results. The 3GC resistance gene most identified in the isolates was the extended-spectrum β-lactamases (ESBL)-encoding gene blaCTX-M-1 (82.3%), followed by blaCTX-M-32 (5.9%), blaCTX-M-14 (5.9%), and blaSHV-12 (5.9%). E. coli isolates mainly belonged to the sequence types (STs) rarely reported from humans. The single nucleotide polymorphism (SNP)-based typing showed that most E. coli genomes from wild animals (wild boars, birds of prey, and buzzards) formed clonal clusters (<5 SNPs), showing a clonal dissemination crossing species boundaries. blaCTX-M-1-harboring IncI1-ST3 plasmid was the predominant ESBL-encoding plasmid (76.4%) in wild animal isolates. Plasmid comparison revealed a 110-kb self-transferable plasmid consisting of a conserved backbone and two variable regions involved in antimicrobial resistance and in interaction with recipient cells during conjugation. Conclusion. Our results highlighted the unexpected clonal dissemination of blaCTX-M-1-encoding clones and the complicity of IncI1-ST3 plasmid in the spread of blaCTX-M-1 within wild fauna.

Comparative phenotypic characterization identifies few differences in the metabolic capacity between Escherichia coli ST131 subclones

Background

Extraintestinal pathogenic Escherichia coli (ExPEC) is responsible for causing many infections such as urinary tract infections (UTIs). The current dissemination of the multidrug resistant (MDR) ExPEC clone, Escherichia coli sequence type 131 (E. coli ST131), poses a real threat to public health worldwide. This study aimed to determine and compare the metabolic capacity of a collection of ExPEC isolates including ST131, non-ST131 and various ST131 subclones, and sought to assess the association between antimicrobial resistance and metabolic capacity of ST131 isolates.

Methods

The metabolic activity of forty urine E. coli isolates, collected from in-patients hospitalized at tertiary hospital in Riyadh, was tested using KB009 Hi carbohydrate kit, and then statistically analysed to assess the difference in the metabolic profiles between ST131 and non-ST131 isolates, and between ST131 subclones.

Results

The data of this study found almost similar metabolic profiles between ST131 and non-ST131, suggesting that ST131 is not a metabolically unique clone of ExPEC. There was also no link between antimicrobial susceptibility profiles and high metabolic capacity of ST131 isolates. Testing the biochemical activity of isolates belonging to ST131 subclones found higher activity of H30 subclone than non-H30 isolates, however it revealed few significant differences between these subclones.

Conclusion

This study demonstrated no difference in the metabolism of ST131 and non-ST131, although it uncovered the presence of few significant differences in the metabolic capacity between ST131 subclones. Carrying out whole-genome based studies on ST131 and its main subclones is essential to elucidate the genetic factors responsible for the success of particular ST131 subclones.