Molecular diversity of extended-spectrum β-lactamases and carbapenemases, and antimicrobial resistance

Epidemiology and Mortality Analysis Related to Carbapenem-Resistant Enterobacterales in Patients After Admission to Intensive Care Units: An Observational Study

Purpose

The prevalence of carbapenem-resistant Enterobacterales (CRE) is rapidly increasing worldwide. Patients in the intensive care unit (ICU) are susceptible to CRE infections, and the related mortality rate is increased. It is necessary to understand CRE strains and risk factors for CRE infection in the ICU, to facilitate development of effective prophylactic strategies and treatments for ICU patients.

Patients and Methods

This observational study was conducted in a tertiary hospital between 2016 and 2021. The subjects were patients with CRE cultured from specimens obtained after ICU admission. Genotypes of strains of CRE and carbapenemase-producing Enterobacterales (CPE) were identified, CRE infection was distinguished from mere colonization, and the clinical course of these patients was investigated.

Results

Among 327 CRE cases, 84 (25.7%) showed infection and 243 (74.3%) showed colonization. Of these patients, 138 (42.2%) died. The CRE strains were Klebsiella pneumoniae (253 cases, 77.4%), Enterobacter cloacae (44 cases, 13.5%), and Escherichia coli (15 cases, 4.6%). Among CRE cases, CPE was found in 249 (76.1%), including Klebsiella pneumoniae carbapenemase (KPC) in 164 (65.9%), and Guiana extended-spectrum (GES) in 64 (25.7%). A bedridden state, longer ICU stay, chronic kidney disease, malignancy, connective tissue disease, ICU admission for cardiac arrest, and CRE infection were associated with higher mortality, but cerebrovascular disease and ICU admission for trauma were associated with lower mortality. GES outbreak was caused by person-to-person transmission and was controlled through active surveillance.

Conclusion

The frequency of K. pneumoniae and KPC was the highest, but E. cloacae and GES was characteristically high in this study. Active CRE surveillance can be helpful for controlling outbreak.

ESBL and carbapenemase-producing Enterobacteriaceae in infectious pleural effusions: current epidemiology at Hôpital du Mali

Background

Antimicrobial resistance (AMR) is a global health concern, with extended-spectrum β-lactamases (ESBLs) and carbapenemases being major contributors. Pleural infection (PI) is a severe condition in West Africa, complicated by AMR. This study aimed to investigate the prevalence and molecular characteristics of ESBL and carbapenemase-producing enterobacteria in pleural effusions in Mali.

Materials and methods

Pleural fluid samples from 526 patients with pleuritis were analyzed. Enterobacterial species were isolated and identified, and the prevalence of resistance genes (blaOXA-48, blaNDM-1, blaKPC, blaTEM, blaSHV) and virulence factors was determined.

Results

Among the patients, 110 were diagnosed with enterobacterial pleuritis. Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis were the main pathogens identified. Resistance to β-lactams and cephalosporins was high, while carbapenems showed good activity. ESBL production was detected in 33.6% of isolates, with blaTEM being the most common gene. Carbapenemase gene (blaNDM-1) was found in three isolates.

Conclusion

The study highlights the high prevalence of multidrug-resistant bacteria and the need for appropriate antibiotic selection based on local resistance patterns. Understanding the molecular characteristics of resistance is crucial for optimizing patient care and developing effective therapeutic strategies. Further research is needed to monitor and control AMR in PIs in Mali.

The threat of multidrug-resistant/extensively drug-resistant Gram-negative respiratory infections: another pandemic

Antibiotic resistance is recognised as a global threat to human health by national healthcare agencies, governments and medical societies, as well as the World Health Organization. Increasing resistance to available antimicrobial agents is of concern for bacterial, fungal, viral and parasitic pathogens. One of the greatest concerns is the continuing escalation of antimicrobial resistance among Gram-negative bacteria resulting in the endemic presence of multidrug-resistant (MDR) and extremely drug-resistant (XDR) pathogens. This concern is heightened by the identification of such MDR/XDR Gram-negative bacteria in water and food sources, as colonisers of the intestine and other locations in both hospitalised patients and individuals in the community, and as agents of all types of infections. Pneumonia and other types of respiratory infections are among the most common infections caused by MDR/XDR Gram-negative bacteria and are associated with high rates of mortality. Future concerns are already heightened due to emergence of resistance to all existing antimicrobial agents developed in the past decade to treat MDR/XDR Gram-negative bacteria and a scarcity of novel agents in the developmental pipeline. This clinical scenario increases the likelihood of a future pandemic caused by MDR/XDR Gram-negative bacteria.

Detection of Extended-Spectrum β-Lactamases (ESBLs) and AmpC in Class A and Class B Carbapenemase-Producing Enterobacterales

In carbapenemase-producing Enterobacterales (CPE) additional β-lactam resistance mechanisms such as extended-spectrum-β-lactamases (ESBL) and/or AmpC-β-lactamases are generally difficult to detect by phenotypical methods. Recently, a modified version of the CLSI ESBL confirmatory combination disc diffusion (CDD) test, which involves the addition of boronic acid and EDTA on discs containing ESBL and AmpC substrates ± inhibitors, has been proposed for the detection of ESBL in class A and class B CPE. Here, the performance of the modified CDD test was evaluated using 121 genotypically characterized class A and class B CPE. Also, the effectiveness of the NG-Test CTX-M-MULTI lateral flow immunoassay was evaluated for ESBL detection. For class A CPE (n = 47), the modified CDD method exhibited an equal specificity (95.7%) and a higher sensitivity (100%) compared to the standard method (91.7%). The CTX-M-MULTI test detected ESBL in all CTX-M-type ESBL producers (n = 23), whereas it was negative for all CTX-M-type ESBL-negative isolates (n = 24). For class B CPE (n = 71), the modified method significantly improved both sensitivity (95%) and specificity (100%) in detecting ESBL compared to the standard method (17.5% sensitivity and 83.9% specificity). In comparison, the CTX-M-MULTI led to identification of ESBL in all CTX-M-ESBL-producers (n = 39) and no false-positive signal was generated with the CTX-M-type-ESBL-negative isolates (n = 30). Furthermore, the modified CDD improved the robustness of the method for AmpC detection (inconclusive results were produced in 53/57 and 10/57 cases with the standard and modified method, respectively), although the sensitivity of the test was poor (23.5%). Here, we propose a practical and cost-effective approach combining the modified CDD and the CTX-M-MULTI test for detection of ESBL and/or AmpC in class A and B CPE. IMPORTANCE Antimicrobial resistance is a growing public health threat of broad concern worldwide. Timely detection of antibiotic resistance mechanisms can help to monitor and to curb the spread of resistant bacteria within the hospital setting as well as in the environment. In this work we report an accurate and affordable method to phenotypically identify difficult-to-detect resistance determinants in highly resistant (carbapenemase-producing) bacteria. This method may be implemented in any diagnostic microbiology lab and may reduce the underreporting of relevant resistance mechanisms.

Characterization of Acinetobacter baumannii Isolated from Raw Milk

Acinetobacter baumannii (A. baumannii) is an opportunistic pathogen associated with nosocomial infections. In this study, 100 raw milk samples were collected from Qena, Egypt, and subjected to conventional and molecular assays to determine the presence of A. baumannii and investigate their antimicrobial resistance and biofilm formation. Our findings revealed that, among the 100 samples, Acinetobacter spp. were found in 13 samples based on CHROM agar results. We further characterized them using rpoB and 16S-23SrRNA sequencing and gyrB multiplex PCR analysis and confirmed that 9 out of the 13 Acinetobacter spp. isolates were A. baumannii and 4 were other species. The A. baumannii isolates were resistant to β-lactam drugs, including cefotaxime (44%), ampicillin-sulbactam and levofloxacin (33.3% for each), imipenem, meropenem and aztreonam (22.2% for each). We observed different antimicrobial resistance patterns, with a multi-antibiotic resistant (MAR) index ranging from 0.2 to 0.3. According to the PCR results, bla_OXA-51 and bla_OXA-23 genes were amplified in 100% and 55.5% of the A. baumannii isolates, respectively, while the bla_OXA-58 gene was not amplified. Furthermore, the metallo-β-lactamases (MBL) genes bla_IMP and bla_NDM were found in 11.1% and 22.2% of isolates, respectively, while bla_VIM was not amplified. Additionally, eight A. baumannii isolates (88.8%) produced black-colored colonies on Congo red agar, demonstrating their biofilm production capacity. These results showed that, besides other foodborne pathogens, raw milk should also be examined for A. baumannii, which could be a public health concern.

Prevalence and Antibiotic Resistance of Staphylococcus aureus and Escherichia coli Isolated from Bovine Raw Milk in Lebanon: A study on Antibiotic Usage, Antibiotic Residues, and Assessment of Human Health Risk Using the One Health Approach

The emergence, persistence, and spread of antibiotic-resistant microbes is a tremendous public health threat that is considered nowadays a critical One Health issue. In Lebanon, the consumption of raw bovine milk has been recently reported as a result of the financial crisis. The objectives of the current study were (1) to evaluate raw bovine milk samples in a comprehensive manner for the types of antibiotics used and their residues, (2) to determine the presence of mesophilic bacteria, extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA), and (3) to determine the associated human health risk caused by drinking raw milk with antibiotic residues among all age categories. LC-MS-MS was used to carry out the analysis. From 200 milk samples, 30 (15%) were found contaminated with four major antibiotics. The highest average concentration detected was for oxytetracyline 31.51 ± 13.23 μg/kg, followed by 5.5 ± 0.55 μg/kg for gentamicin, 4.56 ± 0.73 μg/kg for colistin, and 4.44 ± 0.89 μg/kg for tylosin. The mean contamination among most samples was below the maximum residue limits (MRLs). Upon comparison with the acceptable daily intake (ADI), the estimated daily intake (EDI) across all age groups was acceptable. The hazard quotient (HQ) was also below 1 across all age groups, signifying the absence of associated health risks for the Lebanese consumers. On the other hand, all milk samples were found exceeding the maximum tolerable value of mesophilic flora. Antibiotic-resistant bacteria (ARB) were detected and represented by ESBL-producing E. coli and MRSA isolates. Thus, the greatest threat of antibiotic use in Lebanon does not fall under antibiotic residues but rather the proliferation of antibiotic resistance in potentially pathogenic bacteria. In this study, the virulence profile of detected bacteria was not investigated; thus their pathogenicity remains unknown. Therefore, to mitigate this health threat in Lebanon, a "One Health" action plan against ABR is required. It will provide a framework for continued, more extensive action to reduce the emergence and spread of ABR in Lebanon.

Comparative Evaluation of Three Phenotypic Tests-Carba NP, Modified Carba NP and Rapidec Carba NP Test for Rapid Detection of Carbapenem Resistance in Blood Culture Isolates of Escherichia coli in an ICU Setting

Background

To determine the antibiotic resistance pattern, the prevalence of extended-spectrum beta-lactamases (ESBLs) and carbapenem resistance in blood culture isolates of E. coli. Further, we evaluated and compared Carba NP, Modified Carba NP and a kit-based Rapidec Carba NP test to detect carbapenem resistance rapidly.

Methods

Twenty-six carbapenem-resistant strains and four susceptible strains were selected. The three methods mentioned above were evaluated as per Clinical Laboratory Standards Institute (CLSI). These tests are based on biochemical detection of the hydrolysis of the beta-lactam ring of a carbapenem-imipenem, followed by the colour change of a pH indicator.

Results

Carba NP test was positive in 24 out of 26 isolates; the Modified Carba NP and Rapidec Carba NP tests were positive for all the isolates (26/26). All the carbapenemase non-producers (100%, 04/04) were negative.

Conclusion

Modified Carba NP is a more effortless and inexpensive alternative to the Carba NP test, allowing the detection of carbapenemase activity directly from bacterial cultures of Enterobacteriaceae. The test could be used in low-income countries with large reservoirs for carbapenemase producers and can be implemented in any laboratory worldwide.

Contamination of healthcare environment by carbapenem-resistant Acinetobacter baumannii

Acinetobacter baumannii is frequently found on floors, devices, and environmental sites in hospitals and can survive for prolonged periods and accumulate resistance determinants. The infection and presence of carbapenem-resistant A. baumannii (CRAB) in patients is associated with increased mortality, severe clinical outcomes, and longer lengths of stay at hospitals. This review addresses contamination by CRAB in corporal surfaces of patients and healthcare workers and environmental sites at healthcare-related settings. We summarized published data during the last decade on potential reservoirs for CRAB, including contamination frequency and the involved resistance mechanisms, and some measures associated with the elimination of CRAB from hospital surfaces.

Insight into carbapenem resistance and virulence of Acinetobacter baumannii from a children’s medical centre in eastern China

Carbapenem-resistant Acinetobacter baumannii (CRAB) appeared more frequently in children and caused a great threat to global public health. It is urgent to investigate the carbapenem resistance and virulence of CRAB for clinicians to choose appropriate antibiotics. A retrospective study of 77 nonduplicated CRAB isolates was conducted. The carbapenem resistance and virulence genes were characterized by polymerase chain reaction (PCR) and gel electrophoresis. In the present study, A. baumannii mainly came from the intensive care unit and was mostly isolated from sputum samples. The carbapenem resistant rate of A. baumannii in 2018–2020 increased significantly compared with that in 2016–2017. All isolates had carbapenem resistant genes. They were highly resistant to a variety of antibiotics but were relatively sensitive to fluoroquinolones and tetracyclines. blaVIM and blaOXA-23 were detected in all isolates, whereas blaOXA-51, blaIMP and blaNDM were present in 98.70%, 67.53% and 31.17% of isolates, respectively. Notably, 1 isolate A. baumannii was identified as multidrug-resistant A. baumannii (MDR-AB), and 76 other extensively drug-resistance (XDR) isolates were also detected. Virulence genes were present in 100% of all isolates, including genes in the iron acquisition system (basJ), secretion systems (ompA, plcD), quorum sensing system (abaI) and biofilm formation (csuA). adeH, pgaA, and ptk were present in 98.70%, 98.70% and 94.80% of isolates, respectively. CRAB, which is prevalent in east China, carries a large number of drug resistance and virulence genes. Fluoroquinolones and tetracyclines may be effective antibiotics for the treatment of CRAB infection in children. An in-depth understanding of the resistance and virulence of CRAB is conducive to timely guiding empirical drug use and controlling infection.

In vitro effects of diazabicyclooctane β-lactamase inhibitors relebactam and nacubactam against three subspecies of Mycobacterium abscessus complex

BACKGROUND

Mycobacterium abscessus complex (MABC) pulmonary disease is notoriously difficult to treat due to intrinsic resistance to many common antibiotics. MABC is β-lactam-resistant as it produces class A β-lactamases, such as bla_Mab, which are inhibited by diazabicyclooctane (DBO) β-lactamase inhibitors.

OBJECTIVES

To investigate the microbiological effects of the combination of β-lactam and DBO β-lactamase inhibitors (relebactam and nacubactam) against MABC and determine if the effects are associated with the MABC subspecies and colony morphotype.

METHODS

The antimicrobial susceptibility of three type strains and 20 clinical isolates of MABC to the combination of seven β-lactams with relebactam or nacubactam was evaluated using broth microdilution checkerboard assays. For these strains, expression levels of bla_Mab were assessed using quantitative real-time polymerase chain reaction and genotypic diversity was evaluated using 18-locus variable number tandem repeat assay.

RESULTS

Relebactam and nacubactam lowered the minimum inhibitory concentrations of β-lactams, particularly imipenem, meropenem, and tebipenem, against MABC. There was no difference in efficacy of combination treatment between three subspecies, but rough morphotypes tended to be less susceptible than smooth morphotypes. There were no differences in bla_Mab expression levels and genotypic diversity between the morphotypes.

CONCLUSIONS

The combination of β-lactam with relebactam or nacubactam improved the efficacy of β-lactams against all MABC subspecies, but higher concentrations of β-lactams were needed for rough morphotypes.

Role of Enzymatic Activity in the Biological Cost Associated with the Production of AmpC β-Lactamases in Pseudomonas aeruginosa

In the current scenario of growing antibiotic resistance, understanding the interplay between resistance mechanisms and biological costs is crucial for designing therapeutic strategies. In this regard, intrinsic AmpC β-lactamase hyperproduction is probably the most important resistance mechanism of Pseudomonas aeruginosa, proven to entail important biological burdens that attenuate virulence mostly under peptidoglycan recycling alterations. P. aeruginosa can acquire resistance to new β-lactam-β-lactamase inhibitor combinations (ceftazidime-avibactam and ceftolozane-tazobactam) through mutations affecting ampC and its regulatory genes, but the impact of these mutations on the associated biological cost and the role that β-lactamase activity plays per se in contributing to the above-mentioned virulence attenuation are unknown. The same questions remain unsolved for plasmid-encoded AmpC-type β-lactamases such as FOX enzymes, some of which also provide resistance to new β-lactam-β-lactamase inhibitor combinations. Here, we assessed from different perspectives the effects of changes in the active center and, thus, in the hydrolytic spectrum resistance to inhibitors of AmpC-type β-lactamases on the fitness and virulence of P. aeruginosa, using site-directed mutagenesis; the previously described AmpC variants T96I, G183D, and ΔG229-E247; and, finally, blaFOX-4 versus blaFOX-8. Our results indicate the essential role of AmpC activity per se in causing the reported full virulence attenuation (in terms of growth, motility, cytotoxicity, and Galleria mellonella larvae killing), although the biological cost of the above-mentioned AmpC-type variants was similar to that of the wild-type enzymes. This suggests that there is not an important biological burden that may limit the selection/spread of these variants, which could progressively compromise the future effectiveness of the above-mentioned drug combinations. IMPORTANCE The growing antibiotic resistance of the top nosocomial pathogen Pseudomonas aeruginosa pushes research to explore new therapeutic strategies, for which the resistance-versus-virulence balance is a promising source of targets. While resistance often entails significant biological costs, little is known about the bases of the virulence attenuations associated with a resistance mechanism as extraordinarily relevant as β-lactamase production. We demonstrate that besides potential energy and cell wall alterations, the enzymatic activity of the P. aeruginosa cephalosporinase AmpC is essential for causing the full attenuation associated with its hyperproduction by affecting different features related to pathogenesis, a fact exploitable from the antivirulence perspective. Less encouraging, we also show that the production of different chromosomal/plasmid-encoded AmpC derivatives conferring resistance to some of the newest antibiotic combinations causes no significantly increased biological burdens, which suggests a free way for the selection/spread of these types of variants, potentially compromising the future effectiveness of these antipseudomonal therapies.

Clinically Relevant β-Lactam Resistance Genes in Wastewater Treatment Plants

Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in multiple areas, which is consistent with One Health's concept of close interconnections between people, animals, plants, and their shared environments. Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) circulate constantly in various niches, sediments, water sources, soil, and wastes of the animal and plant sectors, and is linked to human activities. Sewage of different origins gets to the wastewater treatment plants (WWTPs), where ARB and ARG removal efficiency is still insufficient, leading to their transmission to discharge points and further dissemination. Thus, WWTPs are believed to be reservoirs of ARGs and the source of spreading AMR. According to a World Health Organization report, the most critical pathogens for public health include Gram-negative bacteria resistant to third-generation cephalosporins and carbapenems (last-choice drugs), which represent β-lactams, the most widely used antibiotics. Therefore, this paper aimed to present the available research data for ARGs in WWTPs that confer resistance to β-lactam antibiotics, with a particular emphasis on clinically important life-threatening mechanisms of resistance, including extended-spectrum β-lactamases (ESBLs) and carbapenemases (KPC, NDM).

Hypervirulent carbapenem-resistant Klebsiella pneumoniae causing highly fatal meningitis in southeastern China

Klebsiella pneumoniae (K. pneumoniae) is one of the most common causes of bacterial meningitis worldwide. The purpose of this study was to investigate the clinical and microbiological characteristics of K. pneumoniae meningitis, as well as the association of antimicrobial resistance, virulence, and patient prognosis. The clinical data of patients with K. pneumoniae meningitis from 2014 to 2020 in a tertiary teaching hospital were retrospectively evaluated. Antimicrobial susceptibility profiles were performed by the agar dilution method and broth microdilution method. The isolates were detected for virulence-related genes, resistance genes, capsular serotypes, and molecular subtypes. A total of 36 individuals with K. pneumoniae meningitis were included in the study, accounting for 11.3% (36/318) of all cases of bacterial meningitis. Of the 36 available isolates, K1, K47, and K64 were tied for the most frequent serotype (7/36, 19.4%). MLST analysis classified the isolates into 14 distinct STs, with ST11 being the most common (14/36, 38.9%). Carbapenem resistance was found in 44.4% (16/36) of the isolates, while hypervirulent K. pneumoniae (HvKP) was found in 66.7% (24/36) of the isolates. The isolates of hypervirulent carbapenem-resistant K. pneumoniae (Hv-CRKP) were then confirmed to be 36.1% (13/36). Importantly, individuals with meningitis caused by Hv-CRKP had a statistically significant higher mortality than the other patients (92.3%, 12/13 vs. 56.5%, 13/23; P < 0.05). The high percentage and fatality of K. pneumoniae-caused meningitis, particularly in Hv-CRKP strains, should be of significant concern. More effective surveillance and treatment solutions will be required in future to avoid the spread of these life-threatening infections over the world.

Multi-drug resistant bacteria isolates from lymphatic filariasis patients in the Ahanta West District, Ghana

Background

Antimicrobial resistance is associated with increased morbidity in secondary infections and is a global threat owning to the ubiquitous nature of resistance genes in the environment. Recent estimate put the deaths associated with bacterial antimicrobial resistance in 2019 at 4.95 million worldwide. Lymphatic filariasis (LF), a Neglected Tropical Disease (NTD), is associated with the poor living in the tropical regions of the world. LF patients are prone to developing acute dermatolymphangioadenitis (ADLA), a condition that puts them at risk of developing secondary bacterial infections due to skin peeling. ADLA particularly worsens the prognosis of patients leading to usage of antibiotics as a therapeutic intervention. This may result in inappropriate usage of antibiotics due to self-medication and non-compliance; exacerbating antimicrobial resistance in LF patients. In this perspective, we assessed the possibilities of antimicrobial resistance in LF patients. We focused on antibiotic usage, antibiotic resistance in Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa isolates and looked at genes (mecA and Extended-spectrum beta-lactamase [blaCTX-M, blaSHV and blaTEM]) coding for resistance in multi-drug resistant (MDR) bacterial isolates.

Results

Of the sixty (60) participants, fifty-four (n = 54, 90%) were within 31–60 years of age, twenty (n = 20, 33.33%) were unemployed and thirty-eight (n = 38, 50.67%) had wounds aged (in months) seven (7) months and above. Amoxicillin (54%) and chloramphenicol (22%) were the most frequently used antibiotics for self-medication. Staphylococcus aureus isolates (n = 26) were mostly resistant to penicillin (n = 23, 88.46%) and least resistant to erythromycin (n = 2, 7.69%). Escherichia coli isolates (n = 5) were resistant to tetracycline (n = 5, 100%) and ampicillin (n = 5, 100%) but were sensitive to meropenem (n = 5, 100%). Pseudomonas aeruginosa isolates (n = 8) were most resistant to meropenem (n = 3, 37.50%) and to a lesser ciprofloxacin (n = 2, 25%), gentamicin (n = 2, 25%) and ceftazidime (n = 2, 25%). Multi-drug resistant methicillin resistant Staphylococcus aureus (MRSA), cephalosporin resistant Escherichia coli. and carbapenem resistant Pseudomonas aeruginosa were four (n = 4, 15.38%), two (n = 2, 40%) and two (n = 2, 25%) respectively. ESBL (blaCTX-M) and mecA genes were implicated in the resistance mechanism of Escherichia coli and MRSA, respectively.

Conclusion

The findings show presence of MDR isolates from LF patients presenting with chronic wounds; thus, the need to prioritize resistance of MDR bacteria into treatment strategies optimizing morbidity management protocols. This could guide antibiotic selection for treating LF patients presenting with ADLA.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02624-9.

Extended Spectrum- and Carbapenemase-Based β-Lactam Resistance in the Arabian Peninsula-A Descriptive Review of Recent Years

Antimicrobial resistance (AMR) is a global problem that also includes countries of the Arabian Peninsula. Of particular concern, is the continuing development of extended-spectrum β-lactamases (ESBLs) in the countries of this region. Additionally, antibiotic treatment options for ESBL-producing bacteria are becoming limited, primarily due to the continuing development of carbapenem resistance (CR), carbapenems being frequently used to treat such infections. An overview of recent publications (2018-2021) indicates the presence of ESBL and/or CR in patients and hospitals in most countries of the Arabian Peninsula, although the delay between microbial isolation and publication inevitably makes an accurate analysis of the current situation rather difficult. However, there appears to be greater emphasis on CR (including combined ESBL and CR) in recent publications. Furthermore, although publications from Saudi Arabia are the most prevalent, this may simply reflect the increased interest in ESBL and CR within the country. Enhanced ESBL/CR surveillance is recommended for all countries in the Arabian Peninsula.

New antimicrobial treatment options for severe Gram-negative infections

PURPOSE OF REVIEW

This review will provide rationale for the development of new antibiotics to treat severe or multidrug-resistant (MDR) Gram-negative infections. It will also provide an overview of recently approved and pipeline antibiotics for severe/MDR Gram-negative infections.

RECENT FINDINGS

MDR Gram-negative infections are recognized as critical threats by global and national organizations and carry a significant morbidity and mortality risk. Increasing antibiotic resistance amongst Gram-negative bacteria, including carbapenem-resistant Acinetobacter baumannii , extended-spectrum β-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales and Pseudomonas aeruginosa , with difficult-to-treat-resistance has made both empiric and definitive treatment of these infections increasingly problematic. In recent years, several antibiotics have been approved for treatment of MDR Gram-negative infections and ongoing clinical trials are poised to provide additional options to clinicians' armamentarium. These agents include various β-lactam/β-lactamase inhibitor combinations, eravacycline, plazomicin and cefiderocol.

SUMMARY

Severe/MDR Gram-negative infections continue to be important infections due to their impact on patient outcomes, especially in critically ill and immunocompromised hosts. The availability of new antibiotics offers an opportunity to improve empiric and definitive treatment of these infections.

The Mechanism of Bacterial Resistance and Potential Bacteriostatic Strategies

Bacterial drug resistance is rapidly developing as one of the greatest threats to human health. Bacteria will adopt corresponding strategies to crack the inhibitory effect of antibiotics according to the antibacterial mechanism of antibiotics, involving the mutation of drug target, secreting hydrolase, and discharging antibiotics out of cells through an efflux pump, etc. In recent years, bacteria are found to constantly evolve new resistance mechanisms to antibiotics, including target protective protein, changes in cell morphology, and so on, endowing them with multiple defense systems against antibiotics, leading to the emergence of multi-drug resistant (MDR) bacteria and the unavailability of drugs in clinics. Correspondingly, researchers attempt to uncover the mystery of bacterial resistance to develop more convenient and effective antibacterial strategies. Although traditional antibiotics still play a significant role in the treatment of diseases caused by sensitive pathogenic bacteria, they gradually lose efficacy in the MDR bacteria. Therefore, highly effective antibacterial compounds, such as phage therapy and CRISPER-Cas precision therapy, are gaining an increasing amount of attention, and are considered to be the treatments with the moist potential with regard to resistance against MDR in the future. In this review, nine identified drug resistance mechanisms are summarized, which enhance the retention rate of bacteria under the action of antibiotics and promote the distribution of drug-resistant bacteria (DRB) in the population. Afterwards, three kinds of potential antibacterial methods are introduced, in which new antibacterial compounds exhibit broad application prospects with different action mechanisms, the phage therapy has been successfully applied to infectious diseases caused by super bacteria, and the CRISPER-Cas precision therapy as a new technology can edit drug-resistant genes in pathogenic bacteria at the gene level, with high accuracy and flexibility. These antibacterial methods will provide more options for clinical treatment, and will greatly alleviate the current drug-resistant crisis.

The Resistance Mechanisms and Clinical Impact of Resistance to the Third Generation Cephalosporins in Species of Enterobacter cloacae Complex in Taiwan

Enterobacter cloacae complex (ECC) is ubiquitous in the environment and is an important pathogen causing nosocomial infections. Because routine methods used in clinical laboratories cannot identify species within ECC, the clinical significance of each species within ECC is less known. We applied hsp60 gene sequencing to identify the species/clusters of ECC and detected β-lactamase genes and class 1 integrons with PCR for 184 clinical ECC isolates in Taiwan from 2013 to 2014 to investigate the clinical impact of species within ECC. The four most common clusters were E. hormaechei subsp. steigerwaltii (cluster VIII) (29.9%), E. hormaechei subsp. oharae (cluster VI) (20.1%), E. cloacae subsp. cloacae (cluster XI) (12%), and E. kobei (cluster II) (10.3%). E. hormaechei, which consisted of four clusters (clusters III, VI, VII, and VIII), is the predominant species and accounted for 57.1% of the isolates. The ceftazidime resistance rate was 27.2%, and the ceftriaxone resistance rate was 29.3%. Resistance to third generation cephalosporin was associated with a higher 30-day mortality rate. In total, 5 (2.7%), 24 (13.0%), and 1 (0.5%) isolates carried ESBL, AmpC, and carbapenemase genes, respectively. Class 1 integrons were present in 24.5% of the isolates, and most of the cassettes pertain to antibiotic resistance. Resistance to third generation cephalosporins, multidrug resistance, and class 1 integrons were significantly more in E. hormaechei (clusters III, VI, VII, and VIII) than in the other species. The 30-day mortality rate and 100-day mortality did not differ significantly between patients with E. hormaechei and those with infections with the other species. In conclusion, the distribution of third generation cephalosporin resistance, multidrug resistance, and class 1 integrons were uneven among Enterobacter species. The resistance to third generation cephalosporins possessed significant impact on patient outcome.

MALDI-TOF mass spectrometry for direct KPC detection among Enterobacterales

In this study, we evaluate a method for the KPC enzyme detection, using MALDI-TOF MS, for Enterobacterales. A total of 300 clinical Enterobacterales isolates were selected. The collection included 259 carbapenemase-producing (157 KPC and 102 non-KPC) and 41 carbapenemase non-producing isolates. Bacterial proteins were extracted from Mueller-Hinton agar plates using formic acid, isopropyl alcohol, and water (17:33:50). Samples were prepared with a double layer of synapinic acid. Analyses were performed using a Microflex LT mass spectrometer (Bruker Daltonics) and flexAnalysis 4.0 software (Bruker Daltonics). Statistical analyses were performed using SPSS Software. A distinctive peak at m/z 28,643-28,731 was found in all 157 KPC-producing isolates, and it was consistently absent in the 143 KPC non-producing group. KPC-producing peak intensities ranged from 77 to 3893. Considering an intensity cutoff value ≥ 120 for the presence of KPC, this methodology presented 98.09% and 97.90% of sensitivity and specificity, respectively.

Occurrence of Serratia marcescens Carrying blaIMP-26 and mcr-9 in Southern China: New Insights in the Evolution of Megaplasmid IMP-26

The spread of multidrug-resistant enterobacteria strains has posed a significant concern in public health, especially when the strain harbors metallo-beta-lactamase (MBL)-encoding and mobilized colistin resistance (mcr) genes as such genetic components potentially mediate multidrug resistance. Here we report an IncHI2/2A plasmid carrying bla_IMP-26 and mcr-9 in multidrug-resistant Serratia marcescens human isolates YL4. Antimicrobial susceptibility testing was performed by the broth microdilution method. According to the results, S. marcescens YL4 was resistant to several antimicrobials, including β-lactams, fluorquinolones, sulfanilamide, glycylcycline, and aminoglycosides, except for amikacin. To investigate the plasmid further, we conducted whole-genome sequencing and sequence analysis. As shown, S. marcescens YL4 possessed a circular chromosome with 5,171,477 bp length and two plasmids, pYL4.1 (321,744 bp) and pYL4.2 (46,771 bp). Importantly, sharing high similarity with plasmids pZHZJ1 and pIMP-26, pYL4.1 has an IncHI2/2A backbone holding a variable region containing bla_IMP-26, mcr-9, and two copies of bla_TEM-1B. After comprehensively comparing relevant plasmids, we proposed an evolutionary pathway originating from ancestor pZHZJ1. Then, via an acquisition of the mcr-9 element and a few recombination events, this plasmid eventually evolved into pYL4.1 and pIMP-26 through two different pathways. In addition, the phage-like plasmid pYL4.2 also carried a bla_TEM-1B gene. Remarkably, this study first identified a multidrug-resistant S. marcescens strain co-harboring bla_IMP-26 and mcr-9 on a megaplasmid pYL4.1 and also included a proposed evolutionary pathway of epidemic megaplasmids carrying bla_IMP-26.

In vitro activity of aztreonam/avibactam against isolates of Enterobacterales collected globally from ATLAS in 2019

OBJECTIVES

Infections caused by drug-resistant Enterobacterales including those producing metallo-β-lactamases (MBLs) are particularly challenging due to limited therapeutic options. The drug combination aztreonam/avibactam (ATM-AVI) is under clinical development for treating serious infections caused by these strains. This study assessed the in vitro activity of ATM-AVI against Enterobacterales isolates collected globally in the ATLAS surveillance programme in 2019.

METHODS

Clinical isolates of Enterobacterales (N=18713) including Citrobacter freundii, Citrobacter koseri, Enterobacter cloacae complex, Escherichia coli, Klebsiella aerogenes, Klebsiella oxytoca, Klebsiella pneumoniae, Proteus mirabilis, and Serratia marcescens collected from 232 sites in 2019 were analysed. Antimicrobial susceptibility testing was performed by reference broth microdilution. A pharmacokinetic/pharmacodynamic based breakpoint of 8 mg/L was considered for ATM-AVI activity.

RESULTS

ATM-AVI demonstrated potent antimicrobial activity against all Enterobacterales, with 99.9% isolates inhibited at MIC ≤8 mg/L (MIC₉₀, 0.25 mg/L). MICs ≤8 mg/L (>99.0%) were noted for ATM-AVI across regions worldwide. Among other antimicrobials, amikacin, colistin, imipenem, meropenem, and tigecycline were also active (susceptibility >85.0%) against Enterobacterales. Activity of ATM-AVI was sustained against multi-drug resistant, extended-spectrum β-lactamases producing, and carbapenem-resistant isolates (susceptibility >99%; MIC₉₀, 0.25-0.5 mg/L). Importantly, potent activity for ATM-AVI (>99.0%; MIC_90, 0.5 mg/L) was noted among MBL-positive isolates and those producing other carbapenemases, such as KPC and OXA-48.

CONCLUSIONS

Our results demonstrated that ATM-AVI was highly active against a recent collection of Enterobacterales isolates, including those producing MBLs either alone or in combination with other carbapenemases. Thus, ATM-AVI represents a potential option for treating infections caused by antibiotic-resistant Enterobacterales including MBL-producing strains.

In vitro Susceptibility to β-Lactam Antibiotics and Viability of Neisseria gonorrhoeae Strains Producing Plasmid-Mediated Broad- and Extended-Spectrum β-Lactamases

Neisseria gonorrhoeae plasmids can mediate high-level antimicrobial resistance. The emergence of clinical isolates producing plasmid β-lactamases that can hydrolyze cephalosporins, the mainstay treatment for gonorrhea, may be a serious threat. In this work, N. gonorrhoeae strains producing plasmid-mediated broad- and extended-spectrum β-lactamases (ESBLs) were obtained in vitro, and their viability and β-lactam antibiotic susceptibility were studied. Artificial pbla_TEM-1 and pbla_TEM-20 plasmids were constructed by site-directed mutagenesis from a pbla_TEM-135 plasmid isolated from a clinical isolate. Minimum inhibitory concentration (MIC) values for a series of β-lactam antibiotics, including benzylpenicillin, ampicillin, cefuroxime, ceftriaxone, cefixime, cefotaxime, cefepime, meropenem, imipenem, and doripenem, were determined. The N. gonorrhoeae strain carrying the pbla_TEM-20 plasmid exhibited a high level of resistance to penicillins and second–fourth-generation cephalosporins (MIC ≥2 mg/L) but not to carbapenems (MIC ≤0.008 mg/L). However, this strain stopped growing after 6 h of culture. The reduction in viability was not associated with loss of the plasmid but can be explained by the presence of the plasmid itself, which requires additional reproduction costs, and to the expression of ESBLs, which can affect the structure of the peptidoglycan layer in the cell membrane. Cell growth was mathematically modeled using the generalized Verhulst equation, and the reduced viability of the plasmid-carrying strains compared to the non-plasmid-carrying strains was confirmed. The cell death kinetics of N. gonorrhoeae strains without the pbla_TEM-20 plasmid in the presence of ceftriaxone can be described by a modified Chick–Watson law. The corresponding kinetics of the N. gonorrhoeae strain carrying the pbla_TEM-20 plasmid reflected several processes: the hydrolysis of ceftriaxone by the TEM-20 β-lactamase and the growth and gradual death of cells. The demonstrated reduction in the viability of N. gonorrhoeae strains carrying the pbla_TEM-20 plasmid probably explains the absence of clinical isolates of ESBL-producing N. gonorrhoeae.

Klebsiella pneumonia and Its Antibiotic Resistance: A Bibliometric Analysis

The rapid development of antibiotic resistance in K. pneumonia has led to a major concern. In order to analyze the hotspots and develop trends in this field through visual the analysis, this study used CiteSpace software to summarize the available data in the literature to provide insights. A total of 9366 research articles were retrieved from the Web of Science Core Collection, and the number of published papers is increasing year by year. The country with the most articles was the USA, followed by China and India. The institution with the highest number of publications was LERU. The author with the highest number of articles was Li. The journal with the highest citation rate was Antimicrobial Agents and Chemotherapy. In addition, based on keyword coword analysis and cited literature prominence analysis by CiteSpace, the current research focus in the field was therapy, CRKP, and resistance genes. This paper provides a new quantitative visualization way for the development of the field in the recent ten years. The results show global trends that researchers can use to determine future directions.

Whole-Genome Characterisation of ESBL-Producing E. coli Isolated from Drinking Water and Dog Faeces from Rural Andean Households in Peru

E. coli that produce extended-spectrum β-lactamases (ESBLs) are major multidrug-resistant bacteria. In Peru, only a few reports have characterised the whole genome of ESBL enterobacteria. We aimed to confirm the identity and antimicrobial resistance (AMR) profile of two ESBL isolates from dog faeces and drinking water of rural Andean households and determine serotype, phylogroup, sequence type (ST)/clonal complex (CC), pathogenicity, virulence genes, ESBL genes, and their plasmids. To confirm the identity and AMR profiles, we used the VITEK®2 system. Whole-genome sequencing (WGS) and bioinformatics analysis were performed subsequently. Both isolates were identified as E. coli, with serotypes -:H46 and O9:H10, phylogroups E and A, and ST/CC 5259/- and 227/10, respectively. The isolates were ESBL-producing, carbapenem-resistant, and not harbouring carbapenemase-encoding genes. Isolate 1143 ST5259 harboured the astA gene, encoding the EAST1 heat-stable toxin. Both genomes carried ESBL genes (blaEC-15, blaCTX-M-8, and blaCTX-M-55). Nine plasmids were detected, namely IncR, IncFIC(FII), IncI, IncFIB(AP001918), Col(pHAD28), IncFII, IncFII(pHN7A8), IncI1, and IncFIB(AP001918). Finding these potentially pathogenic bacteria is worrisome given their sources and highlights the importance of One-Health research efforts in remote Andean communities.

Genome-wide identification of carbapenem-resistant Gram-negative bacterial (CR-GNB) isolates retrieved from hospitalized patients in Bihar, India

Carbapenemase-producing clinical isolates are becoming more common over the world, posing a severe public health danger, particularly in developing nations like India. Carbapenem-resistant Gram-negative bacterial (CR-GNB) infection has become a fast-expanding global threat with limited antibiotic choice and significant mortality. This study aimed to highlight the carbapenem-resistance among clinical isolates of hospital admitted patients in Bihar, India. A cross-sectional study was conducted with 101 clinical isolates of Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa. All GNB isolates were tested for their antimicrobial susceptibility using Kirby-Bauer disc diffusion method. Double disc synergy test / modified Hodge test (DDST/MHT) were used to detect carbapenemase production by these isolates. Subsequently, these isolates were evaluated for carbapenem-resistance genes using whole-genome sequencing method. The overall percentage of carbapenem-resistance among GNB was (17/101) 16.8%. The genomic analysis of antimicrobial-resistance (AMR) demonstrates a significantly high prevalence of blaCTX-M followed by blaSHV, blaTEM, blaOXA, and blaNDM β-lactam or carbapenem resistance genes among clinical isolates of GNB. Co-occurrence of blaNDM with other beta-lactamase-encoding genes was found in 70.6% of carbapenemase-producing isolates. Our study highlights the mechanism of carbapenem-resistance to curb the overwhelming threat posed by the emergence of drug-resistance in India.

Prevalence of High-Risk β-Lactam Resistance Genes in Family Livestock Farms in Danjiangkou Reservoir Basin, Central China

The propagation of antibiotic resistance genes (ARGs) from domestic livestock manure is an unnegligible important environmental problem. There is an increasing need to understand the role of domestic livestock manure in causing antibiotic resistance in the environment to minimize risks to human health. Here, we targeted β-lactam resistance genes (bla genes), primarily discovered in clinical settings, to compare the high-risk ARG profile and their main spreading vectors of 26 family livestock farms in China and analyze the effects of domestic livestock manure on their receiving farmland environments. Results showed that the high-risk bla genes and their spreading carriers were widely prevalent in livestock and poultry manure from family farms. The bla_ampC gene encoding extended-spectrum AmpC β-lactamases, as well as its corresponding spreading carrier (class-1 integron), had the highest occurrence level. The bla gene abundance in family chicken farms was higher than that in family swine and cattle farms, while the bla gene contamination in the feces of laying hens or beef cattle was worse than that in corresponding broiler chickens or dairy cattle. Notably, the application from domestic livestock manure led to substantial emission of bla genes, which significantly increased the abundance of high-risk resistance genes in farmland soil by 12–46 times. This study demonstrated the prevalence and severity of high-risk resistance genes in domestic livestock and poultry manure; meanwhile, the discharge of bla genes also highlighted the need to mitigate the persistence and spread of these elevated high-risk genes in agricultural systems.

Microbial Resistance to Antibiotics and Effective Antibiotherapy

Currently, the efficacy of antibiotics is severely affected by the emergence of the antimicrobial resistance phenomenon, leading to increased morbidity and mortality worldwide. Multidrug-resistant pathogens are found not only in hospital settings, but also in the community, and are considered one of the biggest public health concerns. The main mechanisms by which bacteria develop resistance to antibiotics include changes in the drug target, prevention of entering the cell, elimination through efflux pumps or inactivation of drugs. A better understanding and prediction of resistance patterns of a pathogen will lead to a better selection of active antibiotics for the treatment of multidrug-resistant infections.

High prevalence of blaVEB , blaGES and blaPER genes in beta-lactam resistant clinical isolates of Pseudomonas aeruginosa

The increased prevalence of β-lactamase is one of the main factors in resistance to β-lactams in Pseudomonas aeruginosa. This study aimed to investigate the prevalence of blaVEB , blaPER , and blaGES genes in β-lactam-resistant P. aeruginosa. We collected 100 non-duplicated clinical isolates of P. aeruginosa and identified them by standard tests. Using disk agar diffusion test, we detected the β-lactam-resistant isolates and extracted the DNAs of the isolates by alkaline lysis method. Then, the prevalence of blaVEB , blaPER and blaGES genes were detected by PCR method. The results were assessed by SPSS 21 software and Chi-square test. Out of 100 isolates, 43% were detected as resistant against at least one of the beta-lactams tested. Piperacillin-tazobactam was the most effective antibiotic, while 39% and 37% of the isolates were resistant to aztreonam and meropenem, respectively. A significant relationship was observed between the resistance to tested antibiotics and the presence of blaVEB , blaGES , and blaPER genes. Among 43 isolates that were resistant to at least one of the tested β-lactams, 93.02%, 83.72%, and 81.39% of them carried blaVEB , blaGES , and blaPER genes, respectively. According to this study and due to high prevalence of β-lactam resistance genes, it is better to check the level of antibiotic resistance and resistance genes for better management of patients with infection caused by this bacterium. Also, high prevalence of class A β-lactamases indicates the significant role of these enzymes in emerging resistance to beta-lactams.

Class C β-Lactamases: Molecular Characteristics

Class C β-lactamases or cephalosporinases can be classified into two functional groups (1, 1e) with considerable molecular variability (≤20% sequence identity). These enzymes are mostly encoded by chromosomal and inducible genes and are widespread among bacteria, including Proteobacteria in particular. Molecular identification is based principally on three catalytic motifs (⁶⁴SXSK, ¹⁵⁰YXN, ³¹⁵KTG), but more than 70 conserved amino-acid residues (≥90%) have been identified, many close to these catalytic motifs. Nevertheless, the identification of a tiny, phylogenetically distant cluster (including enzymes from the genera Legionella, Bradyrhizobium, and Parachlamydia) has raised questions about the possible existence of a C2 subclass of β-lactamases, previously identified as serine hydrolases. In a context of the clinical emergence of extended-spectrum AmpC β-lactamases (ESACs), the genetic modifications observed in vivo and in vitro (point mutations, insertions, or deletions) during the evolution of these enzymes have mostly involved the Ω- and H-10/R2-loops, which vary considerably between genera, and, in some cases, the conserved triplet ¹⁵⁰YXN. Furthermore, the conserved deletion of several amino-acid residues in opportunistic pathogenic species of Acinetobacter, such as A. baumannii, A. calcoaceticus, A. pittii and A. nosocomialis (deletion of residues 304-306), and in Hafnia alvei and H. paralvei (deletion of residues 289-290), provides support for the notion of natural ESACs. The emergence of higher levels of resistance to β-lactams, including carbapenems, and to inhibitors such as avibactam is a reality, as the enzymes responsible are subject to complex regulation encompassing several other genes (ampR, ampD, ampG, etc.). Combinations of resistance mechanisms may therefore be at work, including overproduction or change in permeability, with the loss of porins and/or activation of efflux systems.

Prevalence of enteric opportunistic pathogens and extended-spectrum cephalosporin- and carbapenem-resistant coliforms and genes in wastewater from municipal wastewater treatment plants in Croatia

Extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales are a critical global health problem and wastewater treatment plants (WWTPs) can promote their spread into the environment; yet their efficacy is not well characterized. Here, we have used conventional culturing to monitor coliform bacteria and quantitative PCR to monitor 2 ESBL and 5 carbapenemase (CP) genes and 4 enteric opportunistic pathogens (EOPs) in the influent and effluent of 7 Croatian WWTPs in two seasons. In general, levels of total, cefotaxime- and carbapenem-resistant coliforms were significantly reduced but not eliminated by conventional treatment in most WWTPs. Most WWTPs efficiently removed EOPs such as K. pneumoniae and A. baumannii, while E. coli and Enterococcus spp. were reduced but still present in relatively high concentrations in the effluent. ESBL genes (bla_TEM and bla_CTX-M-32) were only slightly reduced or enriched after treatment. CP genes, bla_KPC-3, bla_NDM and bla_OXA-48-like, were sporadically detected, while bla_IMP and bla_VIM were frequently enriched during treatment and correlated with plant size, number or size of hospitals in the catchment area, and COD effluent concentration. Our results suggest that improvements in wastewater treatment technologies are needed to minimize the risk of environmental contamination with top priority EOPs and ARGs and the resulting public health.

The Collateral Effects of COVID-19 Pandemic on the Status of Carbapenemase-Producing Pathogens

The serious challenge of antimicrobial resistance continues to threaten public health and lingers in the era of the coronavirus disease 2019 (COVID-19), declared pandemic by the World Health Organization. While the pandemic has triggered the importance of infection control practices and preventive measures such as physical distancing, hand hygiene, travel reduction and quarantine, the ongoing alarm of antimicrobial resistance seems to accompany the pandemic too. Antimicrobial resistance has been fostered during COVID-19, possibly due to high rate of empirical antibiotic utilization in COVID-19 patients, increased use of biocides, and the disruption of proper healthcare for other conditions. Specifically, carbapenemase-producing Gram-negative bacteria have shown to cause secondary bacterial infections in patients hospitalized for COVID-19. Clinical and microbiological evidence of such infections is accumulating in different parts of the world. With the resilient nature of carbapenemases, their association with mortality, and the limited treatment options available, concerns regarding this group of antibiotic-hydrolyzing enzymes during the pandemic are expected to upsurge. While the additional burden carbapenemases exert on healthcare is worrisome, it remains hidden or abandoned among the various health consequences of the pandemic. The purpose of this minireview is to shed a light on carbapenemase-associated infections during such unprecedented time of COVID-19. A focused insight shall be made into carbapenemases, their implications for COVID-19 patients, and the features and consequences of co-infection, with a review of available evidence from pertinent literature. The importance of increased surveillance for carbapenemase-producers and optimizing their management in relation to the pandemic, shall be addressed as well.

The occurrence of antibiotic-resistant bacteria on the clothes of nursery teachers in daycare centres

AIMS

Childcare facilities act as microenvironments that facilitate and promote the selection, spread, and transmission of antibiotic-resistant microorganisms in the community. We focused on the study of antimicrobial resistance and genetic predispositions for β-lactamase production in bacterial isolates from nursery teachers' clothing.

METHODS AND RESULTS

Antimicrobial resistance of bacterial strains belonging to Enterobacteriaceae, Enterococcus, Staphylococcus spp., Pseudomonas spp. and Bacillus spp. isolated from 80 samples of nursery teachers' clothing was determined. The selected ESβL genes were found in 30 (44.1%) of 68 strains examined. The CTX-M type ESβL determinants were detected in 15.4%, 71.5%, and 42.5% of the Enterobacteriaceae, Pseudomonas, and Bacillus isolates, respectively. The OXA-type coding genes were detected only in strains of the genera Pseudomonas (57.1%) and Bacillus (48.6%). Thus, most B. cereus strains were sensitive to the recommended antibiotics used to treat infections caused by these bacteria. Methicillin resistance was phenotypically confirmed in 27 (14.6%) of 185 staphylococcal isolates. Four isolates (2.2%) were identified as MRSA. Vancomycin resistance was not observed in any of the staphylococcal and enterococci strains.

CONCLUSIONS

This study has shown that potential pathogens have been isolated from the clothing of nursery teachers, posing a risk of transmission to children. These clothes should be maintained and properly laundered to avoid cross-contamination and the spread of multidrug-resistant (MDR) bacteria in childcare centres.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides insight into the route of transmission of MDR microorganisms through the clothing of nursery teachers, to which greater importance should be given in the future. Proper procedures for the cleaning and use of clothing in daycare centres should be clarified and standardised.

Phylogenomics, Epigenomics, Virulome, and Mobilome of Gram-negative Bacteria Co-resistant to Carbapenems and Polymyxins: A One-Health Systematic Review and Meta-analyses

Gram-negative bacteria (GNB) continue to develop resistance against important antibiotics including last-resort ones such as carbapenems and polymyxins. An analysis of GNB with co-resistance to carbapenems and polymyxins from a One Health perspective is presented. Data of species name, country, source of isolation, resistance genes (ARGs), plasmid type, clones, and mobile genetic elements (MGEs) were deduced from 129 articles from January 2016 to March 2021. Available genomes and plasmids were obtained from PATRIC and NCBI. Resistomes and methylomes were analysed using BAcWGSTdb and REBASE whilst Kaptive was used to predict capsule typing. Plasmids and other MEGs were identified using MGE Finder and ResFinder. Phylogenetic analyses were done using RAxML and annotated with MEGA 7. A total of 877 isolates, 32 genomes and 44 plasmid sequences were analysed. Most of these isolates were reported in Asian countries and were isolated from clinical, animal, and environmental sources. Colistin resistance was mostly mediated by mgrB inactivation (37%; n = 322) and mcr-1 (36%; n = 312), while OXA-48/181 was the most reported carbapenemase. IncX and IncI were the most common plasmids hosting carbapenemases and mcr genes. The isolates were co-resistant to other antibiotics, with floR (chloramphenicol) and fosA3 (fosfomycin) being common; E. coli ST156 and K. pneumoniae ST258 strains were common globally. Virulence genes and capsular KL-types were also detected. Type I, II, III and IV restriction modification systems were detected, comprising various MTases and restriction enzymes. The escalation of highly resistant isolates drains the economy due to untreatable bacterial infections, which leads to increasing global mortality rates and healthcare costs. This article is protected by copyright. All rights reserved.

Dissemination Routes of Carbapenem and Pan-Aminoglycoside Resistance Mechanisms in Hospital and Urban Wastewater Canalizations of Ghana

Wastewater has a major role in antimicrobial resistance (AMR) dynamics and public health. The impact on AMR of wastewater flux at the community-hospital interface in low- and middle-income countries (LMICs) is poorly understood. Therefore, the present study analyzed the epidemiological scenario of resistance genes, mobile genetic elements (MGEs), and bacterial populations in wastewater around the Tamale metropolitan area (Ghana). Wastewater samples were collected from the drainage and canalizations before and after three hospitals and one urban waste treatment plant (UWTP). From all carbapenem/pan-aminoglycoside-resistant bacteria, 36 isolates were selected to determine bacterial species and phenotypical resistance profiles. Nanopore sequencing was used to screen resistance genes and plasmids, whereas, sequence types, resistome and plasmidome contents, pan-genome structures, and resistance gene variants were analyzed with Illumina sequencing. The combination of these sequencing data allowed for the resolution of the resistance gene-carrying platforms. Hospitals and the UWTP collected genetic and bacterial elements from community wastewater and amplified successful resistance gene-bacterium associations, which reached the community canalizations. Uncommon carbapenemase/β-lactamase gene variants, like bla_DIM-1, and novel variants, including bla_VIM-71, bla_CARB-53, and bla_CMY-172, were identified and seem to spread via clonal expansion of environmental Pseudomonas spp. However, bla_NDM-1, bla_CTX-M-15, and armA genes, among others, were associated with MGEs that allowed for their dissemination between environmental and clinical bacterial hosts. In conclusion, untreated hospital wastewater in Ghana is a hot spot for the emergence and spread of genes and gene-plasmid-bacterium associations that accelerate AMR, including to last-resort antibiotics. Urgent actions must be taken in wastewater management in LMICs in order to delay AMR expansion.

IMPORTANCE Antimicrobial resistance (AMR) is one the major threats to public health today, especially resistance to last-resort compounds for the treatment of critical infections, such as carbapenems and aminoglycosides. Innumerable works have focused on the clinical ambit of AMR, but studies addressing the impact of wastewater cycles on the emergence and dissemination of resistant bacteria are still limited. The lack of knowledge is even greater when referring to low- and middle-income countries, where there is an absence of accurate sanitary systems. Furthermore, the combination of short- and long-read sequencing has surpassed former technical limitations, allowing the complete characterization of resistance genes, mobile genetic platforms, plasmids, and bacteria. The present study deciphered the multiple elements and routes involved in AMR dynamics in wastewater canalizations and, therefore, in the local population of Tamale, providing the basis to adopt accurate control measures to preserve and promote public health.

Diversity of bacterial pathogens and their antimicrobial resistance profile among commensal rodents in Qatar

Rodents are sources of many zoonotic pathogens that are of public health concern. This study investigated bacterial pathogens and assessed their antimicrobial resistance (AMR) patterns in commensal rodents in Qatar. A total of 148 rodents were captured between August 2019 and February 2020, and blood, ectoparasites, and visceral samples were collected. Gram-negative bacteria were isolated from the intestines, and blood plasma samples were used to detect antibodies against Brucella spp., Chlamydophila abortus, and Coxiella burnetii. PCR assays were performed to detect C. burnetii, Leptospira spp., Rickettsia spp., and Yersinia pestis in rodent tissues and ectoparasite samples. Antimicrobial resistance by the isolated intestinal bacteria was performed using an automated VITEK analyzer. A total of 13 bacterial species were isolated from the intestine samples, namely Acinetobacter baumannii, Aeromonas salmonicida, Citrobacter freundii, Citrobacter koseri, Enterobacter aerogenes, Enterobacter cloacae, Escherichia coli, Hafnia alvei, Klebsiella pneumoniae, Providencia stuartii, Proteus mirabilis, Pseudomonas aeruginosa, and Salmonella enterica. The majority of them were E. coli (54.63%), followed by P. mirabilis (17.59%) and K. pneumoniae (8.33%). Most of the pathogens were isolated from rodents obtained from livestock farms (50.46%), followed by agricultural farms (26.61%) and other sources (22.94%). No antibodies (0/148) were detected against Brucella spp., C. abortus, or C. burnetii. In addition, 31.58% (6/19) of the flea pools and one (1/1) mite pool was positive for Rickettsia spp., and no sample was positive for C. burnetii, Leptospira spp., and Y. pestis by PCR. A total of 43 (38%) bacterial isolates were identified as multidrug resistant (MDR), whereas A. salmonicida (n = 1) did not show resistance to any tested antimicrobials. Over 50% of bacterial MDR isolates were resistant to ampicillin, cefalotin, doxycycline, nitrofurantoin, and tetracycline. The presence of MDR pathogens was not correlated with rodent species or the location of rodent trapping. Seven (11.86%) E. coli and 2 (22.2%) K. pneumoniae were extended-spectrum beta-lactamases (ESBL) producers. These findings suggest that rodents can be a source of opportunistic bacteria for human and animal transmission in Qatar. Further studies are needed for the molecular characterization of the identified bacteria in this study.

Surveillance of carbapenem-resistant Klebsiella pneumoniae in a paediatric hospital in China revealed the dynamics of carbapenemase and the prevalence of ST2735 K. pneumoniae

Background. Carbapenem-resistant Klebsiella pneumoniae (CRKP) is increasingly isolated in paediatric wards, posing a severe threat to these vulnerable populations. This study investigated the clinical features, determinants of carbapenem resistance and clonal relatedness among CRKP in our hospital.

Hypothesis. The prevalence of carbapenem-resistant K. pneumoniae in paediatric patients differs from the strains isolated from adult patients in carbapenemase and predominant clones.

Aim. To investigate the pattern of carbapenemase and the clonal relationships between carbapenem-resistant Klebsiella pneumoniae in a paediatric hospital in Jiangxi Province.

Methodology. Forty-five CRKP isolates were consecutively collected from October 2016 to October 2020. Medical records were reviewed to analyse clinical features. Detection of carbapenemase genes was used to determine CRKP resistance mechanisms and clonal relatedness among CRKP was identified through multi-locus sequence typing (MLST).

Results. Forty-three (95.6 %) patients developed CRKP infection, and two (4.4 %) were colonized by CRKP in the urinary tract. The overall mortality rate was 13.3 %. In total, 42 (93.3 %) strains were positive for carbapenemase genes, and bla NDM (62.2 %) was the predominant gene. The MLST identified 24 different sequence types (STs) of CRKP, in which ST11 (n=8, 17.8 %) and ST2735 (n=8, 17.8 %) were the most common STs.

Conclusion. The pattern of CRKP in paediatric patients reflects evolving changes. The ST2735 K. pneumoniae may present as a dangerous CRKP clone circulating in paediatric patients.

[Regional dissemination of carbapenem-resistant Enterobacteriaceae accompanying with enhanced resistance in Northern Osaka, Japan]

With the rapid spread of multidrug-resistant bacteria, carbapenem-resistant Enterobacteriaceae (CRE) has been reported worldwide as a major concern because of limited treatment options. Carbapenem resistance is mainly due to carbapenem-ase, a carbapenem-degrading enzyme, which is mainly encoded on a plasmid to spread across bacterial species. However, there have been only small-scale attempts to determine the similarities or accommodations of the plasmids disseminating regionwide. We analysed the 230 CRE isolates carrying bla_IMP from 43 medical facilities in the northern Osaka area focusing on the plasmids, the main carriers of the drug resistance genes. Combination of whole genome sequencing and Southern blotting revealed the predominant dissemination of bla_IMP-6 by the pKPI-6 plasmid among genetically distinct isolates, as well as the emergences of derivatives that acquired various advantages. We iden-tified heteroresistance likely causing stealth transmissions, which was generated by the transcriptional regu-lation of bla_IMP-6, stabilization of bla_IMP-6 through chromosomal integration, enhanced carbapenem resistance through plasmid multimerization, or broadened antimicrobial resistance due to a single point mutation in bla_IMP-6. In this article, I dis-cussed the mechanisms of regional spread of CRE and enhancement of carbapenem resistance providing the insights to prevent their disseminations.

Worldwide distribution and environmental origin of the Adelaide imipenemase (AIM-1), a potent carbapenemase in Pseudomonas aeruginosa

Carbapenems are potent broad-spectrum β-lactam antibiotics reserved for the treatment of serious infections caused by multidrug-resistant bacteria such as Pseudomonas aeruginosa. The surge in P. aeruginosa resistant to carbapenems is an urgent threat, as very few treatment options remain. Resistance to carbapenems is predominantly due to the presence of carbapenemase enzymes. The assessment of 147 P. aeruginosa isolates revealed that 32 isolates were carbapenem non-wild-type. These isolates were screened for carbapenem resistance genes using PCR. One isolate from wastewater contained the Adelaide imipenemase gene (bla _AIM-1) and was compared phenotypically with a highly carbapenem-resistant clinical isolate containing the bla _AIM-1 gene. A further investigation of wastewater samples from various local healthcare and non-healthcare sources as well as river water, using probe-based qPCR, revealed the presence of the bla _AIM-1 gene in all the samples analysed. The widespread occurrence of bla _AIM-1 throughout Adelaide hinted at the possibility of more generally extensive spread of this gene than originally thought. A blast search revealed the presence of the bla _AIM-1 gene in Asia, North America and Europe. To elucidate the identity of the organism(s) carrying the bla _AIM-1 gene, shotgun metagenomic sequencing was conducted on three wastewater samples from different locations. Comparison of these nucleotide sequences with a whole-genome sequence of a P. aeruginosa isolate revealed that, unlike the genetic environment and arrangement in P. aeruginosa, the bla _AIM-1 gene was not carried as part of any mobile genetic elements. A phylogenetic tree constructed with the deduced amino acid sequences of AIM-1 suggested that the potential origin of the bla _AIM-1 gene in P. aeruginosa might be the non-pathogenic environmental organism, Pseudoxanthomonas mexicana.

Vegetables and Fruit as a Reservoir of β-Lactam and Colistin-Resistant Gram-Negative Bacteria: A Review

Antibacterial resistance is one of the 2019 World Health Organization’s top ten threats to public health worldwide. Hence, the emergence of β-lactam and colistin resistance among Gram-negative bacteria has become a serious concern. The reservoirs for such bacteria are increasing not only in hospital settings but in several other sources, including vegetables and fruit. In recent years, fresh produce gained important attention due to its consumption in healthy diets combined with a low energy density. However, since fresh produce is often consumed raw, it may also be a source of foodborne disease and a reservoir for antibiotic resistant Gram-negative bacteria including those producing extended-spectrum β-lactamase, cephalosporinase and carbapenemase enzymes, as well as those harboring the plasmid-mediated colistin resistance (mcr) gene. This review aims to provide an overview of the currently available scientific literature on the presence of extended-spectrum β-lactamases, cephalosporinase, carbapenemase and mcr genes in Gram-negative bacteria in vegetables and fruit with a focus on the possible contamination pathways in fresh produce.

Antibacterial effect of cerium oxide nanoparticle against Pseudomonas aeruginosa

BACKGROUND

Antibiotics have been widely used for the treatment of bacterial infections for decades. However, the rapid emergence of antibiotic-resistant bacteria has created many problems with a heavy burden for the medical community. Therefore, the use of nanoparticles as an alternative for antibacterial activity has been explored. In this context, metal nanoparticles have demonstrated broad-spectrum antimicrobial activity. This study investigated the antimicrobial activity of naked cerium oxide nanoparticles dispersed in aqueous solution (CNPs) and surface-stabilized using Pseudomonas aeruginosa as a bacterial model.

METHODS

Gelatin-polycaprolactone nanofibers containing CNPs (Scaffold@CNPs) were synthesized, and their effect on P. aeruginosa was investigated. The minimum inhibitory and bactericidal concentrations of the nanoparticls were determined in an ATCC reference strain and a clinical isolate strain. To determine whether the exposure to the nanocomposites might change the expression of antibiotic resistance, the expression of the genes shv, kpc, and imp was also investigated. Moreover, the cytotoxicity of the CNPs was assessed on fibroblast using flow cytometry.

RESULTS

Minimum bactericidal concentrations for the ATCC and the clinical isolate of 50 µg/mL and 200 µg/mL were measured, respectively, when the CNPs were used. In the case of the Scaffold@CNPs, the bactericidal effect was 50 µg/mL and 100 µg/mL for the ATCC and clinical isolate, respectively. Interestingly, the exposure to the Scaffold@CNPs significantly decreased the expression of the genes shv, kpc, and imp.

CONCLUSIONS

A concentration of CNPs and scaffold@CNPs higher than 50 μg/mL can be used to inhibit the growth of P. aeruginosa. The fact that the scaffold@CNPs significantly reduced the expression of resistance genes, it has the potential to be used for medical applications such as wound dressings.

Advances in novel antibiotics to treat multidrug-resistant gram-negative bacterial infections

Antimicrobial resistance is a growing threat to public health and an increasingly common problem for acute care physicians to confront. Several novel antibiotics have been approved in the past decade to combat these infections; however, physicians may be unfamiliar with how to appropriately utilize them. The purpose of this review is to evaluate novel antibiotics active against resistant gram-negative bacteria and highlight clinical information regarding their use in the acute care setting. This review focuses on novel antibiotics useful in the treatment of infections caused by resistant gram-negative organisms that may be seen in the acute care setting. These novel antibiotics include ceftolozane/tazobactam, ceftazidime/avibactam, meropenem/vaborbactam, imipenem/cilistatin/relebactam, cefiderocol, plazomicin, eravacycline, and omadacycline. Acute care physicians should be familiar with these novel antibiotics so they can utilize them appropriately.

Prevalence of β-lactamase-encoding genes and molecular typing of Acinetobacter baumannii isolates carrying carbapenemase OXA-24 in children

Background

β-Lactam antibiotics have been broadly used for the treatment of Acinetobacter baumannii infections, resulting in development of β-lactam inactivating β-lactamases. Here, we described antibiotic resistance rate, prevalence of β-lactamase-encoding genes, and clonal relationships of A. baumannii strains isolated from children referred to Children’s Medical Center in Tehran, Iran, during 2019–2020.

Methods

A total of 60 non-replicate A. baumannii isolates were recovered from clinical specimens of pediatric patients. Antibiotic susceptibility testing was done by the disc diffusion method. Colistin susceptibility of isolates was performed by the broth microdilution method. β-lactamase-encoding genes were characterized by PCR. The presence of ISAba1 element upstream of the several oxacillinase genes was also checked. Genetic relatedness of isolates was determined by using random amplification of polymorphic DNA (RAPD) typing.

Results

The antimicrobial susceptibility tests showed that 83.3% of A. baumannii isolates were MDR, and 40% XDR. Both MDR and XDR A. baumannii isolates were susceptible to colistin. The frequency of bla_OXA-51-like, bla_OXA-23-like, bla_TEM, bla_OXA-24-like, bla_PER, bla_SHV, bla_CTX-M, bla_OXA-58-like, and bla_IMP was 100, 93.33, 60, 36.67, 28.33, 8.33, 5, 3.33, and 1.67%, respectively. Coexistence of ISAba1/bla_OXA-23-like and ISAba1/bla_OXA-51-like was observed in 65% and 85% of isolates, respectively. RAPD analysis revealed 4 common types and 2 single types of A. baumannii isolates.

Conclusions

The multiple clones harboring bla_OXA-23-like, ISAba1-bla_OXA-51-like, and ISAba1-bla_OXA-23-like were responsible for the spread of A. baumannii isolates in our clinical wards. Dissemination of the well-established clones is worrisome and would become therapeutic challenges due to the possible transferring genetic elements associated with resistance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-021-00480-5.

Detection of Multidrug-Resistant Enterobacterales-From ESBLs to Carbapenemases

Multidrug-resistant Enterobacterales (MDRE) are an emerging threat to global health, leading to rising health care costs, morbidity and mortality. Multidrug-resistance is commonly caused by different β-lactamases (e.g., ESBLs and carbapenemases), sometimes in combination with other resistance mechanisms (e.g., porin loss, efflux). The continuous spread of MDRE among patients in hospital settings and the healthy population require adjustments in healthcare management and routine diagnostics. Rapid and reliable detection of MDRE infections as well as gastrointestinal colonization is key to guide therapy and infection control measures. However, proper implementation of these strategies requires diagnostic methods with short time-to-result, high sensitivity and specificity. Therefore, research on new techniques and improvement of already established protocols is inevitable. In this review, current methods for detection of MDRE are summarized with focus on culture based and molecular techniques, which are useful for the clinical microbiology laboratory.

Molecular Detection of Carbapenemases and Extended-Spectrum β-Lactamases-Encoding Genes in Clinical Isolates of Pseudomonas aeruginosa in Iran

Background: Pseudomonas aeruginosa is a unique Gram-negative opportunistic pathogen that is the leading cause of nosocomial infections. Objectives: This study aimed to investigate the prevalence of the main carbapenemase and extended-spectrum β-lactamases encoding genes in P. aeruginosa clinical isolates. Methods: In the present study, we collected 85 P. aeruginosa clinical isolates from different wards of three military hospitals in Tehran, Iran. We used disk diffusion and agar dilution methods to determine resistance to 12 different antibiotics in these isolates. Also, we assessed the blaIMP, blaVIM, blaSHV, blaTEM, and blaCTX genes by polymerase chain reaction methods among all isolates. Results: Our results revealed that all isolates were resistant to two antibiotics, and 76 (89.4%) of isolates were multidrug-resistant. We observed maximum and minimum resistance rates against ticarcillin (n = 77; 90.5%) and colistin (n = 7; 8.2%), respectively. The blaVIM, blaIPM, blaTEM, blaSHV, and blaCTX genes were harbored by 44 (51.8%), 20 (23.5%), 41 (48.2%), 24 (28.2%), and 16 (18.8%) isolates, respectively. Conclusions: The resistance rate among P. aeruginosa strains is significantly increasing that causes nosocomial infections due to different mechanisms, including the high frequency of metallo-β-lactamases and extended-spectrum β-lactamases genes.

Virulence characterization and clonal analysis of uropathogenic Escherichia coli metallo-beta-lactamase-producing isolates

Background

Uropathogenic Escherichia coli (UPEC) is a major cause of urinary tract infection (UTI); however, treatment of UTI has been challenging due to increased antimicrobial resistance (AMR). One of the most important types of AMR is carbapenem resistance (CR). CR bacteria are known as an important threat to global public health today. Class B metallo-beta-lactamases (MBLs) are one of the major factors for resistance against carbapenems. We aimed to investigate the characteristics of UPEC isolates producing MBL.

Methods

A cross-sectional study was conducted from October 2018 to December 2019 in Ahvaz; Iran. UPEC isolates were identified by biochemical and molecular methods. Metallo-beta-lactamase-producing isolates were detected using modified carbapenem inactivation method (mCIM) and EDTA-CIM (eCIM) tests. MBL genes, phylogenetic group, and virulence genes profile of carbapenem resistant isolates were determined. Conjugation assay and plasmid profiling were conducted to evaluate the ability of transferring of CR to other E. coli isolates. Clonal similarity of isolates were assessed using Enterobacterial intergenic repetitive element sequence (ERIC)-PCR.

Results

Among 406 UPEC isolates, 12 (2.95%) carbapenem-resistant were detected of which 11 were phenotypically MBL-producing strains. Four isolates were resistant to all investigated antimicrobial agents and were considered possible pandrug-resistant (PDR). bla_NDM, bla_OXA-48, bla_IMP-1, and bla_IMP-2 genes were found in 9, 5, 1, and 1 isolates, respectively. Among 30 virulence genes investigated, the traT, fyuA followed by fimH, and iutA with the frequency of 8 (66.7%), 8 (66.7%), 7 (58.3%), and 7 (58.3%) were the most identified genes, respectively. Siderophore production was the main virulence trait among carbapenem-resistant UPEC isolates. Except for two, all other isolates showed weak to moderate virulence index. In all recovered isolates, CR was readily transmitted via plasmids to other isolates during conjugation experiments.

Conclusion

MBL and carbapenemase genes, especially bla_NDM and bla_OXA-48 are spreading rapidly among bacteria, which can be a threat to global public health. Therefore monitoring the emergence and dissemination of new AMR is necessary to continuously refine guidelines for empiric antimicrobial therapy. Understanding the mechanisms of resistance and virulence in this group of bacteria can play an effective role in providing new therapeutic methods.