Current epidemiology, genetic evolution and clinical impact of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae

Characteristics of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae and Contact to Animals in Estonia

We have attempted to define the prevalence and risk factors of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-Enterobacteriaceae) carriage, and to characterize antimicrobial susceptibility, beta-lactamase genes, and major types of isolated strains in volunteers, with a specific focus on humans in contact with animals. Samples were collected from 207 volunteers (veterinarians, pig farmers, dog owners, etc.) and cultured on selective agar. Clonal relationships of the isolated ESBL-Enterobacteriaceae were determined by whole genome sequencing and multi-locus sequence typing. Beta-lactamases were detected using a homology search. Subjects filled in questionnaires analyzed by univariate and multiple logistic regression. Colonization with ESBL-Enterobacteriaceae was found in fecal samples of 14 individuals (6.8%; 95%CI: 3.75–11.09%). In multiple regression analysis, working as a pig farmer was a significant risk factor for ESBL-Enterobacteriaceae carriage (OR 4.8; 95%CI 1.2–19.1). The only species isolated was Escherichia coli that distributed into 11 sequence types. All ESBL-Enterobacteriaceae isolates were of CTX-M genotype, with the blaCTX-M-1 being the most prevalent and more common in pig farmers than in other groups. Despite the generally low prevalence of ESBL-Enterobacteriaceae in Estonia, the pig farmers may still pose a threat to transfer resistant microorganisms. The clinical relevance of predominant blaCTX-M-1 carrying E. coli is still unclear and needs further studies.

Restoration of the Antibiotic Susceptibility of Methicillin-Resistant Staphylococcus aureus and Extended-Spectrum β-Lactamases Escherichia coli Through Combination with Chelerythrine

Multidrug resistance poses a severe threat to public health and urgently requires new solutions. The natural product chelerythrine (CHE) is a benzophenanthridine alkaloid with antimicrobial potential. In this study, CHE was effective against seven gram-positive bacterial strains, and the minimum inhibitory concentrations (MICs) ranged from 2 to 4 μg/mL. By contrast, CHE showed inferior antibacterial activities against 11 gram-negative strains, and the MICs varied from 16 to 256 μg/mL. We also determined the synergistic/additive effects of combining CHE with nine currently used antibiotics. CHE restored the antibacterial efficacy of the antibiotics against methicillin-resistant Staphylococcus aureus and extended-spectrum β-lactamases producing Escherichia coli. This study suggests that the combination of CHE with conventional antibiotics may be a promising strategy to combat infections caused by multidrug-resistant organisms.

Antibiotic multi-drug-resistance of Escherichia coli causing device- and procedure-related infections in the United States reported to the National Healthcare Safety Network (NHSN), 2013-2017

BACKGROUND

Escherichia coli is one of the most common causes of healthcare-associated infections (HAI); multidrug resistance reduces available options for antibiotic treatment. We examined factors associated with the spread of multidrug-resistant E. coli phenotypes responsible for device- and procedure-related HAI from acute care hospitals, long term acute care hospitals and inpatient rehabilitation facilities, using isolate and antimicrobial susceptibility data reported to the National Healthcare Safety Network (NHSN) from 2013-2017.

METHODS

We used multivariable logistic regression to examine associations between co-resistant phenotypes, patient and healthcare facility characteristics, and time. We also examined the geographic distributione of co-resistant phenotypes each year by state and by hospital referral region to identify hot spots.

RESULTS

A total of 96,672 E. coli isolates were included. Patient median age was 62 years; 60% were females; over half (54%) were reported from catheter-associated urinary tract infections. From 2013-2017, 35% of the isolates were non-susceptible to FQs; 17% to ESCs; and 13% to both ESCs and FQs. The proportion of isolates co-resistant to ESCs and FQs was higher in 2017 (14%) than in 2013 (11%) (P<0.0001); overall prevalence and increases were heterogeneously distributed across healthcare referral regions. Co-resistance to FQs and ESCs was independently associated with male sex, central line-associated bloodstream infections, long-term acute care hospitals, and the 2016-17 (v. 2013-14) reporting period.

CONCLUSIONS

Multidrug-resistance among E.coli causing device- and procedure-related HAIs has increased in the United States. FQ and ESC co-resistant strains appear to be spreading heterogeneously across hospital referral regions.

Molecular Mechanisms, Epidemiology, and Clinical Importance of β-Lactam Resistance in Enterobacteriaceae

Despite being members of gut microbiota, Enterobacteriaceae are associated with many severe infections such as bloodstream infections. The β-lactam drugs have been the cornerstone of antibiotic therapy for such infections. However, the overuse of these antibiotics has contributed to select β-lactam-resistant Enterobacteriaceae isolates, so that β-lactam resistance is nowadays a major concern worldwide. The production of enzymes that inactivate β-lactams, mainly extended-spectrum β-lactamases and carbapenemases, can confer multidrug resistance patterns that seriously compromise therapeutic options. Further, β-lactam resistance may result in increases in the drug toxicity, mortality, and healthcare costs associated with Enterobacteriaceae infections. Here, we summarize the updated evidence about the molecular mechanisms and epidemiology of β-lactamase-mediated β-lactam resistance in Enterobacteriaceae, and their potential impact on clinical outcomes of β-lactam-resistant Enterobacteriaceae infections.

Dissemination of the blaCTX-M-15 gene among Enterobacteriaceae via outer membrane vesicles

Background

Bacterial outer membrane vesicles (OMVs) are an emerging source of antibiotic resistance transfer but their role in the spread of the blaCTX-M-15 gene encoding the most frequent CTX-M ESBL in Enterobacteriaceae is unknown.

Objectives

To determine the presence of blaCTX-M-15 and other antibiotic resistance genes in OMVs of the CTX-M-15-producing MDR Escherichia coli O104:H4 outbreak strain and the ability of these OMVs to spread these genes among Enterobacteriaceae under different conditions.

Methods

OMV-borne antibiotic resistance genes were detected by PCR; OMV-mediated transfer of blaCTX-M-15 and the associated blaTEM-1 was quantified under laboratory conditions, simulated intraintestinal conditions and under ciprofloxacin stress; resistance to antibiotics and the ESBL phenotype were determined by the CLSI disc diffusion methods and the presence of pESBL by plasmid profiling and Southern blot hybridization.

Results

E. coli O104:H4 OMVs carried blaCTX-M-15 and blaTEM-1 located on the pESBL plasmid, but not chromosomal antibiotic resistance genes. The OMVs transferred blaCTX-M-15, blaTEM-1 and the associated pESBL into Enterobacteriaceae of different species. The frequencies of the OMV-mediated transfer were significantly increased under simulated intraintestinal conditions and under ciprofloxacin stress when compared with laboratory conditions. The ‘vesiculants’ (i.e. recipients that received the blaCTX-M-15- and blaTEM-1-harbouring pESBL via OMVs) acquired resistance to cefotaxime, ceftazidime and cefpodoxime and expressed the ESBL phenotype. They were able to further spread pESBL and the blaCTX-M-15 and blaTEM-1 genes via OMVs.

Conclusions

OMVs are efficient vehicles for dissemination of the blaCTX-M-15 gene among Enterobacteriaceae and may contribute to blaCTX-M-15 transfer in the human intestine.

Clinical and computed tomography features of extended-spectrum β-lactamase-producing Klebsiella pneumoniae liver abscess

Background

Klebsiella pneumoniae (KP) is the primary pathogen associated with pyogenic liver abscesses (PLAs). Moreover, there has been an increase in the proportion of extended-spectrum beta-lactamase (ESBL)-producing KP. However, the clinical and computed tomography (CT) features of liver abscesses caused by ESBL-producing KP have not been separately described. We aimed to compare the clinical and CT features present in patients with ESBL-producing and non-ESBL-producing KP as well as to determine the risk factors for ESBL-producing KP liver abscesses (KPLAs).

Methods

We performed a retrospective analysis of data obtained from the medical records of patients with a first episode of KPLA admitted to Shengjing Hospital of China Medical University between May 2015 and May 2019. We compared the clinical and CT features between patients with ESBL-producing and non-ESBL-producing KPLA.

Results

We enrolled 100 patients with KPLA (14 and 86 in the ESBL-producing and non-ESBL-producing groups, respectively). There was no significant between-group difference in the proportion of patients with comorbid diabetes (71.43% vs. 66.2%, p = 0.086). The ESBL-producing KPLA group had a greater proportion of patients with a history of biliary disease (78.57% vs. 26.74%, p < 0.001) and gastrointestinal malignancy (50% vs. 6.98%, p < 0.001). Multivariate regression analysis showed that a history of biliary disease was an independent risk factor for ESBL-producing KPLA. Compared with the non-ESBL-producing KPLA group, the ESBL-producing KPLA group had a significantly higher intensive care unit (ICU) admission rate (28.57% vs. 2.33%, p < 0.001). All ESBL-producing KP isolates were susceptible to carbapenems and amikacin. Only the presence of multiloculation on CT was found to be significantly different between the groups (50% vs. 82.56%, p = 0.012).

Conclusions

The presence of biliary disease was an independent risk factor for ESBL-producing KPLA. Patients with ESBL-producing KPLA had a higher ICU admission rate, with only half of patients having evidence of multiloculation on CT.

Multi-Drug-Resistant Diarrheagenic Escherichia coli Pathotypes in Pediatric Patients with Gastroenteritis from Central Iran

Background

Diarrheagenic Escherichia coli (DEC) is a significant cause of gastroenteritis and a major public health problem. This study investigates the prevalence and the antibiotic resistance patterns of DEC that were isolated from infectious diarrhea samples of pediatric patients from central Iran.

Patients and Methods

Pediatric diarrhea samples were collected from 230 pediatric patients visiting the hospital. E. coli pathotypes were diagnosed by using conventional culture methods and PCR. Antibiotic resistance profiles, the frequency of multi-drug resistance (MDR), and the phenotypic and genotypic characteristics of extended spectrum-β-lactamase (ESBL), AmpC and integron-associated genes were analyzed.

Results

Of the 230 samples of infectious diarrhea, 91 (39.5%) produced E. coli isolates. Of these, 32 cases (35.1%) were identified as DEC by culture and PCR. The frequency of the E. coli pathotypes obtained was as follows: EAEC 11/32 (34.3%), EPEC 9/32 (28.1%), ETEC 6/32 (18.7%), EIEC 3/32 (9.3%), and EHEC 3/32 (9.3%). The antibiotic resistance rates were greater for nalidixic acid (30/32; 93.7%), ampicillin (29/32; 90.6%), and tetracycline (25/32; 78.1%) than for any of the other tested antibiotics. High levels of MDR (25/32; 78.1%) and the presence of ESBL (18/32; 56.2%) and AmpC (9/32; 28.1%) were observed in the DEC isolates. The isolates showed a higher frequency of the ESBL genes [bla_TEM (18/18; 100%), bla_CTX-M15 (17/18; 94.4%)], and AmpC [bla _CIT (4/9; 44.4%) and bla_DHA (4/9; 44.4%)] than of the other ESBL and AmpC genes.

Conclusion

Compared to the previous study, DEC appeared to be the second-most abundant agent of diarrhea in pediatric patients after Campylobacter jejuni, with frequent MDR and ESBL presence.

Antibiotic Resistance of Escherichia coli from Humans and Black Rhinoceroses in Kenya

Upsurge of antibiotic resistance in wildlife poses unprecedented threat to wildlife conservation. Surveillance of antibiotic resistance at the human-wildlife interface is therefore needed. We evaluated differences in antibiotic resistance of Escherichia coli isolates from human and the endangered black rhinoceros in Lambwe Valley, Kenya. We used standard microbiological techniques to carry out susceptibility assays using eight antibiotics of clinical and veterinary importance. Standard PCR method was used to characterize antibiotic resistance genes. There was no difference in resistance between E. coli isolates from human and those from rhinoceros (U = 25, p = 0.462). However, higher resistance in isolates from humans was noted for cotrimoxazole (p = 0.000, OR = 0.101), ceftriaxone (p = 0.005, OR = 0.113) and amoxicillin/clavulanic acid (p = 0.017, OR = 0.258), whereas isolates from rhinoceros showed higher gentamicin resistance (p = 0.001, OR = 10.154). Multi-drug resistance phenotype was 69.0% in humans and 43.3% in rhinoceros. Isolates from both species contained bla_TEM, tetA, tetB, dfrA1 and sul1 genes. Resistance profiles in the two species suggest potential for cross-transfer of resistance genes or exposure to comparable selective pressure and call for a multi-sectorial action plan on surveillance of antibiotic resistance at the human-wildlife interface. Genome-wide studies are needed to explicate the direction of transfer of genes that confer antibiotic resistance at the human-wildlife interface.

Global Evolution of Pathogenic Bacteria With Extensive Use of Fluoroquinolone Agents

It is well-established that the spread of many multidrug-resistant (MDR) bacteria is predominantly clonal. Interestingly the international clones/sequence types (STs) of most pathogens emerged and disseminated during the last three decades. Strong experimental evidence from multiple laboratories indicate that diverse fitness cost associated with high-level resistance to fluoroquinolones contributed to the selection and promotion of the international clones/STs of hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA), extended-spectrum β-lactamase-(ESBL)-producing Klebsiella pneumoniae, ESBL-producing Escherichia coli and Clostridioides difficile. The overwhelming part of the literature investigating the epidemiology of the pathogens as a function of fluoroquinolone use remain in concordence with these findings. Moreover, recent in vitro data clearly show the potential of fluoroquinolone exposure to shape the clonal evolution of Salmonella Enteritidis. The success of the international clones/STs in all these species was linked to the strains' unique ability to evolve multiple energetically beneficial gyrase and topoisomerase IV mutations conferring high-level resistance to fluorquinolones and concomittantly permitting the acquisition of an extra resistance gene load without evoking appreciable fitness cost. Furthermore, by analyzing the clonality of multiple species, the review highlights, that in environments under high antibiotic exposure virulence factors play only a subsidiary role in the clonal dynamics of bacteria relative to multidrug-resistance coupled with favorable fitness (greater speed of replication). Though other groups of antibiotics should also be involved in selecting clones of bacterial pathogens the role of fluoroquinolones due to their peculiar fitness effect remains unique. It is suggested that probably no bacteria remain immune to the influence of fluoroquinolones in shaping their evolutionary dynamics. Consequently a more judicious use of fluoroquinolones, attuned to the proportion of international clone/ST isolates among local pathogens, would not only decrease resistance rates against this group of antibiotics but should also ameliorate the overall antibiotic resistance landscape.

Molecular characteristics of extended-spectrum β-lactamase/AmpC-producing Salmonella enterica serovar Virchow isolated from food-producing animals during 2010-2017 in South Korea

Global dissemination of non-typhoidal Salmonella producing extended-spectrum β-lactamase (ESBL) is a public-health concern. Recently, the prevalence of Salmonella spp. resistant to third-generation cephalosporins has been increasing in food-producing animals in Korea. In this study, we investigated resistance mechanisms and molecular characteristics of S. Virchow isolates resistant to extended-spectrum cephalosporins (ESCs). We obtained 265 S. Virchow isolates from fecal and carcasses samples of cattle (n = 2), pigs (n = 7), and chickens (n = 256) during 2010-2017, and observed high ESC-resistance (63.8%, 169/265); most of the resistant isolates (96.4%) were obtained from chickens. ESC-resistant S. Virchow isolates (n = 169) showed significantly higher resistance rates to other antimicrobials (especially aminoglycosides and tetracycline, p-value <0.0001), as well as prevalence of multidrug resistance, than did ESC-susceptible S. Virchow isolates (n = 96). All ESC-resistant S. Virchow produced CTX-M-15-type ESBL (n = 147) and/or CMY-2-type AmpC β-lactamase (n = 23). ESC-resistant S. Virchow represented seven pulsotypes, predominantly composed of type II (58.6%) and III (26.0%), detected in 69 farms in 10 provinces, and 33 farms in 7 provinces, respectively. Genes encoding ESC-resistance were horizontally transferred by conjugation to recipient E. coli J53; this was demonstrated in 28.8% (42/146) of bla_CTX-M-15-positive isolates and in 50.0% (11/22) of bla_CMY-2-positive isolates. All conjugative plasmids carrying bla_CTX-M-15 and bla_CMY-2 genes belonged to ST2-IncHI2 and ST12/CC12-IncI1, respectively. Genetic features of transferred bla genes were involved with ISEcp1 in both bla_CTX-M-15 and bla_CMY-2; ISEcp1 plays a critical role in the efficient capture, expression, and mobilization of bla genes. In addition to bla_CTX-M-15 genes, resistance markers to aminoglycosides and/or tetracycline were co-transferred to recipient E. coli J53. Our results show a high prevalence of ESBL-producing S. Virchow in chickens and chicken carcasses. Specific bla_CTX-M-15 and bla_CMY-2-carrying S. Virchow clones and plasmids were predominant in food-producing animals nationwide. Restriction of antimicrobial use and proper biosecurity practices at the farm level should be urgently implemented in the poultry industry.

Avibactam Sensitizes Carbapenem-Resistant NDM-1-Producing Klebsiella pneumoniae to Innate Immune Clearance

Infections caused by New Delhi metallo-β-lactamase (NDM)–producing strains of multidrug-resistant Klebsiella pneumoniae are a global public health threat lacking reliable therapies. NDM is impervious to all existing β-lactamase inhibitor (BLI) drugs, including the non–β-lactam BLI avibactam (AVI). Though lacking direct activity against NDMs, AVI can interact with penicillin-binding protein 2 in a manner that may influence cell wall dynamics. We found that exposure of NDM-1–producing K. pneumoniae to AVI led to striking bactericidal interactions with human cathelicidin antimicrobial peptide LL-37, a frontline component of host innate immunity. Moreover, AVI markedly sensitized NDM-1–producing K. pneumoniae to killing by freshly isolated human neutrophils, platelets, and serum when complement was active. Finally, AVI monotherapy reduced lung counts of NDM-1–producing K. pneumoniae in a murine pulmonary challenge model. AVI sensitizes NDM-1–producing K. pneumoniae to innate immune clearance in ways that are not appreciated by standard antibiotic testing and that merit further study.

Molecular characterization of Extended-spectrum β lactamase- producing E. coli recovered from community-acquired urinary tract infections in Upper Egypt

Treatment of community urinary tract infections (UTIs) caused by extended-spectrum β lactamase (ESBL)- producing Escherichia coli (E. coli) is more expensive than treating ESBL-negative opposites. Evaluation of the prevalence of ESBL-production among urinary E. coli isolates is crucial due to its great impact on the choice of proper antimicrobials. Accordingly, the aim of this work was to detect and characterize ESBL-producing E. coli isolated from outpatients with signs of UTIs in Upper Egypt. Urinary E. coli isolates were identified by 16S rRNA and their ESBL-production was confirmed by Modified Double Disc Synergy Test (MDDST) and ESBL- CHROMagar media. Isolates were then subjected to Polymerase Chain Reaction (PCR) for new Clermont phylogrouping, ESBL genes detection and CTX-M typing. The study enrolled 583 patients with clinically diagnosed UTIs. Uropathogens were found in 400 urine samples (68.6%) out of which 134 E. coli isolates were identified. Among the examined uropathogenic E. coli (UPEC), 80 (59.7%) were recognized as ESBL-producers. Greater than half of the ESBL-producers were multi-drug resistant (MDR) (62%). All of them were susceptible to meropenem. Most of the E. coli isolates were distributed in 4 phylogenetic groups: B2 = 42 (52.5%), F = 17 (21.25%) and Clade I or II = 10 (12.5%). The predominant gene types were TEM 60 (75%) and CTX-M gene 45 (56.25%). The CTX-M-1 group was the most prevalent (62.2%), including the CTX-M-15 enzyme, followed by the CTX-M-2 group, CTX-M-8 group and CTX-M-9 group. In conclusion, the results present alarming evidence of a serious spread of ESBL genes in Egypt, especially the epidemiological CTX-M 15, with the potential for the dissemination of MDR UPEC strains in the community.

Molecular characterization of Extended-spectrum β lactamase- producing E. coli recovered from community-acquired urinary tract infections in Upper Egypt

Treatment of community urinary tract infections (UTIs) caused by extended-spectrum β lactamase (ESBL)- producing Escherichia coli (E. coli) is more expensive than treating ESBL-negative opposites. Evaluation of the prevalence of ESBL-production among urinary E. coli isolates is crucial due to its great impact on the choice of proper antimicrobials. Accordingly, the aim of this work was to detect and characterize ESBL-producing E. coli isolated from outpatients with signs of UTIs in Upper Egypt. Urinary E. coli isolates were identified by 16S rRNA and their ESBL-production was confirmed by Modified Double Disc Synergy Test (MDDST) and ESBL- CHROMagar media. Isolates were then subjected to Polymerase Chain Reaction (PCR) for new Clermont phylogrouping, ESBL genes detection and CTX-M typing. The study enrolled 583 patients with clinically diagnosed UTIs. Uropathogens were found in 400 urine samples (68.6%) out of which 134 E. coli isolates were identified. Among the examined uropathogenic E. coli (UPEC), 80 (59.7%) were recognized as ESBL-producers. Greater than half of the ESBL-producers were multi-drug resistant (MDR) (62%). All of them were susceptible to meropenem. Most of the E. coli isolates were distributed in 4 phylogenetic groups: B2 = 42 (52.5%), F = 17 (21.25%) and Clade I or II = 10 (12.5%). The predominant gene types were TEM 60 (75%) and CTX-M gene 45 (56.25%). The CTX-M-1 group was the most prevalent (62.2%), including the CTX-M-15 enzyme, followed by the CTX-M-2 group, CTX-M-8 group and CTX-M-9 group. In conclusion, the results present alarming evidence of a serious spread of ESBL genes in Egypt, especially the epidemiological CTX-M 15, with the potential for the dissemination of MDR UPEC strains in the community.

Functional and Structural Roles of the Major Facilitator Superfamily Bacterial Multidrug Efflux Pumps

Pathogenic microorganisms that are multidrug-resistant can pose severe clinical and public health concerns. In particular, bacterial multidrug efflux transporters of the major facilitator superfamily constitute a notable group of drug resistance mechanisms primarily because multidrug-resistant pathogens can become refractory to antimicrobial agents, thus resulting in potentially untreatable bacterial infections. The major facilitator superfamily is composed of thousands of solute transporters that are related in terms of their phylogenetic relationships, primary amino acid sequences, two- and three-dimensional structures, modes of energization (passive and secondary active), and in their mechanisms of solute and ion translocation across the membrane. The major facilitator superfamily is also composed of numerous families and sub-families of homologous transporters that are conserved across all living taxa, from bacteria to humans. Members of this superfamily share several classes of highly conserved amino acid sequence motifs that play essential mechanistic roles during transport. The structural and functional importance of multidrug efflux pumps that belong to the major facilitator family and that are harbored by Gram-negative and -positive bacterial pathogens are considered here.

The increased recurrence rate of liver abscess caused by extended-spectrum β-lactamase-producing Klebsiella pneumoniae

The pathogenic bacterium Klebsiella pneumoniae (KP) is the major causative agent of pyogenic liver abscess (PLA). But reports about the prognosis of KP-caused PLA (KPLA) are rare. This study aimed to ascertain the recurrence rate of KPLA after initial treatment and its contributing factors. A total of 110 patients who had first-time episodes of KPLA were included into the study. The average follow-up time was 3.65 ± 2.18 years. Twenty (18.18%) KPLA patients experienced recurrence. Those in the recurrence group had a significantly greater incidence of extended-spectrum β-lactamase (ESBL) production compared with the non-recurrence group (30.0% vs 8.89%, P = 0.018). Diabetes, biliary tract disease, and history of malignancy were not associated with recurrence (all P > 0.05). No difference in the CT characteristics of KPLA (including abscess size, location, whether multilocular, gas production of KPLA, and thrombophlebitis) was found between the two groups. Multivariate regression analysis showed that ESBL production (OR, 6.3; 95% CI, 1.02-38.59; P = 0.04) was an independent risk factor for the recurrence of KPLA. Our findings emphasize that KPLA has a high recurrence rate and ESBL production is an independent risk factor for recurrent KPLA.

Carbapenem-Sparing Strategies for ESBL Producers: When and How

Extended spectrum β-lactamase (ESBL)-producing bacteria are prevalent worldwide and correlated with hospital infections, but they have been evolving as an increasing cause of community acquired infections. The spread of ESBL constitutes a major threat for public health, and infections with ESBL-producing organisms have been associated with poor outcomes. Established therapeutic options for severe infections caused by ESBL-producing organisms are considered the carbapenems. However, under the pressure of carbapenem overuse and the emergence of resistance, carbapenem-sparing strategies have been implemented. The administration of carbapenem-sparing antibiotics for the treatment of ESBL infections has yielded conflicting results. Herein, the current available knowledge regarding carbapenem-sparing strategies for ESBL producers is reviewed, and the optimal conditions for the "when and how" of carbapenem-sparing agents is discussed. An important point of the review focuses on piperacillin-tazobactam as the agent arousing the most debate. The most available data regarding non-carbapenem β-lactams (i.e., ceftolozane-tazobactam, ceftazidime-avibactam, temocillin, cephamycins and cefepime) are also thoroughly presented as well as non β-lactams (i.e., aminoglycosides, quinolones, tigecycline, eravacycline and fosfomycin).

Molecular characteristics of carbapenemase-producing Enterobacterales in the Netherlands; results of the 2014-2018 national laboratory surveillance

OBJECTIVES

Carbapenem resistance mediated by mobile genetic elements has emerged worldwide and has become a major public health threat. To gain insight into the molecular epidemiology of carbapenem resistance in The Netherlands, Dutch medical microbiology laboratories are requested to submit suspected carbapenemase-producing Enterobacterales (CPE) to the National Institute for Public Health and the Environment as part of a national surveillance system.

METHODS

Meropenem MICs and species identification were confirmed by E-test and MALDI-TOF and carbapenemase production was assessed by the Carbapenem Inactivation Method. Of all submitted CPE, one species/carbapenemase gene combination per person per year was subjected to next-generation sequencing (NGS).

RESULTS

In total, 1838 unique isolates were received between 2014 and 2018, of which 892 were unique CPE isolates with NGS data available. The predominant CPE species were Klebsiella pneumoniae (n = 388, 43%), Escherichia coli (n = 264, 30%) and Enterobacter cloacae complex (n = 116, 13%). Various carbapenemase alleles of the same carbapenemase gene resulted in different susceptibilities to meropenem and this effect varied between species. Analyses of NGS data showed variation of prevalence of carbapenemase alleles over time with bla_OXA-48 being predominant (38%, 336/892), followed by bla_NDM-1 (16%, 145/892). For the first time in the Netherlands, bla_OXA-181, bla_OXA-232 and bla_VIM-4 were detected. The genetic background of K. pneumoniae and E. coli isolates was highly diverse.

CONCLUSIONS

The CPE population in the Netherlands is diverse, suggesting multiple introductions. The predominant carbapenemase alleles are bla_OXA-48 and bla_NDM-1. There was a clear association between species, carbapenemase allele and susceptibility to meropenem.

High quantities of multidrug-resistant Escherichia coli are present in the Machángara urban river in Quito, Ecuador

Urban river pollution by multidrug-resistant (MDR) bacteria constitutes an important public health concern. Epidemiologically important strains of MDR Escherichia coli transmissible at the human-animal-environment interfaces are especially worrying. Quantifying and characterizing MDR E. coli at a molecular level is thus imperative for understanding its epidemiology in natural environments and its role in the spread of resistance in precise geographical areas. Cefotaxime-resistant E. coli was characterized along the watercourse of the major urban river in Quito. Our results showed high quantities of cefotaxime-resistant E. coli (2.7 × 10³-5.4 × 10⁵ CFU/100 mL). The antimicrobial resistance index (ARI) revealed the exposure of the river to antibiotic contamination, and the multiple antibiotic resistance index indicated a high risk of contamination. The bla_CTX-M-15 gene was the most prevalent in our samples. Isolates also had class 1 integrons carrying aminoglycoside-modifying enzymes and folate pathway inhibitors. The isolates belonged to phylogroups A, B1 and D. Clonal complex 10 was found to be the most prevalent (ST10, ST44 and ST 167), followed by ST162, ST394 and ST46. Our study provides a warning about the high potential of the major urban river in Quito for spreading the epidemiologically important MDR E. coli.

Bacteriochlorin-bis(spermine) conjugate affords an effective photodynamic action to eradicate microorganisms

A novel bacteriochlorin bearing two spermine units (BCS) was synthesized from 3,13-dibromo-8,8,18,18-tetramethylbacteriochlorin (BC-Br ^3,13 ). The synthesis involved the Suzuki coupling of BC-Br ^3,13 to obtain a bacteriochlorin-dibenzaldehyde (BCA), which was subjected to reductive amination with spermine. The resulting bacteriochlorin BCS presents a strong near-infrared absorption band at 747 nm, emits at 750 nm with fluorescence quantum yield of 0.14, and generates singlet molecular oxygen, O₂ (¹ Δ_g ), with a quantum yield of 0.27. Photokilling capacities mediated by BCS were evaluated in microbial cells. The viability of Staphylococcus aureus decreased 7 logs when cells were incubated with 1 μM BCS and irradiated for 15 minutes. Comparable photocytotoxic effect was obtained with Escherichia coli, when cells were treated for 30 minutes with visible light. BCS was also an effective photosensitizer to inactivate Candida albicans. In addition, this bacteriochlorin was able to eradicate bacteria at short incubation times. The structure of BCS contains eight basic amino groups that, when protonated in water, increase the binding to the cell envelope. In summary, the readily accessible bacteriochlorin BCS was highly effective at low concentrations as a broad-spectrum antimicrobial photosensitizer.

Genome analysis of enterobacteriaceae with non-wild type susceptibility to third-generation cephalosporins recovered from diseased dogs and cats in Europe

BACKGROUND

Extended-spectrum-β-lactamases (ESBL) and plasmid-mediated cephalosporinases (pAmpC)-producing Enterobacteriaceae isolates are now reported worldwide in humans, animals, and in the environment. We identified the determinants of resistance to β-lactams and associated resistance genes as well as phylogenetic diversity of 53 ESBL- or pAmpC-producing Enterobacteriaceae isolated from dogs and cats in Europe.

MATERIALS/METHODS

Of a collection of 842 Enterobacteriaceae isolates that were recovered in 2013 and 2014 from 842 diseased and untreated dogs and cats, for 242 ampicillin or amoxicillin resistant isolates (MIC ≥ 16 mg/L), cefotaxime (CTX) and ceftazidime (CAZ) MICs were determined. Isolates with CTX and/or CAZ MIC ≥ 1 mg/L (n = 63) were selected, and their genomes were fully sequenced using Illumina Technology. Genomic data were explored to identify the resistance determinants, the plasmid incompatibility groups, and the sequence types (STs). Plasmid location of bla_ESBL and bla_AmpC was evaluated for all isolates based on the co-localization of resistance and plasmid incompatibility group genes on the same contig. Phylogenetic trees were constructed using core-genome MLST.

RESULTS

Of the 63 sequenced isolates, 53 isolates harbored a bla_ESBL or bla_AmpC gene. Ten CTX and/or CAZ non-wild type isolates had neither bla_ESBL nor bla_AmpC. Among the 63 isolates, 44 (69.8 %) were Escherichia coli, 11 (17.5 %) were Klebsiella pneumoniae, and 8 (12.7 %) were Proteus mirabilis. Fifty-one (80.9 %) isolates originated from dogs and 12 (19.1 %) from cats. Isolates were sampled from urinary tract (n = 36), skin and soft tissue (n = 22) and respiratory tract infections (n = 5). Thirty-two isolates (32/53, 60.4 %) carried bla_ESBL genes, including bla_CTX-M-15 (n = 12), bla_CTX-M-14 (n = 6), bla_CTX-M-1 (n = 5), bla_CTX-M-2 (n = 3), bla_CTX-M-27 (n = 3), bla_SHV-28 (n = 4), bla_SHV-12 (n = 2), and bla_VEB-6 (n = 1). Four isolates of K. pneumoniae had both bla_CTX-M-15 and bla_SHV-28. Twenty-one isolates (21/53, 39.6 %) carried genes encoding pAmpC, including bla_CMY-2 (n = 19) and bla_DHA-1 (n = 2). Thirteen E. coli isolates harbored both bla_ESBL or bla_AmpC genes and plasmids of incompatibility groups IncIB (9/13), IncI1 (8/13), and IncFII (6/13). In addition to the reduced susceptibility to CTX and/or CAZ, reduced susceptibility or evidence of acquired resistance to at least one other relevant class of antibiotics was observed for all 63 isolates. E. COLI: isolates clustered in 23 STs, including B2 virulent clones from humans such as ST131 (n = 5), K. pneumoniae isolates mostly clustered in 3 STs: ST11 (n = 4), ST307 (n = 3), and ST16 (n = 2). Phylogenetic analysis identified the spread of E. coli ST131 bla_CTX-M-27, and of K. pneumoniae ST307 harboring bla_CTX-M-15 and bla_SHV-28 or ST11 bla_CTX-M-15.

CONCLUSIONS

We report here a 6.3 % prevalence of ESBL/pAmpC producing Enterobacteriaceae in diseased dogs and cats. This EU survey confirms that dogs and cats can be infected with epidemic multidrug resistant clones that may also spread in humans.

Detection and Whole-Genome Analysis of a High-Risk Clone of Klebsiella pneumoniae ST340/CG258 Producing CTX-M-15 in a Companion Animal

The emergence and dissemination of high-risk clones of Klebsiella pneumoniae producing extended-spectrum β-lactamases (ESBLs) in animal infections is a critical issue. We report the detection and genomic features of a multidrug-resistant (MDR) ESBL (CTX-M-15)-producing K. pneumoniae infecting a domestic cat. Whole-genome sequencing analysis identified the international ST340 (clonal group CG258), and genes and mutations conferring resistance to β-lactams, aminoglycosides, macrolides, phenicols, fosfomycin, sulfonamides, tetracycline, trimethoprim, and fluoroquinolones. In addition, the presence of genes encoding resistance to disinfectant and heavy metals hazardous to humans was also confirmed. The MDR profile exhibited by the strain contributed to treatment failure and death of the companion animal. Therefore, active surveillance of critical priority lineages of K. pneumoniae should not only focus on human infections but also on veterinary infections.

Phenotypic and Molecular Epidemiology of ESBL-, AmpC-, and Carbapenemase-Producing Escherichia coli in Northern and Eastern Europe

Extended-spectrum beta-lactamases (ESBL) and AmpC producing-Escherichia coli have spread worldwide, but data about ESBL-producing-E. coli in the Northern and Eastern regions of Europe is scant. The aim of this study has been to describe the phenotypical and molecular epidemiology of different ESBL/AmpC/Carbapenemases genes in E. coli strains isolated from the Baltic States (Estonia, Latvia, and Lithuania), Norway and St. Petersburg (Russia), and to determine the predominant multilocus sequence type and single nucleotide polymorphisms diversity of E. coli isolates deduced by whole genome sequencing (WGS). A total of 10,780 clinical E. coli strains were screened for reduced sensitivity to third-generation cephalosporins. They were collected from 21 hospitals located in Estonia, Latvia, Lithuania, Norway and St. Petersburg during a 5 month period in 2012. The overall prevalence of ESBL/AmpC strains was 4.7% by phenotypical test and 3.9% by sequencing. We found more strains with the ESBL/AmpC phenotype and genotype in St. Petersburg and Latvia than other countries. Of phenotypic E. coli strains, 85% contained confirmed ESBL genes (including bla_CTX–M, bla_TEM–29, bla_TEM–71), AmpC genes (bla_CMY–59, bla_{ACT–12/–15/–20}, bla_ESC–6, bla_FEC–1, bla_DHA–1), or carbapenemase genes (bla_NDM–1). bla_CTX–M–1, bla_CTX–M–14 and bla_CTX–M–15 were found in all countries, but bla_CTX–M–15 prevalence was higher in Latvia than in St. Petersburg (Russia), Estonia, Norway and Lithuania. The dominating AmpC genes were bla_CMY–59 in the Baltic States and Norway, and bla_DHA–1 in St. Petersburg. E. coli strains belonged to 83 different sequence types, of which the most prevalent was ST131 (40%). In conclusion, we generally found low ESBL/AmpC/Carbapenemase prevalence in E. coli strains isolated in Northern/Eastern Europe. However, several inter-country differences in distribution of particular genes and multilocus sequence types were found.

In vitro activity of ceftolozane/tazobactam against phenotypically defined extended-spectrum β-lactamase (ESBL)-positive isolates of Escherichia coli and Klebsiella pneumoniae isolated from hospitalized patients (SMART 2016)

The Clinical and Laboratory Standards Institute (CLSI)-defined broth microdilution testing method (M07, 11th edition, 2018) was used to determine MICs for ceftolozane/tazobactam and eight comparator agents against 21,952 isolates of Enterobacteriaceae submitted by 161 clinical laboratories in 51 countries in 2016 as a part of the SMART global surveillance program. MICs were interpreted using CLSI breakpoints (M100 29th edition, 2019). 89.7% of isolates of Enterobacteriaceae were susceptible to ceftolozane/tazobactam, compared to 70.0%, 76.3%, 77.7%, 84.7%, 93.6%, and 96.4%, respectively, for ceftriaxone, ceftazidime, cefepime, piperacillin-tazobactam, ertapenem, and meropenem. 82.4% of isolates of ESBL-positive, carbapenemase-negative Enterobacteriaceae were susceptible to ceftolozane/tazobactam, compared to 1.5%, 7.8%, 20.3%, 71.1%, 94.7%, and 98.7%, respectively, for ceftriaxone, cefepime, ceftazidime, piperacillin-tazobactam, ertapenem, and meropenem. In vitro susceptibility to ceftolozane/tazobactam was >60% higher than susceptibility to other advanced-generation cephalosporins among all Enterobacteriaceae and >10% higher than susceptibility to piperacillin-tazobactam among ESBL-positive Enterobacteriaceae collected globally in 2016.

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

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

Eravacycline: a new treatment option for complicated intra-abdominal infections in the age of multidrug resistance

Aim: Recently approved for use in complicated intra-abdominal infection, eravacycline is a novel fluorocycline with broad spectrum of activity against resistant Gram-negative pathogens. This manuscript is a pooled analysis of two Phase III trials. Clinical efficacy: Clinical cure rates were 86.8% for eravacycline versus 87.6% for ertapenem, and 90.8% for eravacycline versus 91.2% for meropenem in the Intent to Treat (micro-ITT) populations, and 87.0% for eravacycline versus 88.8% ertapenem, and 92.4 versus 91.6% for meropenem in the Modified Intent to Treat (MITT) populations. Safety: Eravacycline is well tolerated, with lower rates of nausea, vomiting and diarrhea than other tetracyclines. Conclusion: Eravacycline is an effective new option for use in complicated intra-abdominal infections, and in particular, for the treatment of extended-spectrum β-lactamase- and carbapenem-resistant Enterobacteriaceae-expressing organisms.

Risk factors and outcomes in non-transplant patients with extended-spectrum beta-lactamase-producing Escherichia coli bacteremia: a retrospective study from 2013 to 2016

Background

Escherichia coli is one of the most common strains of extended-spectrum β-lactam (ESBL)-producing bacteria, and the prevention and treatment of ESBL-producing E. coli infections is an ongoing challenge. The clinical characteristics and outcomes of ESBL-producing E. coli bacteremia in non-transplant patients remain to be elucidated.

Methods

This retrospective study included 491 non-transplant patients with E. coli bloodstream infections (BSIs) from January 2013 to December 2016 and was conducted to investigate the risk factors, clinical features, and outcomes of these infections.

Results

Of the 491 E. coli BSI patients, 57.6% suffered from infections with ESBL-producing strains. A multivariate analysis showed that urinary tract infection, prior use of cephalosporin, and treatment with β-lactam-β-lactamase inhibitor (BLBLI) combination antibiotics were independent risk factors for the development of ESBL-producing E. coli BSIs. The overall mortality rate in E. coli BSI patients was 14.46%, and there was no significant difference in the 28 day mortality rate between ESBL-producing E. coli and non-ESBL-producing E. coli BSI patients (14.8% vs. 14.0%, respectively; P = 0.953). Similarly, there was no difference between the community-acquired infection group and the nosocomial infection group. Hepatobiliary disease, carbapenem exposure, high APACHE II score, and hypoproteinemia were independent risk factors for death in E. coli BSI patients. Multivariate analysis showed that hypoproteinemia and severe disease were independent risk factors for death from ESBL-producing E. coli BSIs. Furthermore, there was no significant difference in the 28 day mortality between patients with ESBL-producing E. coli BSIs treated with carbapenem monotherapy versus those treated with BLBLI combination antibiotics (12.8% vs. 17.9%, respectively; P = 0.384).

Conclusions

Prior use of cephalosporin or BLBLI combination antibiotics increased the risk ratio for ESBL-producing E. coli infection. Hypoproteinemia and severe disease are independent risk factors for death in patients with E. coli BSIs. There was no significant difference in the 28 day prognosis of patients with ESBL-producing E. coli and those with non-ESBL-producing E. coli BSIs. These data do not support the conclusion that carbapenems might be more effective than BLBLI antibiotics for treatment of patients with BSIs caused by ESBL-producing E. coli.

Electronic supplementary material

The online version of this article (10.1186/s13756-019-0599-y) contains supplementary material, which is available to authorized users.

β-Lactamases and β-Lactamase Inhibitors in the 21st Century

The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli) and non-fermenting organisms (e.g., Pseudomonas aeruginosa). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.

Carbapenem-Resistant KPC- and TEM-Producing Escherichia coli ST131 Isolated from a Hospitalized Patient with Urinary Tract Infection: First Isolation in Molise Region, Central Italy, July 2018

In July 2018, a Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli ST131 was isolated from a patient admitted to the Vascular Surgery Unit of the main hospital of Molise region, Central Italy. Sequencing and alignment with the available sequences revealed that the isolate harbored the KPC-2 variant and TEM-1 beta-lactamase. This observation raises great concerns about the spread of carbapenem resistance in national and local settings with high endemicity level of KPC in K. pneumoniae, and underlines the importance of strengthening a proactive surveillance.

The Interaction of Klebsiella pneumoniae With Lipid Rafts-Associated Cholesterol Increases Macrophage-Mediated Phagocytosis Due to Down Regulation of the Capsule Polysaccharide

Klebsiella pneumoniae successfully colonizes host tissues by recognizing and interacting with cholesterol present on membrane-associated lipid rafts. In this study, we evaluated the role of cholesterol in the expression of capsule polysaccharide genes of K. pneumoniae and its implication in resistance to phagocytosis. Our data revealed that exogenous cholesterol added to K. pneumoniae increases macrophage-mediated phagocytosis. To explain this event, the expression of capsular galF, wzi, and manC genes was determined in the presence of cholesterol. Down-regulation of these capsular genes occurred leading to increased susceptibility to phagocytosis by macrophages. In contrast, depletion of cholesterol from macrophage membranes led to enhanced expression of galF, wzi, and manC genes and to capsule production resulting in resistance to macrophage-mediated phagocytosis. Cholesterol-mediated repression of capsular genes was dependent on the RcsA and H-NS global regulators. Finally, cholesterol also down-regulated the expression of genes responsible for LPS core oligosaccharides production and OMPs. Our results suggest that cholesterol plays an important role for the host by reducing the anti-phagocytic properties of the K. pneumoniae capsule facilitating bacterial engulfment by macrophages during the bacteria-eukaryotic cell interaction mediated by lipid rafts.

Antimicrobial Resistance and Molecular Characterization of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Ducks in South Korea

Ducks are potential carriers of pathogenic bacteria, which are capable of transmitting zoonotic diseases to humans. The global spread of Enterobacteriaceae carrying extended-spectrum β-lactamase (ESBL) genes is a public health concern. This study investigated the prevalence of antimicrobial resistance in Escherichia coli isolated from ducks in Korea and described the molecular characteristics of the ESBLs they produced. A total of 146 E. coli isolates from 404 duck fecal and carcass samples in 85 duck farms were tested for antimicrobial resistance using the broth dilution method and were further characterized using molecular methods. We observed high resistance rates to tetracycline, trimethoprim/sulfamethoxazole, nalidixic acid, ampicillin, and ciprofloxacin. In total, six ceftiofur-resistant isolates (4.1%) were observed, which produced CTX-M-55 (n = 3) or CTX-M-65 β-lactamase (n = 3). All CTX-M-producing E. coli isolates were also resistant to ciprofloxacin, with mutations in the quinolone resistance determining region of GyrA (S83L with or without D87N) and ParC (S80I), and three CTX-M-producing E. coli isolates carried plasmid-mediated quinolone resistance (PMQR) genes, qepA (n = 1), qnrS, and acc(6')-Ib-cr (n = 2). The transfer of bla_CTX-M genes was observed in one isolate mediated by IncF-family plasmids but not in the co-resistant isolates carrying both bla_CTX-M and PMQR genes. Pulsed-field gel electrophoresis and multilocus sequence typing demonstrated that CTX-M-producing isolates were heterogeneous; however, identical isolates were found in different farms and slaughterhouses. This study presents baseline data on antimicrobial resistance of E. coli derived from duck samples and is the first report of CTX-M-55 and CTX-M-65 β-lactamase-producing E. coli isolated from ducks in Korea. The dissemination of ESBL-producing E. coli poses a potential risk to public health and therefore should be monitored.

Prevalence and distribution of blaCTX-M, blaSHV, blaTEM genes in extended- spectrum β- lactamase- producing E. coli isolates from broiler farms in the Philippines

BACKGROUND

Antimicrobial resistance is a worldwide problem causing serious health threats. Escherichia coli is one of the most important bacteria that causes resistance problem. These bacteria produce an enzyme called extended-spectrum β-lactamase (ESBL) that allows it to become resistant to a wide variety of penicillins and cephalosporins. Currently, no information or published studies on ESBL-producing E.coli in broilers are available in the Philippines. This cross-sectional study was conducted to determine the prevalence and distribution of extended-spectrum β-lactamase (ESBL)-encoding genes, blaCTX-M, blaSHV, and blaTEM, among E. coli isolates from broiler farms in Luzon, Philippines.

RESULTS

Results showed a farm prevalence of 66. 67%. A total of 69 (44.23%) ESBL-producing E. coli were isolated from boot swabs and cloacal swab samples from broiler farms. All major blaCTX-M groups except blaCTX-M-25 group were identified in the isolates. The most prevalent group was blaCTX-M-1, 72.46% (CI: 60.38-82.54%), followed by blaCTX-M-2, blaCTX-M-9 group and blaCTX-M-8. The blaTEM and blaSHV genes were identified in 57.97 and 27.54% of isolates, respectively. The blaCTX-M and blaTEM were the most common gene combinations (33.33%). Coexistence of blaCTX-M types was observed in 50 (73.53%) isolates.

CONCLUSION

This study shows the high prevalence, diversity of patterns and coexistence of ESBL genes in the E. coli isolates from cloacal and boot swabs from broiler farms which pose risks of possible transmission to the environment, other animals and human.

Multidrug-resistant Gram-negative Bacterial Bloodstream Infections in Children's Hospitals in Japan, 2010-2017

BACKGROUND

The risk factors of multidrug-resistant (MDR) Gram-negative bacilli (GNB) bloodstream infection (BSI) are not yet known in children. Our aim was to evaluate risk factors and outcomes associated with MDR GNB BSI in children.

METHODS

Patients with GNB BSI were enrolled between April 2010 and March 2017 at 8 children's hospitals in Japan. Clinical and microbiologic data were collected retrospectively. The risk factors and outcomes of MDR and non-MDR GNB BSI were compared.

RESULTS

In total, 629 GNB BSI episodes met the case definition. The median age and proportion of males were 2 years (interquartile range, 0.3-8.7) and 50.7%, respectively. An underlying disease was found in 94% of patients. The proportion of BSI cases that developed >48 hours after admission was 76.2%. MDR comprised 24.5% of BSI cases. The MDR rate did not change over time (P = 0.540). The effective coverage rate of the initial empiric therapy for the MDR and non-MDR BSI cases was 60.4% and 83.4%, respectively (P < 0.001). The all-cause mortality rate at 28 days for all BSI, MDR-BSI and non-MDR BSI cases was 10.7%, 13.6% and 9.7%, respectively (P = 0.167). MDR BSI was independently associated with cancer chemotherapy within 30 days (odds ratio [OR] 43.90), older age (OR 1.05) and admission to the neonatal ward (OR 0.019).

CONCLUSIONS

One-fourth of GNB BSI cases were MDR. Cancer chemotherapy and older age were risk factors for MDR GNB BSI in children's hospitals. MDR did not increase the all-cause mortality rate.

Dissemination of Multidrug-Resistant Commensal Escherichia coli in Feedlot Lambs in Southeastern Brazil

Antimicrobial resistance (AR) is a public health issue since it limits the choices to treat infections by Escherichia coli in humans and animals. In Brazil, the ovine meat market has grown in recent years, but studies about AR in sheep are still scarce. Thus, this study aims to investigate the presence of AR in E. coli isolated from lambs during feedlot. To this end, feces from 112 lambs with 2 months of age, after weaning, were collected on the first day of the animals in the feedlot (day 0), and on the last day before slaughtering (day 42). Isolates were selected in MacConkey agar supplemented with 4 mg/L of ceftiofur and identified by biochemical methods. Isolates were submitted to an antimicrobial susceptibility test by disc-diffusion and PCR to investigate genes for phylogenetic group, virulence determinants and resistance to the several antimicrobial classes tested. The genetic localization of the bla genes detected was elucidated by S1-PFGE followed by Southern blot-hybridizations. The isolates were typed by XbaI-PFGE and MLST methods. Seventy-eight E. coli were isolated from 8/112 (7.1%) animals on day 0, and from 55/112 (49.1%) animals on day 42. Since only fimH was present in almost all E. coli (97.4%) as a virulence gene, and also 88.5% belonged to phylogroups B1 or A, we consider that isolates represent intestinal commensal bacteria. The dendrogram separated the 78 non-virulent isolates in seven clusters, two of which comprised 50 E. coli belonging to ST/CC 1727/446 or ST 3994 recovered on day 42 commonly harboring the genotype bla CMY -2-aac(3)-IIa -tetA-sul1-sul2-floR-cmlA. Special attention should be given to the presence of bla CTX-M-15, a worldwide gene spread, and bla CTX-M-14, a hitherto undetected gene in Enterobacteriaceae from food-producing animals in Brazil. Importantly, E. coli lineages and plasmids carrying bla genes detected here have already been reported as sources of infection in humans either from animals, food, or the environment, which raises public health concerns. Hence, two types of commensal E. coli carrying important AR genes clearly prevailed during feedlot, but lambs are also reservoirs of bacteria carrying important AR genes such as bla CTX-M-14 and bla CTX-M-15, mostly related to antimicrobial treatment failure.

Multiomics Assessment of Gene Expression in a Clinical Strain of CTX-M-15-Producing ST131 Escherichia coli

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strain C999 was isolated of a Spanish patient with urinary tract infection. Previous genotyping indicated that this strain presented a multidrug-resistance phenotype and carried beta-lactamase genes encoding CTX-M-15, TEM-1, and OXA-1 enzymes. The whole-cell proteome, and the membrane, cytoplasmic, periplasmic and extracellular sub-proteomes of C999 were obtained in this work by two-dimensional gel electrophoresis (2DE) followed by fingerprint sequencing through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). A total of 602 proteins were identified in the different cell fractions, several of which are related to stress response systems, cellular responses, and antibiotic and drug responses, consistent with the multidrug-resistance phenotype. In parallel, whole genome sequencing (WGS) and RNA sequencing (RNA-Seq) was done to identify and quantify the genes present and expressing. The in silico prediction following WGS confirmed our strain as being serotype O25:H4 and sequence type ST131. The presence of proteins related to antibiotic resistance and virulence in an O25:H4-ST131 E. coli clone are serious indicators of the continued threat of antibiotic resistance spread amongst healthcare institutions. On a positive note, a multiomics approach can facilitate surveillance and more detailed characterization of virulent bacterial clones from hospital environments.

A Clinical Prediction Tool for Extended-Spectrum Cephalosporin Resistance in Community-Onset Enterobacterales Urinary Tract Infection

Background

Bacterial resistance to first line antibiotics used to treat community-onset urinary tract infections (UTIs) continues to increase. We sought to create a clinical prediction tool for community-onset UTIs due to extended-spectrum cephalosporin-resistant (ESC-R) Enterobacterales (formerly Enterobacteriaceae, EB).

Methods

A case-control study was performed. The source population included patients presenting to an emergency department (ED) or outpatient practice with an EB UTI between 2010 and 2013. Case patients had ESC-R EB UTIs. Control patients had ESC-susceptible EB UTIs and were matched to cases 1:1 on study year. Multivariable conditional logistic regression was performed to develop the predictive model by maximizing the area under the receiver-operating curve (AUC). Internal validation was performed via bootstrapping.

Results

A total of 302 patients with a community-onset EB UTI were included, with 151 cases and 151 controls. After multivariable analysis, we found that presentation with an ESC-R EB community-onset UTI could be predicted by the following: (1) a history of malignancy; (2) a history of diabetes; (3) recent skilled nursing facility or hospital stay; (4) recent trimethoprim-sulfamethoxazole exposure; and (5) pyelonephritis at the time of presentation (AUC 0.73, Hosmer-Lemeshow goodness-of-fit P value 0.23). With this model, each covariate confers a single point, and a patient with ≥ 2 points is considered high risk for ESC-R EB (sensitivity 80%, specificity 54%). The adjusted AUC after bootstrapping was 0.71.

Conclusions

Community-onset ESC-R EB UTI can be predicted using the proposed scoring system, which can help guide diagnostic and therapeutic interventions.

A survey of extended-spectrum β-lactamase-producing Enterobacteriaceae in environmental water in Okinawa Prefecture of Japan and relationship with indicator organisms

Surveys of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-pE) in stream water and untreated wastewater were carried out in Okinawa Prefecture, Japan. Thirty-six samples of water were collected from 18 streams in Okinawa Prefecture, as well as ten samples of wastewater flowing into four wastewater treatment plants (WWTPs). We investigated bacterial species, Escherichia coli O antigen, ESBL phenotype, ESBL genotype, and pulsed-field gel electrophoresis (PFGE) type of isolates, and total viable count and fecal coliforms as indicator organisms. The relation between indicator organisms and ESBL-pE was also validated using the same samples. A total of 141 ESBL-pE including 107 E. coli, 15 Klebsiella pneumoniae, 2 Proteus mirabilis, and 17 other species was isolated from stream water and wastewater. Of the 141 ESBL-pE, 14.9% and 54.6% were found to be blaCTX-M-15 and blaCTX-M-14-like types, respectively, which have been found in hospital isolates in Okinawa. Two pairs of possibly related patterns according to PFGE criteria were isolated from stream water and wastewater in two districts. When ESBL-pE was significantly isolated, total viable count and fecal coliform boundaries were ≥ 6.0 × 10³ CFU/ml and ≥ 4.3 × 10² most probable number/100 ml, respectively. These results suggested that ESBL-pE isolated from stream water is human derived, and that total viable count and fecal coliforms will be useful as indicators for confirming the spread of ESBL-pE to the environment by means of simple hygiene surveys.

Complete genome sequence of a novel bacteriophage, PBKP05, infecting Klebsiella pneumoniae

An increasing number of Klebsiella pneumoniae isolates have been found to be multi-drug resistant. A novel bacteriophage, PBKP05, which infects K. pneumoniae, was isolated and characterized. It has a linear double-stranded DNA genome of 30,240 base pairs in length. Its G+C content is 53%, and 47 putative open reading frames are functionally annotated. This phage can be a candidate material for phage therapy.

Phenotypic and genotypic characterizations of extended-spectrum beta-lactamase-producing Escherichia coli in Thailand

Purpose

Extended-spectrum β-lactamases (ESBLs) have become an issue in community worldwide due to an increase in antibiotic resistance over the past decade. This study was aimed to investigate the phenotypic and genotypic characteristics of ESBL-producing Escherichia coli in Thailand.

Materials and methods

In this study, all clinical isolates collected from tertiary hospitals in Thailand were identified as E. coli by biochemical tests and MALDI-TOF mass spectrometry. ESBL-producing E. coli was preliminary screened with disk diffusion method by cephalosporin disks and confirmed by the method of combination disk diffusion. Antimicrobial susceptibility test was used to determine MIC values of all ESBL-producing E. coli. For genotypic detection, a variety of ESBL genes were determined by PCR. Moreover, multilocus sequence typing (MLST) analysis was performed on internal portions of seven housekeeping genes for the diversity and phylogenetic relatedness of E. coli clonal group.

Results

Of the 285 ESBL-producing E. coli, most were susceptible to carbapenems. These strains showed a high resistance rate to ciprofloxacin (85.26%). The most frequently detected gene was bla_CTX-M1 group at about 71.23% followed by bla_CTX-M9 group (38.95%). The bla_TEM, bla_PER, bla_GES, bla_VEB, and bla_SHV genes were identified in 31.93%, 5.96%, 4.56%, 3.51%, and 0.70% of ESBL-producing isolates, respectively. The bla OXA-10 gene was detected in only one strain. ESBL-producing E. coli isolates with high antimicrobial resistance were further investigated. Among those, E. coli sequence type ST38 was mostly found, followed by ST405, ST410, and ST131. It is noteworthy that the bla_CTX-M gene was mainly detected in all four ST-type E. coli clones (ST38, ST405, ST410, and ST131).

Conclusion

This study provided a recent evidence of the genetic diversity of ESBL-producing E. coli in Thailand. In addition, the profile related to antimicrobial resistance pattern in this region was also demonstrated.