NDM-1 Introduction in Portugal through a ST11 KL105 Klebsiella pneumoniae Widespread in Europe

The changing epidemiology of carbapenem-resistant Klebsiella pneumoniae in Southern European countries is challenging for infection control, and it is critical to identify and track new genetic entities (genes, carbapenemases, clones) quickly and with high precision. We aimed to characterize the strain responsible for the first recognized outbreak by an NDM-1-producing K. pneumoniae in Portugal, and to elucidate its diffusion in an international context. NDM-1-producing multidrug-resistant K. pneumoniae isolates from hospitalized patients (2018–2019) were characterized using FTIR spectroscopy, molecular typing, whole-genome sequencing, and comparative genomics with available K. pneumoniae ST11 KL105 genomes. FT-IR spectroscopy allowed the rapid (ca. 4 h after incubation) identification of the outbreak strains as ST11 KL105, supporting outbreak control. Epidemiological information supports a community source but without linkage to endemic regions of NDM-1 producers. Whole-genome comparison with previous DHA-1-producing ST11 KL105 strains revealed the presence of different plasmid types and antibiotic resistance traits, suggesting the entry of a new strain. In fact, this ST11 KL105 clade has successfully disseminated in Europe with variable beta-lactamases, but essentially as ESBL or DHA-1 producers. We expand the distribution map of NDM-1-producing K. pneumoniae in Europe, at the expense of a successfully established ST11 KL105 K. pneumoniae clade circulating with variable plasmid backgrounds and beta-lactamases. Our work further supports the use of FT-IR as an asset to support quick infection control.

Penicillinase plasmid Australia type in Neisseria gonorrhoeae isolated in Poland

Purpose Neisseria gonorrhoeae is an etiological agent of gonorrhea which remains a major public health problem the mechanisms that determine resistance to drugs of the beta-lactam class, which are recommended for the treatment of gonorrhea, are currently the most important problem in its treatment. Chromosomal mutations are responsible for resistance to ceftriaxone and cefepime. The possibility of mutations in the gene encoding beta-lactamase (blaTEM) in the penicillinase plasmid may also turn out to be a serious threat. Methods The occurrence of resistance encoded on penicillinase plasmid has been investigated. For this purpose, the susceptibility of bacteria was determined and the gene for resistance to beta-lactams as well as the plasmids themselves was typed. Results Of the 333 strains tested, 21 (6.3%) had the beta-lactamase gene and produced penicillinase. Two of the beta-lactamase: TEM-1 and TEM-135 occurred among the tested strains of N. gonorrhoeae. Most of the known penicillinase plasmid types of N. gonorrhoeae were demonstrated: the Asian, the African, the Toronto/Rio plasmids and Australian variants. Conclusions In the first 3 years, TEM-1 beta-lactamases dominated in N. gonorrhoeae, which were replaced by TEM-135 in the following years of the study. Not all molecular methods are capable of varying the types of penicillinase plasmids. A particularly noteworthy observation is the fact that the Australia-type of penicillinase plasmid (3270 bp) was identified for the first time in Europe, and the second time in the world.

Role of AmpC-Inducing Genes in Modulating Other Serine Beta-Lactamases in Escherichia coli

The consistently mutating bacterial genotypes appear to have accelerated the global challenge with antimicrobial resistance (AMR); it is therefore timely to investigate certain less-explored fields of targeting AMR mechanisms in bacterial pathogens. One of such areas is beta-lactamase (BLA) induction that can provide us with a collection of prospective therapeutic targets. The key genes (ampD, ampE and ampG) to which the AmpC induction mechanism is linked are also involved in regulating the production of fragmented muropeptides generated during cell-wall peptidoglycan recycling. Although the involvement of these genes in inducing class C BLAs is apparent, their effect on serine beta-lactamase (serine-BLA) induction is little known. Here, by using ∆ampD and ∆ampE mutants of E. coli, we attempted to elucidate the effects of ampD and ampE on the expression of serine-BLAs originating from Enterobacteriaceae, viz., CTX-M-15, TEM-1 and OXA-2. Results show that cefotaxime is the preferred inducer for CTX-M-15 and amoxicillin for TEM-1, whereas oxacillin for OXA-2. Surprisingly, exogenous BLA expressions are elevated in ∆ampD and ∆ampE mutants but do not always alter their beta-lactam susceptibility. Moreover, the beta-lactam resistance is increased upon in trans expression of ampD, whereas the same is decreased upon ampE expression, indicating a differential effect of ampD and ampE overexpression. In a nutshell, depending on the BLA, AmpD amidase moderately facilitates a varying level of serine-BLA expression whereas AmpE transporter acts likely as a negative regulator of serine-BLA.

Extensive outbreak of colistin resistant, carbapenemase (blaOXA-48, blaNDM) producing Klebsiella pneumoniae in a large tertiary care hospital, India

Background Extensive drug resistance in Klebsiella pneumoniae (K. pneumoniae) causing major outbreaks in large hospitals is an emerging challenge. We describe a near fatal outbreak of colistin resistant, carbapenem resistant K. pneumoniae (CRKp) producing metallo beta-lactamases (blaNDM) and blaOXA-48 in the neonatal intensive care unit (NICU) at the background of a larger outbreak involving multiple parts of the hospital and the challenges in its containment. Methods Following identification of an outbreak due to colistin resistant CRKp between April to June 2017 in the NICU, a thorough surveillance of similar cases and the hospital environment was performed to trace the source. All the isolated K. pneumoniae were tested for susceptibility to standard antibiotics by disc diffusion and microbroth dilution methods. Molecular detection of extended spectrum beta lactamases (ESBLs) and carbapenemases (classes A, B, D) genes was done. Enterobacterial repetitive intergenic consensus (ERIC) PCR and multi-locus sequence typing (MLST) was done to determine the genetic relatedness of the isolates. Characteristics of different sequence types were statistically compared (Student’s t-test). Results A total of 45 K. pneumoniae isolates were studied from NICU (14 cases of neonatal sepsis), ICU (18 cases), other wards (7 cases) along with 6 isolates from hospital environment and human colonizers. The primary case was identified in the ICU. All the K. pneumoniae from NICU and 94.4% from the ICU were colistin resistant CRKp. Majority (59.37% and 56.25%) harbored blaSHV/blaCTXM and blaOXA-48 genes, respectively. Two distinct sequence types ST5235 and ST5313 were noted with colistin resistance, distribution within the NICU and mortality as significant attributes of ST5235 (p < 0.05). The outbreak was contained with strengthening of the infection control practices and unintended short duration closure of the hospital. Conclusion Large hospital outbreaks with considerable mortality can be caused by non-dominant clones of colistin resistant CRKp harboring blaOXA-48 and blaNDM carbapenemases in endemic regions. The exact global impact of these sequence types should be further studied to prevent future fatal outbreaks.

Impact of SARS-COV-2 on the diagnosis of community bacteremia in a tertiary hospital

Objective. We carry out an analysis of the bacteremia diagnosed in the Emergency Department during 2020, coinciding with the period of the pandemic. Method. We performed a retrospective analysis from March 4, 2020 to December 31, 2020. Results. The number of patients who went to the Emergency Department during the study period and the number of extracted blood cultures decreased by 46.79% and 35.7% compared to the same period in 2019 (p <0.05). 320 bacteremia occurred while 507 occurred in 2019, assuming a decrease of 36.8% (p <0.05). The positivity rate of blood cultures was 7.09% in 2020 and 7.23% in 2019 and the contamination rate was 7.07 % in 2020 and 5.67% in 2019. The most frequently isolated microorganism was Escherichia coli, followed by Staphylococcus aureus and Klebsiella pneumoniae. A 6.62% of the isolated E. coli were carriers of extended-spectrum beta-lactamases (ESBL). The percentage of methicillin-resistant S. aureus was 12.9 % and that of K. pneumoniae ESBL was 11.54%. Conclusion. During the SARS-CoV-2 pandemic there has been a decrease in the number of bacteremia diagnoses, it is possible that attention was focused especially on COVID, forgetting other diseases, such as bacteremia.

KARAKTERISTIK ANTIBIOGRAM ISOLAT Escherichia coli DAN Klebsiella pneumoniae DARI RUANG INTENSIVE CARE UNIT DAN NON-INTENSIVE CARE UNIT DI RSUP SANGLAH SELAMA TAHUN 2018-2020

Resistesi antibiotik meningkat secara global dalam beberapa tahun ini, terutama kejadian Escherichia coli (E.coli) dan Klebsiella pneumoniae (K.pneumoniae) penghasil Extended Spektrum Beta Lactamases (ESBL). Tujuan dari penelitian ini adalah untuk memberikan gambaran prevalensi keberadaan dan antibiogram isolat E.coli dan K. pneumoniae penghasil ESBL di rumah sakit tersier di Bali. Penelitian retrospektif potong lintang ini dlikaukan pada Januari 2018- Desember 2020 di Rumah Sakit Umum Pusat Sanglah, Bali. Identifikasi bakteri dan uji sensitivitas antibiotik dilakukan dengan alat otomatis Vitek®2 Compact. Hasil penelitian menunjukkan dari 2972 isolat, 1067 (63,82%) isolat adalah E. coli penghasil ESBL dan 902 isolat (69,39%) adalah K. pneumoniae penghasil ESBL. Isolat penghasil ESBL ditemukan terbanyak pada non-ICU (89,39%). Bakteri E.coli penghasil ESBL menunjukkan sensitivitas > 80% terhadap Amikacin, Ertapenem, Meropenem, Nitrofurantoin, Piperacillin-tazobactam, dan Tigecycline. Sedangkan, K. pneumoniae penghasil ESBL menunjukkan sensitivitas > 80% terhadap Amikacin, Ertapenem, Meropenem, dan Tigecycline. Penelitian ini menyoroti tingginya prevalensi E.coli dan K.pneumoniae penghasil ESBL di rumah sakit rujukan tersier di Bali. Analisis yang seksama dari antibiogram kedua spesies penghasil ESBL tersebut akan membantu menyusun kebijakan penggunaan antibiotik dan pencegahan, pengendalian penyebaran bakteri penghasil ESBL.Kata Kunci: Escherichia coli; Klebsiella pneumoniae; Extended Spectrum Beta Lactamases; ICU dan Non-ICU

βLact-Pred: A Predictor Developed for Identification of Beta-Lactamases Using Statistical Moments and PseAAC via 5-Step Rule

Beta-lactamase (β-lactamase) produced by different bacteria confers resistance against β-lactam-containing drugs. The gene encoding β-lactamase is plasmid-borne and can easily be transferred from one bacterium to another during conjugation. By such transformations, the recipient also acquires resistance against the drugs of the β-lactam family. β-Lactam antibiotics play a vital significance in clinical treatment of disastrous diseases like soft tissue infections, gonorrhoea, skin infections, urinary tract infections, and bronchitis. Herein, we report a prediction classifier named as βLact-Pred for the identification of β-lactamase proteins. The computational model uses the primary amino acid sequence structure as its input. Various metrics are derived from the primary structure to form a feature vector. Experimentally determined data of positive and negative beta-lactamases are collected and transformed into feature vectors. An operating algorithm based on the artificial neural network is used by integrating the position relative features and sequence statistical moments in PseAAC for training the neural networks. The results for the proposed computational model were validated by employing numerous types of approach, i.e., self-consistency testing, jackknife testing, cross-validation, and independent testing. The overall accuracy of the predictor for self-consistency, jackknife testing, cross-validation, and independent testing presents 99.76%, 96.07%, 94.20%, and 91.65%, respectively, for the proposed model. Stupendous experimental results demonstrated that the proposed predictor “βLact-Pred” has surpassed results from the existing methods.

Antibiotic Resistance Pattern and Prevalence of blaOXA-51, blaNDM, blaVIM, blaPER, blaVEB, blaCTX, tetA and tetB Genes in Acinetobacter baumannii Isolated from Clinical Specimens of Hospitals in Tabriz city, Iran

Background: Nowadays, the resistance of pathogenic bacteria to antibiotics has become a global problem. Acinetobacter baumannii is an important opportunistic nosocomial pathogen. Acinetobacter baumannii plays a significant role in antibiotic resistance. Objectives: The purpose of this study was to investigate the prevalence of the blaOXA-51, blaNDM, blaVIM, blaPER, blaVEB, blaCTX-M, tetA and tetB genes and antibiotic resistance pattern of A. baumannii isolated from hospitals in Tabriz city, Iran. Methods: This study was descriptive cross-sectional research, performed on 129 isolates of Acinetobacter from different clinical specimens. The Isolates were identified using standard laboratory methods and culture in selective mediums. The antibiotic resistance pattern of isolates was also determined by the Kirby-Bauer disk diffusion susceptibility test. Phenotypic and genotypic detection of blaOXA-51, blaNDM, blaVIM, blaPER, blaVEB, blaCTX-M, tetA and tetB genes in the isolates was carried out by a combined disk test (CDT) and polymerase chain reaction (PCR), respectively. Results: The highest resistance of isolates was determined to cefotaxime (100%) and ceftazidime (100%). The results of CDT showed that 14 (12.96%) isolates could produce extended-spectrum Beta-lactamases (ESBLs). However, the PCR results blaOXA-51, blaNDM, blaVIM, blaPER, blaVEB, blaCTX-M, tetA and tetB genes showed that these genes were in 100%, 18.51%, 16.66%, 32.40%, 16.66%, 31.48%, 32.40% and 21.29% of isolates, respectively. Conclusions: Due to the high prevalence of antimicrobial resistance in strains, rapid and timely detection of antibiotic-resistant A. baumannii strains is necessary for the selection of an appropriate therapeutic approach and prevention of their prevalence.

The Ultra-Broad-Spectrum Beta-lactamase Inhibitor QPX7728 Restores the Potency of Multiple Oral Beta-lactam Antibiotics against Beta-lactamase Producing Strains of Resistant Enterobacterales

QPX7728 is a cyclic boronate ultra-broad-spectrum beta-lactamase inhibitor, with potent activity against both serine and metallo beta-lactamases. QPX7728 can be delivered systemically by the IV or oral route of administration. Oral β-lactam antibiotics alone or in combination with QPX7728 were evaluated for 1) sensitivity to hydrolysis by various common beta-lactamases and inhibition of hydrolysis by QPX7728; 2) the impact of non-beta-lactamase-mediated resistance mechanisms on potency of beta-lactams; and 3) in vitro activity against a panel of clinical strains producing diverse beta-lactamases. The carbapenem tebipenem had stability for many serine beta-lactamases from all molecular classes followed by cephalosporin ceftibuten. Addition of QPX7728 to tebipenem, ceftibuten and mecillinam completely reversed beta-lactamase-mediated resistance in cloned beta-lactamases from serine and metallo enzyme classes; the degree of potentiation of other beta-lactams varied according to the beta-lactamase produced. Tebipenem, ceftibuten and cefixime had the lowest MICs against laboratory strains with various combinations of beta-lactamases and the intrinsic drug-resistance mechanisms of porin and efflux mutations. There was a high degree of correlation between potency of various combinations against cloned beta-lactamases and efflux/porin mutants and the activity against clinical isolates, showing the importance of both inhibition of beta-lactamase along with minimal impact of general intrinsic resistance mechanisms affecting the beta-lactam. Tebipenem and ceftibuten appeared to be the best beta-lactam antibiotics when combined with QPX7728 for activity against Enterobacterales that produce serine or metallo beta-lactamases.

Antimicrobial resistance profile of extended-spectrum beta-lactamases, adenosine-monophosphate-cyclic, and carbapenemase-producing Gram-negative bacteria isolated from domestic animals

Background and Aim: The production of beta-lactamase enzymes, such as extended-spectrum beta-lactamase (ESBL), adenosine-monophosphate-cyclic (AmpC), and Klebsiella pneumoniae carbapenemase (KPC), is one of the most important mechanisms of bacterial resistance to antimicrobials. Gram-negative bacteria show significant resistance due to various intrinsic and acquired factors. These intrinsic factors include low permeability of the outer membrane, various efflux systems, and the production of beta-lactamases, while acquired factors include chromosomal mutation and acquisition of resistance genes by horizontal transfer. Mobile elements such as plasmids, integrative conjugative elements, mobilizable islands, or transposable elements are involved in horizontal transfer. At present, the Gram-negative pathogens of most concern are Acinetobacter baumannii, Pseudomonas aeruginosa, and those belonging to the Enterobacteriaceae family (e.g., Escherichia coli, K. pneumoniae, and Proteus mirabilis). This study aimed to evaluate the profile of antimicrobial resistance and the production of the enzymes ESBL, AmpC, and KPC, in 21 gram-negative bacteria isolated from domestic animals treated at the University Veterinary Hospital (HVU) of the Federal University of Western Bahia (UFOB). Materials and Methods: The biological samples (21) were inoculated to brain heart infusion broth, blood agar, and MacConkey agar and incubated for 24-72 h at 37°C. Gram staining and identification through biochemical tests and matrix-associated laser desorption/ionization time-of-flight mass spectrometry were conducted. To evaluate the antimicrobial resistance profile, the disk diffusion method was used, and 25 antibiotics were employed. For the detection of ESBL, the disk approximation method was applied using chromogenic agar. The presence of KPC was observed using chromogenic agar and the Hodge test. For AmpC evaluation, the disk approximation method was used. Results: The most isolated agent was E. coli (66.66%, 14/21), followed by K. pneumoniae and P. mirabilis (both 14.29%, 3/21), and then Pasteurella spp. (4.76%, 1/21). The bacterial isolates showed high levels of resistance against clindamycin, penicillin, imipenem, polymyxin, cefoxitin, gentamycin, cefotaxime, ceftazidime, cephalothin, ceftriaxone, ciprofloxacin, trimethoprim/sulfamethoxazole, chloramphenicol, and tetracycline. The best effectiveness rates were observed for cefepime, streptomycin, amoxicillin-clavulanate, aztreonam, nalidixic acid, tobramycin, levofloxacin, amikacin, and meropenem. All biological isolates showed multiple resistance to at least three of the antibiotics tested (3/25), and some showed resistance to 24 of the antibiotics tested (24/25). Among the 21 pathogens analyzed, 8 were ESBL producers (38.09%); of these, 6 were identified as E. coli (28.57%), and 2 were identified as K. pneumoniae (9.52%). Two strains of K. pneumoniae produced both ESBL and KPC. None of the isolates were producers of AmpC. Conclusion: The results found in the present work raise concern about the level of antimicrobial resistance among pathogens isolated from domestic animals in Brazil. The results highlight the need for the development and implementation of anti-resistance strategies to avoid the dissemination of multiresistant pathogens, including the prudent use of antimicrobials and the implementation of bacterial culture, antimicrobial sensitivity, and phenotypic tests for the detection of beta-lactamase enzymes in bacteria isolated from animals.