Characterization of extended-spectrum β-lactamase (ESBL)-producing Klebsiella, Enterobacter , and Citrobacter obtained in environmental samples of a Tunisian hospital

Metagenomic insights into isolable bacterial communities and antimicrobial resistance in airborne dust from pig farms

This study aims to investigate bacterial communities and antimicrobial resistance (AMR) in airborne dust from pig farms. Airborne dust, pig feces and feed were collected from nine pig farms in Thailand. Airborne dust samples were collected from upwind and downwind (25 meters from pig house), and inside (in the middle of the pig house) of the selected pig house. Pig feces and feed samples were individually collected from the pen floor and feed trough from the same pig house where airborne dust was collected. A direct total bacteria count on each sampling plate was conducted and averaged. The ESKAPE pathogens together with Escherichia coli, Salmonella, and Streptococcus were examined. A total of 163 bacterial isolates were collected and tested for MICs. Pooled bacteria from the inside airborne dust samples were analyzed using Metagenomic Sequencing. The highest bacterial concentration (1.9-11.2 × 103 CFU/m3) was found inside pig houses. Staphylococcus (n = 37) and Enterococcus (n = 36) were most frequent bacterial species. Salmonella (n = 3) were exclusively isolated from feed and feces. Target bacteria showed a variety of resistance phenotypes, and the same bacterial species with the same resistance phenotype were found in airborne dust, feed and fecal from each farm. Metagenomic Sequencing analysis revealed 1,652 bacterial species across all pig farms, of which the predominant bacterial phylum was Bacillota. One hundred fifty-nine AMR genes of 12 different antibiotic classes were identified, with aminoglycoside resistance genes (24%) being the most prevalent. A total of 251 different plasmids were discovered, and the same plasmid was detected in multiple farms. In conclusion, the phenotypic and metagenomic results demonstrated that airborne dust from pig farms contained a diverse array of bacterial species and genes encoding resistance to a range of clinically important antimicrobial agents, indicating the significant role in the spread of AMR bacterial pathogens with potential hazards to human health. Policy measurements to address AMR in airborne dust from livestock farms are mandatory.

CTX-M, TEM, and SHV Genes in Escherichia coli, Klebsiella pneumoniae, and Enterobacter spp Isolated from Hematologic Cancer Patients with Bacteremia in Uganda

Purpose

We determined the phenotypic resistance to third-generation cephalosporins, phenotypic extended spectrum beta-lactamase (ESBL) prevalence, and genotypic prevalence of ESBL-encoding genes blaCTX-M, blaTEM, and blaSHV in Enterobacteriaceae isolated from hematologic cancer patients with febrile neutropenia and bacteremia at the Uganda Cancer Institute (UCI).

Patients and Methods

Blood cultures from hematologic cancer patients with febrile neutropenia were processed in BACTEC 9120. E. coli, K. pneumoniae, and Enterobacter spp. isolates were identified using conventional biochemical methods. Antimicrobial susceptibility tests, phenotypic ESBL characterization, and genotypic characterization of the ESBL-encoding genes blaCTX-M, blaTEM, and blaSHV were determined for pure isolates of E. coli, K. pneumoniae, and Enterobacter spp.

Results

Two hundred and two patients were included in the study. Median age of patients was 19 years (IQR: 10-30 years). Majority (N=119, 59%) were male patients. Sixty (30%) of the participants had at least one febrile episode due to Enterobacteriaceae. Eighty-three organisms were isolated with E. coli being predominant (45, 54%). Seventy-nine (95%) Enterobacteriaceae were multidrug resistant. The ESBL phenotype was detected in 54/73 (74%) of Enterobacteriaceae that were resistant to third-generation cephalosporins. A higher proportion of Enterobacteriaceae with ESBL-positive phenotype were resistant to piperacillin-tazobactam (p=0.024), gentamicin (p=0.000), ciprofloxacin (p=0.000), and cotrimoxazole (p=0.000) compared to Enterobacteriaceae, which were sensitive to third-generation cephalosporins. The organisms were more susceptible to carbapenems and chloramphenicol than resistant. ESBL-encoding genes (blaCTX-M, blaTEM, and blaSHV) were detected in 55 (75%) of the 73 Enterobacteriaceae that were resistant to third-generation cephalosporins. BlaCTX-M, was the most common ESBL-encoding gene identified with 50 (91%).

Conclusion

ESBL-producing Enterobacteriaceae are a predominant cause of bacteremia in hematologic cancer patients at UCI. The most common ESBL-encoding gene identified in the ESBL-PE was blaCTX-M. Resistance to imipenem and meropenem was low.

Clinically relevant pathogens on surfaces display differences in survival and transcriptomic response in relation to probiotic and traditional cleaning strategies

Indoor surfaces are paradoxically presumed to be both colonized by pathogens, necessitating disinfection, and "microbial wastelands." In these resource-poor, dry environments, competition and decay are thought to be important drivers of microbial community composition. However, the relative contributions of these two processes have not been specifically evaluated. To bridge this knowledge gap, we used microcosms to evaluate whether interspecies interactions occur on surfaces. We combined transcriptomics and traditional microbiology techniques to investigate whether competition occurred between two clinically important pathogens, Acinetobacter baumannii and Klebsiella pneumoniae, and a probiotic cleaner containing a consortium of Bacillus species. Probiotic cleaning seeks to take advantage of ecological principles such as competitive exclusion, thus using benign microorganisms to inhibit viable pathogens, but there is limited evidence that competitive exclusion in fact occurs in environments of interest (i.e., indoor surfaces). Our results indicate that competition in this setting has a negligible impact on community composition but may influence the functions expressed by active organisms. Although Bacillus spp. remained viable on surfaces for an extended period of time after application, viable colony forming units (CFUs) of A. baumannii recovered following exposure to a chemical-based detergent with and without Bacillus spp. showed no statistical difference. Similarly, for K. pneumoniae, there were small statistical differences in CFUs between cleaning scenarios with or without Bacillus spp. in the chemical-based detergent. The transcriptome of A. baumannii with and without Bacillus spp. exposure shared a high degree of similarity in overall gene expression, but the transcriptome of K. pneumoniae differed in overall gene expression, including reduced response in genes related to antimicrobial resistance. Together, these results highlight the need to fully understand the underlying biological and ecological mechanisms for community assembly and function on indoor surfaces, as well as having practical implications for cleaning and disinfection strategies for infection prevention.

Clinical characteristics and antimicrobial susceptibility of Klebsiella pneumoniae, Klebsiella variicola and Klebsiella quasipneumoniae isolated from human urine in Japan

Introduction. The three Klebsiella species K. pneumoniae, K. variicola and K. quasipneumoniae are difficult to distinguish, owing to their similar biochemical properties, and are often confused in medical practice.Gap statement. There is a scarcity of data comparing the clinical characteristics and antimicrobial susceptibility of K. pneumoniae, K. variicola and K. quasipneumoniae. We believe that knowledge of the characteristics of each species will help in their better identification. Further, knowing the antimicrobial susceptibility of the species will help physicians in prescribing an effective treatment course for Klebsiella infections.Aim. This study aimed to determine the clinical characteristics and antimicrobial resistance of K. pneumoniae, K. variicola and K. quasipneumoniae isolated from human urine samples.Methodology. This study included 125 K. pneumoniae strains isolated from human urine samples. Multiplex polymerase chain reaction was performed to identify K. pneumoniae, K. variicola and K. quasipneumoniae. We retrospectively investigated the patient background, complications of bacteraemia, antimicrobial susceptibility and extended-spectrum β-lactamase (ESBL).Results. We identified 84 (67.2 %), 31 (24.8 %) and 10 strains (8 .0%) of K. pneumoniae, K. variicola and K. quasipneumoniae, respectively. There was no difference in patient background and frequency of bacteraemia complications among these species. K. pneumoniae was significantly less susceptible than K. variicola to ampicillin/sulbactam (P=0.03) and piperacillin (P<0.01). Furthermore, K. pneumoniae (79.8 %) was less susceptible to trimethoprim/sulfamethoxazole than K. variicola (96.8 %) and K. quasipneumoniae (100 %). There were nine ESBL-producing strains (7.2 %), all of which were K. pneumoniae.Conclusion. There was no difference in patient background and frequency of bacteraemia complications between K. pneumoniae, K. variicola and K. quasipneumoniae isolated from urine. The three Klebsiella species showed a varying extent of antimicrobial susceptibility and ESBL production, and accurate identification is needed to understand the epidemiology of these species.

Antibiotic resistance and random amplified polymorphic DNA typing of Klebsiella pneumoniae isolated from clinical and water samples

The study aimed to screen for the presence of multidrug-resistant Klebsiella pneumoniae from diarrheal stool and environmental water samples and to check the epidemiological link between the two categories. Isolates obtained after culturing on different media were tested for antibiotic resistance and extended-spectrum beta-lactamase (ESBL) production. Polymerase chain reaction (PCR) analysis was done for important β-lactamase encoding genes. Random amplified polymorphic DNA (RAPD) typing was done using two primers. Results showed a high prevalence of K. pneumoniae from fish market effluents compared with stool and well water. Stool isolates showed high resistance to ceftazidime (80.0%) and cefepime (80.0%), fish market effluent isolates to cefoperazone-sulbactam (92.1%), and erythromycin (78.9%), while well water isolates to erythromycin (72.7%) and cefuroxime (54.4%). The ESBL genes bla_CTX , bla_SHV , and bla_TEM were detected in 22.85%, 14.28%, and 42.85% of K. pneumoniae isolates, respectively. The results of RAPD-PCR showed high genetic similarities between the isolates from different sources. PRACTITIONER POINTS: Detection of multi-drug resistant Klebsiella strains in hospital wastewater and drinking water sources has progressively increased since its emerging resistance to third-generation cephalosporins and carbapenems. Detection of beta-lactamase encoding genes by molecular techniques and typing by random amplified polymorphic DNA (RAPD) can be useful in identifying the genetic fingerprints for epidemiological study. Implementation of effective antimicrobial stewardship program and infection control policy thereby helps assess the risk factors associated with infections.

Whole Genome Sequencing of a Citrobacter freundii Strain Isolated from the Hospital Environment: An Extremely Multiresistant NDM-1 and VIM-48 Coproducing Isolate

Citrobacter freundii has acquired resistance to several antimicrobial drugs, including last-resort antibiotics affecting, therefore, clinical efficacy and causing high rates of mortality. In this study, we investigate the whole genome sequence of a carbapenem-resistant C. freundii strain isolated from the hospital environment in Tunisia. A total of 210 samples were taken using sterile swabs, from inanimate surfaces, medical devices, and care staff, during the period extended between March and April 2019. After the microbiological analysis of samples and antimicrobial susceptibility testing, only one strain identified as C. freundii showing resistance to carbapenems was selected for the whole genome sequencing. The genome analysis revealed a high-level resistance to most antibiotics. Interestingly, we have noted the coexistence of bla_NDM-1 and bla_VIM-48 metallo-β-lactamase (MBL) encoding genes conferring resistance to carbapenems. Other β-lactamases encoding genes have also been detected, including bla_TEM-1, bla_CMY-48, and bla_OXA-1. Moreover, genes conferring resistance to aminoglycoside [aac(3)-IId, ant(3″)-Ia, aadA, aac(6')-Ib], macrolide [mph(A)], sulfonamide (sul1), trimethoprim (dfrA1), tetracycline [tet(D)], chloramphenicol [cat(B3)], rifamycin (arr-3), and quinolone (qnrB) have been revealed. The multi-locus sequence typing analysis showed that this isolate could not be assigned to an existing sequence type (ST), but it is almost identical to ST22. The plasmid investigation revealed the presence of five plasmids belonging to diverse incompatibility groups (IncFII, IncHI1A, IncHI1B, IncN, and IncX3). To the best of our knowledge, our findings report the first detection of NDM-1 and VIM-48 coproducing C. freundii in Tunisia and the second detection in the world of the bla_VIM-48.

Molecular Characterization of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae Isolates Collected from Inanimate Hospital Environments in Addis Ababa, Ethiopia

INTRODUCTION

The hospital environment contributes to the spread of Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE), which are contributing to increased morbidity and mortality rates. The present study was carried out to detect environmental contamination, antimicrobial susceptibility testing of ESBL-PE, and to explore molecular characterization of ESBL encoding genes.

METHODS

A cross-sectional study was conducted within the intensive care units (ICUs) of Tikur Anbessa Specialized Hospital from June to July 2018. A total of 97 swabs were taken from high-contact inanimate surfaces near immediate patient environments. All isolates were cultured by using ESBL ChromoSelect Agar and identified with conventional bacteriological methods. Antimicrobial susceptibility testing was performed as recommended by Clinical and Laboratory Standards Institute. Combination disk test was used to confirm ESBL production, while molecular characterizations of ESBL genes were performed by polymerase chain reaction.

RESULTS

Out of 97 swabbed sample, 24 (24.7%) were confirmed as ESBL-PE. The most predominant ESBL-PE was from E. coli (41.7%) and K. pneumoniae (25%). The Pediatrics and Neonatal ICU (29.2%, 7/24) exhibited highest ESBL-PE. The most contaminated materials were bed linens (33.3%). Most of ESBL-PE isolates were resistant to ampicillin (100%) and ceftriaxone (91.7%). A low resistance level was recorded for amikacin (25%). Among ESBL-producing genes, bla_CTX-M (35.7%) was the most prevalent, followed by bla_TEM and bla_SHV gene 32.1% for each.

CONCLUSIONS

Appearance of ESBL-PE in ICUs environment is posing a serious threat to control healthcare associated infections. The high level of resistance shows the need of policies for devising infection control procedures and detection of ESBL-PE.

Extended spectrum beta-lactamase producing Enterobacterales faecal carriage in a medical intensive care unit: low rates of cross-transmission and infection

Background

Extended-spectrum beta-lactamases-producing Enterobacterales (ESBL-E) are disseminating worldwide especially in Intensive Care Units (ICUs) and are responsible for increased health costs and mortality. The aims of this work were to study ESBL-E dissemination in ICU and to assess the impact of ESBL-E fecal carriage on subsequent infections during a non-outbreak situation.

Methods

We therefore screened every patient at admission then once a week in a medical ICU between January and June 2015. Each ESBL-E isolate was characterized by ESBL genes PCR amplification and the clonal dissemination was assessed by Pulsed-Field Gel Electrophoresis (PFGE).

Results

Among the 608 screened patients, 55 (9%) were colonized by ESBL-E. Forty-four isolates were available for further analysis. Most of them (43/44, 98%) contained a ESBL gene from the CTX-M group. Only one case of ESBL-E cross-transmission occurred, even for acquired ESBL-E colonization. Subsequent infection by ESBL-E occurred in 6/55 (11%) patients and infecting ESBL-E strains were the colonizing ones. ESBL-E faecal carriage had a negative predictive value of 100% and a positive predictive value of 40% to predict ESBL-E ventilator associated-pneumonia (VAP). Alternatives to carbapenems consisting in piperacillin-tazobactam, ceftolozane-tazobactam and ceftazidime-avibactam were all active on this panel of ESBL-E.

Conclusions

ESBL-E expansion and acquisition in ICU in a non-outbreak situation are not any more fully explained by cross-transmission. Mechanisms underlying ESBL-E dissemination in ICU are still to investigate. Interestingly, as far as we know, our study demonstrates for the first time by PFGE that the colonizing strain is indeed the infecting one in case of subsequent ESBL-E infection. Nevertheless, subsequent ESBL-E infection remains a rare event conferring poor positive predictive value for ESBL-E colonization to predict ESBL-E VAP. Relevance of systematic ESBL-E faecal screening at ICU admission and during ICU stay needs further investigation.

Extended spectrum beta-lactamase-producing Klebsiella pneumoniae outbreak reveals incubators as pathogen reservoir in neonatal care center

In the context of a 3-month extended-spectrum beta-lactamase-producing Klebsiella pneumonia (ESBL-KP) outbreak in a neonatal care center (NCC), hygiene practices and hospital environment were investigated. ESBL-KP strains isolated from patients and environment were compared by molecular typing. The density of incidence of multi-drug-resistant bacteria (MDRB) was calculated from January 2014 to September 2016. The 3-month ESBL-KP outbreak involved 19 patients. Clinical strains from the 19 patients displayed the same molecular profile between them, and with a strain isolated from an incubator after cleaning. Furthermore, 52.4% of incubator mattresses were positive for diverse pathogens. Hygiene practices were acceptable except for external practitioners and parents. In addition to classical infection control (IC) measures, the replacement of mattresses and the improvement of incubators disinfection stopped the outbreak. The protocol of disinfection was revised and microbiological control was implemented. A significant decrease of MDRB incidence was concomitant (p value = 0.03219) but 3 months later, MDRB incidence increased again.Conclusion: This investigation highlighted incubators and mattresses as critical materials associated to infectious risk in NCC. NCC and IC teams should implement efficient protocol for incubators disinfection and monitoring. What is Known: • Environment in neonatal intensive care units is often suspected as reservoir for Enterobacteriaceae outbreaks but is scarcely investigated. • Incubators and mattresses offer wet and warm conditions suitable for pathogens multiplication, but microbiological survey is not performed routinely for assessing bacterial contamination. What is New: • Incubators and mattresses serve as reservoir for pathogens and relay in outbreak. • An infection control protocol associating efficient disinfection and microbiology analysis is proposed.

Extended-spectrum β-lactamase-producing and carbapenemase-producing Enterobacteriaceae

Antimicrobial resistance (AMR) is a global public-health emergency, which threatens the advances made by modern medical care over the past century. The World Health Organization has recently published a global priority list of antibiotic-resistant bacteria, which includes extended-spectrum β-lactamase-producing Enterobacteriaceae and carbapenemase-producing Enterobacteriaceae. In this review, we highlight the mechanisms of resistance and the genomic epidemiology of these organisms, and the impact of AMR.

First Report of SHV-148-Type ESBL and CMY-42-Type AmpC β-Lactamase in Klebsiella pneumoniae Clinical Isolates in Tunisia

Extended-spectrum beta-lactamase producing Enterobacteriaceae present a real problem worldwide. We aimed to investigate the molecular mechanisms of resistance to antibiotics among Klebsiella pneumoniae clinical isolates collected from a Hospital in the southeast of Tunisia. Eighteen cephalosporin-resistant K. pneumoniae were recovered between April 2015 and August 2016. Molecular characterization of antimicrobial resistance encoding genes was performed by PCR and sequencing. Results revealed several types of Ambler class A β-lactamase encoding genes among our isolates: [blaCTXM-15 (15), blaSHV-28 (6), blaSHV-1 (2), blaSHV-148 (1), blaSHV-61 (1), blaSHV-76 (1), blaSHV-186 (1), blaTEM-1 (8)]. The association of blaOXA-1 was observed in nine isolates. However, the class C β-lactamase encoding genes were detected in four isolates [blaCMY-4 (2), blaCMY-42 (1), blaACT-35 (1)]. Molecular typing of K. pneumoniae isolates by pulsed-field gel electrophoresis showed 16 unrelated pulsotypes proving a high diversity among our isolates. Our study provides new epidemiological information showing a huge diversity of β-lactamase encoding genes among our isolates. In fact, this is the first report of SHV-76, SHV-148, and SHV-186 in Tunisia. This is also the first report of CMY-42 and ACT-35 producing K. pneumoniae in our country.

CTX-M-15 is Established in Most Multidrug-Resistant Uropathogenic Enterobacteriaceae and Pseudomonaceae from Hospitals in Nigeria

β-Lactam antibiotics are widely used to treat urinary tract infections in Nigeria. This study aimed to determine the presence and characteristics of extended spectrum β-lactamases in commonly isolated uropathogenic Gram-negative bacteria (GNB) in Nigeria. Fifty non-duplicate GNB isolates consisting of Escherichia coli, 19; Klebsiella pneumoniae, 21; and Pseudomonas aeruginosa, 10 were obtained from three tertiary hospitals in Nigeria. The antibiotic susceptibility testing of all isolates to a panel of antibiotics including minimum inhibitory concentrations (MICs) and extended spectrum β-lactamases was determined. Polymerase chain reactions and sequencing were used to detect β-lactam genes. Polymerase chain reactions and sequencing identified varying extended spectrum β-lactamases (ESBLs) encoding genes for 24 isolates (48.0%). Cefotaximase-Munich (CTX-M) 15 was the dominant gene with 20/24 of the isolates positive at 83.3%; multiple genes (2 to 6 ESBL genes) were found in 20 of the isolates. The isolates encoded other genes such as CTX-M-14, 33.3%; sulfhydryl variable (SHV) variants, 58.3%; oxacillinase (OXA) variants, 70.8%; OXA-10, 29.2%; and Vietnamese extended β-lactamase (VEB) 1, 25.0%. There was no difference between the MIC₅₀ and MIC₉₀ of all the isolates. The high-level multidrug resistance of uropathogens to third generation cephalosporins including other antibiotics used in this study is strongly associated with carriage of ESBLs, predominantly CTX-M-15, as well as CTX-X-M-14, OXA-10, and VEB-1.

Prevalence of Extended-Spectrum Beta-Lactamases-Producing Microorganisms in Patients Admitted at KRRH, Southwestern Uganda

The emergence of extended-spectrum beta-lactamase- (ESBL-) producing pathogenic bacteria at Kabale Regional Referral Hospital (KRRH), located in southwestern Uganda, is of great concern: a phenomenon that worries clinicians and other healthcare workers due to the serious threat they pose to patients. This current study aimed at determining the phenotypic detection of ESBL-producing strains of E. coli, Klebsiella sp., and Proteus sp. isolated from clinical specimens and their prevalence in patients admitted at KRRH. We used combined disc diffusion technique to detect and establish the presence of ESBLs-producing bacteria. Of the 100 tested bacterial isolates, 89 (89%) were identified as ESBL-producing bacteria. Klebsiella sp. predominated in the samples (46 (52%)), presenting the highest frequency of ESBLs producing followed by E. coli (39 (44%)) and Proteus mirabilis (4 (4.5%)) from the combined disk diffusion.