Competition assays between ESBL-producing E. coli and K. pneumoniae isolates collected from Lebanese elderly: An additional cost on fitness

Landscape of plasmids encoding β-lactamases in disinfection residual Enterobacteriaceae from wastewater treatment plants

Conventional disinfection processes, such as chlorination and UV radiation, are ineffective in controling antibiotic-resistant bacteria, especially disinfection residual Enterobacteriaceae (DRE) encoding β-lactamases, some of which have been classified as "critical priority pathogens" by the World Health Organization. However, few studies have focused on the transferability, phenotype, and genetic characteristics of DRE-derived plasmids encoding β-lactamases, especially extended-spectrum β-lactamases and carbapenemases. In this study, we isolated 10 typical DRE harboring plasmid-mediated blaNDM, blaCTX-M, or blaTEM in post-disinfection effluent from two wastewater treatment plants (WWTPs), with transfer frequency ranging from 1.69 × 10-6 to 3.02 × 10-5. According to genomic maps of plasmids, all blaNDM and blaTEM were cascaded with IS26, and blaCTX-M was adjacent to ISEcp1 or IS26, indicating the important role of these elements in the movement of β-lactamase-encoding genes. The presence of intact class 1 integrons on pWTPN-01 and pWTPC-03 suggested the ability of these DRE-derived plasmids to integrate other exogenous antibiotic resistance genes (ARGs). The coexistence of antibiotic, disinfectant, and heavy metal resistance genes on the same plasmid (e.g., pWTPT-03) implied the facilitating role of disinfectants and heavy metals in the transmission of DRE-derived ARGs. Notably, two plasmid transconjugants exhibited no discernible competitive fitness cost, suggesting a heightened environmental persistence. Furthermore, enhanced virulence induced by β-lactamase-encoding plasmids in their hosts was confirmed using Galleria mellonella infection models, which might be attributed to plasmid-mediated virulence genes. Overall, this study describes the landscape of β-lactamase-encoding plasmids in DRE, and highlights the urgent need for advanced control of DRE to keep environmental and ecological security.

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.

Deciphering Multidrug-Resistant Plasmids in Disinfection Residual Bacteria from a Wastewater Treatment Plant

Current disinfection processes pose an emerging environmental risk due to the ineffective removal of antibiotic-resistant bacteria, especially disinfection residual bacteria (DRB) carrying multidrug-resistant plasmids (MRPs). However, the characteristics of DRB-carried MRPs are poorly understood. In this study, qPCR analysis reveals that the total absolute abundance of four plasmids in postdisinfection effluent decreases by 1.15 log units, while their relative abundance increases by 0.11 copies/cell compared to investigated wastewater treatment plant (WWTP) influent. We obtain three distinctive DRB-carried MRPs (pWWTP-01-03) from postdisinfection effluent, each carrying 9-11 antibiotic-resistant genes (ARGs). pWWTP-01 contains all 11 ARGs within an ∼25 Kbp chimeric genomic island showing strong patterns of recombination with MRPs from foodborne outbreaks and hospitals. Antibiotic-, disinfectant-, and heavy-metal-resistant genes on the same plasmid underscore the potential roles of disinfectants and heavy metals in the coselection of ARGs. Additionally, pWWTP-02 harbors an adhesin-type virulence operon, implying risks of both antibiotic resistance and pathogenicity upon entering environments. Furthermore, some MRPs from DRB are capable of transferring and could confer selective advantages to recipients under environmentally relevant antibiotic pressure. Overall, this study advances our understanding of DRB-carried MRPs and highlights the imminent need to monitor and control wastewater MRPs for environmental security.

OmpC-Dependent Bile Tolerance Contributes to E. coli Colonization of the Mammalian Intestine

Escherichia coli persistently colonizes the mammalian intestine by mechanisms that are not fully understood. Previously, we found when streptomycin-treated mice were fed E. coli MG1655, the intestine selected for envZ missense mutants that outcompeted the wild type. The better-colonizing envZ mutants had a higher level of OmpC and reduced OmpF. This suggested the EnvZ/OmpR two-component system and outer membrane proteins play a role in colonization. In this study, we show that wild-type E. coli MG1655 outcompetes an envZ-ompR knockout mutant. Moreover, ompA and ompC knockout mutants are outcompeted by the wild type, while an ompF knockout mutant colonizes better than the wild type. Outer membrane protein gels show the ompF mutant overproduces OmpC. An ompC mutant is more sensitive to bile salts than the wild type and ompF mutant. The ompC mutant initiates colonization slowly because it is sensitive to physiological concentrations of bile salts in the intestine. Overexpression of ompC under the control of a constitutive promoter confers a colonization advantage only when ompF is deleted. These results indicate that fine-tuning of OmpC and OmpF levels is needed to maximize competitive fitness in the intestine. RNA sequencing reveals the EnvZ/OmpR two-component system is active in the intestine: ompC is upregulated and ompF is downregulated. While other factors could also contribute to the advantage provided by OmpC, we provide evidence that OmpC is important for E. coli to colonize the intestine because its smaller pore size excludes bile salts or other unknown toxic substances, while OmpF is deleterious because its larger pore size allows bile salts or other unknown toxic substances to enter the periplasm. IMPORTANCE Every mammalian intestine is colonized with Escherichia coli. Although E. coli is one of the most studied model organisms, how it colonizes the intestine is not fully understood. Here, we investigated the role of the EnvZ/OmpR two-component system and outer membrane proteins in colonization of the mouse intestine by E. coli. We report that an ompC mutant is a poor colonizer, while an ompF mutant, which overproduces OmpC, outcompetes the wild type. OmpF has a larger pore size that allows toxic bile salts or other toxic compounds into the cell and is deleterious for colonization of the intestine. OmpC has a smaller pore size and excludes bile salts. Our findings provide insights into why E. coli fine-tunes the levels of OmpC and OmpF during colonization via the EnvZ/OmpR two-component system.

Phenotypic and molecular characterization of ESBL producing Escherichia coli and Klebsiella pneumoniae among Lebanese patients

Introduction

Antimicrobial resistance is a major public health issue worldwide and became one of the principal international healthcare crises of the 21st century. The production of ESBLs is one of the resistance mechanisms in Enterobacteriaceae, and they are increasingly detected in Escherichia coli and Klebsiella pneumoniae globally. Therefore, the aim of this study was to determine the phenotypic and molecular characteristics of ESBL-producing E. coli and K. pneumoniae among Lebanese patients.

Methods

A total of 152 ESBL-producing E. coli and K. pneumoniae were obtained from Geitaoui Hospital in Beirut between September 2019 and October 2020 from various clinical samples. The phenotype of ESBL producers was confirmed by a double-disc synergy test and antibiotic susceptibility was determined using the disc diffusion method. Genotypically, multiplex PCR was used to detect the ESBL genes (bla_TEM, bla_CTX-M and bla_SHV).

Results

All strains were confirmed to be ESBL producers (121 isolates were E. coli and 31 isolates were K. pneumoniae). All isolates showed resistance to cefotaxime, cefuroxime, ampicillin and piperacillin. On the other hand, they showed a low susceptibility rate to trimethoprim/sulfamethoxazole and ciprofloxacin. Almost all the isolates were susceptible to ertapenem, imipenem and amikacin. In our study, ESBL genes were detected among 48 (39.67%) E. coli isolates and 8 (58.06%) K. pneumoniae isolates, and the most prevalent gene was bla_TEM (25%), followed by bla_CTX-M (19.08%) and bla_SHV (16.45%).

Conclusion

Imipenem and ertapenem are the most effective drugs to treat ESBL producers. However, antibiotic stewardship programs must be implemented immediately to combat antibiotic resistance.

ESBL Escherichia coli Isolates Have Enhanced Gut Colonization Capacity Compared to Non-ESBL Strains in Neonatal Mice

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli can cause invasive infections in infants and immunocompromised children with high associated morbidity and mortality. The gut is a major reservoir of these strains in the community. Current dogma dictates that antimicrobial resistance is associated with a fitness cost. However, recent data show that some contemporary ESBL E. coli strains may be more "fit" compared to nonresistant E. coli strains. Here, we use whole-genome sequencing to first characterize 15 ESBL E. coli strains isolated from infants in a Pakistani community, a clinical extraintestinal pathogenic ESBL E. coli ST131 strain, and a non-ESBL commensal E. coli strain, and then use a novel animal model of early life gut colonization to assess the ability of these strains to colonize the infant mouse gut. We determined that CTX-M-15 was present in all the ESBL strains, as well as additional beta-lactamases and genes conferring resistance to multiple antibiotic classes. In the animal model, 11/16 ESBL E. coli strains had significantly higher burden of colonization at week four of life compared to commensal strains, even in the absence of selective antibiotic pressure, suggesting that these strains may have enhanced fitness despite being highly antimicrobial resistant. IMPORTANCE Antimicrobial resistance is a global public health emergency. Infants, especially preterm infants and those in the neonatal intensive care unit, immunocompromised hosts, and those with chronic illnesses are at highest risk of adverse outcomes from invasive infections with antimicrobial-resistant strains. It has long been thought that resistance is associated with a fitness cost, i.e., antimicrobial-resistant strains are not able to colonize the gut as well as nonresistant strains, and that antibiotic exposure is a key risk factor for persistent colonization with resistant strains. Here, we use a novel infant mouse model to add to the growing body of literature that some highly-resistant contemporary Escherichia coli strains can persist in the gut with a significant burden of colonization despite absence of antibiotic exposure.

Novel insights related to the rise of KPC-producing Enterobacter cloacae complex strains within the nosocomial niche

According to the World Health Organization, carbapenem-resistant Enterobacteriaceae (CRE) belong to the highest priority group for the development of new antibiotics. Argentina-WHONET data showed that Gram-negative resistance frequencies to imipenem have been increasing since 2010 mostly in two CRE bacteria: Klebsiella pneumoniae and Enterobacter cloacae Complex (ECC). This scenario is mirrored in our hospital. It is known that K. pneumoniae and the ECC coexist in the human body, but little is known about the outcome of these species producing KPC, and colonizing or infecting a patient. We aimed to contribute to the understanding of the rise of the ECC in Argentina, taking as a biological model both a patient colonized with two KPC-producing strains (one Enterobacter hormaechei and one K. pneumoniae) and in vitro competition assays with prevalent KPC-producing ECC (KPC-ECC) versus KPC-producing K. pneumoniae (KPC-Kp) high-risk clones from our institution. A KPC-producing E. hormaechei and later a KPC-Kp strain that colonized a patient shared an identical novel conjugative IncM1 plasmid harboring blaKPC-2. In addition, a total of 19 KPC-ECC and 58 KPC-Kp strains isolated from nosocomial infections revealed that high-risk clones KPC-ECC ST66 and ST78 as well as KPC-Kp ST11 and ST258 were prevalent and selected for competition assays. The competition assays with KCP-ECC ST45, ST66, and ST78 versus KPC-Kp ST11, ST18, and ST258 strains analyzed here showed no statistically significant difference. These assays evidenced that high-risk clones of KPC-ECC and KPC-Kp can coexist in the same hospital environment including the same patient, which explains from an ecological point of view that both species can exchange and share plasmids. These findings offer hints to explain the worldwide rise of KPC-ECC strains based on the ability of some pandemic clones to compete and occupy a certain niche. Taken together, the presence of the same new plasmid and the fitness results that showed that both strains can coexist within the same patient suggest that horizontal genetic transfer of blaKPC-2 within the patient cannot be ruled out. These findings highlight the constant interaction that these two species can keep in the hospital environment, which, in turn, can be related to the spread of KPC.

Replacement of the Dominant ST191 Clone by ST369 Among Carbapenem-Resistant Acinetobacter baumannii Bloodstream Isolates at a Tertiary Care Hospital in South Korea

The clonal dissemination of carbapenem-resistant Acinetobacter baumannii (CRAB) bacteremia is a serious clinical problem worldwide. However, the factors related to the emergence and replacement of predominant CRAB clones in nosocomial settings are unclear. By multilocus sequence typing (MLST), we evaluated the genetic relatedness of CRAB bloodstream isolates at a tertiary care hospital over a 3.5-year period and investigated the clinical and microbiologic characteristics of the predominant sequence types (STs). One hundred and seventy-nine CRAB bloodstream isolates were collected from June 2016 to December 2019, and their MLSTs according to Oxford scheme and clinical data were obtained. The predominant STs were assessed for in vitro growth, competitive growth, and virulence in a mouse model of intraperitoneal infection. Two dominant clones—ST369 (n = 98) and ST191 (n = 48)—belonging to international clone 2 (IC2) were recovered from patients admitted to intensive care units (ICUs) or wards. ST191 predominated (61%, 27/43) from June 2016 to July 2017, whereas ST369 (72%, 98/136), which was first isolated from a patient admitted to the emergency room, replaced ST191 (15%, 21/136) after August 2017. In a multivariate analysis, leukopenia (OR = 3.62, 95% CI 1.04–12.6, p = 0.04) and ST191 or 369 (OR = 5.32, 95% CI 1.25–22.65, p = 0.02) were independent risk factors for 7-day mortality. Compared with non-ST369, ST369 was associated with a shorter time to bacteremia from ICU admission (7 vs. 11 days, p = 0.01), pneumonia as an origin of bacteremia (67 vs. 52%, p = 0.04), leukopenia (28 vs. 11%, p < 0.01), and a lower 7-day survival rate (41 vs. 70%, p < 0.01). In vitro, ST 369 isolates had significantly higher growth rates and enhanced competitive growth compared to ST191. Finally, ST369 had greater virulence and a higher mortality rate than other STs in a mouse infection model. We report almost-complete replacement of the predominant ST191 clone by ST369 within an 8-month period at our hospital. ST369 had a high incidence density rate of CRAB bacteremia, a short time to bacteremia after ICU admission, and a high early mortality rate, which may be in part explained by its faster competitive growth rate and higher virulence than ST191.

The Spread of Plasmidic AmpC in a General Lebanese Hospital Over Nine Consecutive Years and the Relationship With Restricted Isolation Protocols

Background: The dreaded bacterial infection by extended-spectrum β-lactamases (ESBL)-producers has always troubled the medical field whether on the public, scientific, or clinical levels. One of the lesser known β-lactamases, which is capable of hydrolyzing broad and extended-spectrum cephalosporins—i.e., cephamycins plus oxyimino-β-lactams—are the AmpC β-lactamases. This group, which has also been termed occasionally—and incorrectly—as ESBL Class C, confers resistance to β-lactamase inhibitors. The prevalence of plasmidic AmpC (pAmpC) strains is possibly still a matter of debate considering the unevenly matched data between phenotypically-detected and molecularly-detected pAmpC.

Aim: In the absence of any study in Lebanon addressing the AmpC, our intention was to determine the numbers and percentages of AmpC Enterobacteriaceae isolates, notably plasmid-mediated ones, across different wards at the Centre Hospitalier du Nord (CHN), Lebanon, and highlight the importance of infection control protocols.

Materials and Methods: Carriage and infection with pAmpC Enterobacteriaceae were retrospectively investigated between 2011 and 2015 and prospectively between 2016 and 2019 at the Centre Hospitalier du Nord Hospital, North Lebanon. The rise or decline in the numbers of such strains, in concordance with the allegedly intensive isolation of the patients, were analyzed.

Results: Intensive care unit (ICU) data shows an initial rise in infection isolates from 2012 to 2014 and in the carriage isolates from 2012 to 2013 with later notable overall decrease in the both isolates' numbers with the application of the isolation protocols at CHN from 2014 onwards. Floors 2, 3, and 4 seemed to house the bulk of the isolates as well.

Conclusion: Preventive measures, such as on-going surveillance of the hospital wards by specialized healthcare personnel and strict implementation of infection control practices, should be a top priority in any medical center in order to isolate such strains and try to put a limit for the development and the dissemination of any possible multidrug resistant strains.

Characterize carbapenem-resistant Klebsiella pneumoniae isolates for nosocomial pneumonia and their Gram-negative bacteria neighbors in the respiratory tract

This study was conducted to perform an epidemiological survey of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates for nosocomial pneumonia (NP) and visit their Gram-negative bacteria neighbors (GNNs) from the respiratory tracts. Pulsed-field gel electrophoresis and multi locus sequence typing were performed to evaluate the clonal relationships of these isolates. Statistical methods were then used to understand their possible relationship between CRKP and their GNNs. Among the 63 CRKP isolates, 84.1% produced a KPC-2 carbapenemase gene, followed by blaNDM-1 and blaIMP-38 like. 13 different STs and 29 clones were identified. Less heterogeneous clone backgrounds were observed in 53 KPC-2 K. pneumoniae isolates, and 6 STs have been found to contain KPC-2, of which the predominant ST11 harbored 47 KPC-2-producing K. pneumoniae isolates. Particularly, the two infrequent isolates co-possessing blaKPC-2 and blaIMP-38 like shared a different clonal relationship. 87 GNNs isolates of CRKP were established, the analysis present that different strains showed significant or no difference with CRKP upon antibiotics susceptibility. Conclusion, ST11 harboring KPC-2-producing K. pneumoniae isolates were dominant for NP, and both clonal spread and horizontal transfer contributed to the dissemination of CRKP. However, additional studies are needed to explore the biological relationship with their GNNs.