Environmental Prevalence of Carbapenem Resistance Enterobacteriaceae (CRE) in a Tropical Ecosystem in India: Human Health Perspectives and Future Directives

Carbapenemase-producing bacteria recovered from Nairobi River, Kenya surface water and from nearby anthropogenic and zoonotic sources

Carbapenem-resistant bacteria (CRB) present a significant global public health concern. Sub-Saharan Africa has borne a heavy burden of CRB with a reported prevalence of up to 60% in some patient populations. es in Africa focus on clinical CRB isolates, with limited data on their spread in the natural environment. Therefore, the purpose of this study was to report the recovery of CRB from Nairobi River surface waters and nearby anthropogenic and zoonotic sources in Nairobi County, Kenya. A total of 336 CRB were recovered from 336 (250 mL) samples, with 230 of the samples (68.5%) producing one or more CRB isolates. CRB were recovered most commonly from untreated sewage influent (100% of 36 samples; 79 total isolates), treated effluent (93% of 118 samples; 116 total isolates), Nairobi River surface waters upstream (100% of 36 samples; 57 total isolates), downstream (100% of 36 samples; 45 total isolates), and way downstream from the wastewater treatment plant (73% of 11 samples; 19 total isolates), slaughterhouse effluent discharges 1.5%, (5/336), animal contact areas 0.9%, (3/336), a manhole sewer from the affluent neighborhood of Karen at 2.7%, (9/336) respectively. The CRB included Escherichia coli (158, 47%), Klebsiella pneumoniae (74, 22%), and Enterobacter spp (43, 13%). Aeromonas spp (29, 9%) Acinetobacter baumannii (12, 3.6%), Citrobacter freundii (7, 2.1%), Pseudomonas aeruginosa (5, 1.5%) and other species (8, 2.4%). CRB genotypes included blaNDM (246, 73.2%), blaKPC (40, 12%), blaVIM (51, 15.2%), blaOXA-48-like (65, 19.3%), blaIMP (15, 4.5%), and blaGES (7, 2.1%). Sixty-nine of the CRB isolates (20.5%) harbored multiple carbapenemase-encoding genes. Our results indicate that clinically important CRB are commonly present in Nairobi River surface water and from nearby wastewater and livestock sources. These pose an important public health threat that requires urgent intervention strategies and additional investigation.

Application of CRISPR-Cas system in the diagnosis and therapy of ESKAPE infections

Antimicrobial-resistant ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. ESKAPE pathogens are the most common opportunistic pathogens in nosocomial infections, and a considerable number of their clinical isolates are not susceptible to conventional antimicrobial therapy. Therefore, innovative therapeutic strategies that can effectively deal with ESKAPE pathogens will bring huge social and economic benefits and ease the suffering of tens of thousands of patients. Among these strategies, CRISPR (clustered regularly interspaced short palindromic repeats) system has received extra attention due to its high specificity. Regrettably, there is currently no direct CRISPR-system-based anti-infective treatment. This paper reviews the applications of CRISPR-Cas system in the study of ESKAPE pathogens, aiming to provide directions for the research of ideal new drugs and provide a reference for solving a series of problems caused by multidrug-resistant bacteria (MDR) in the post-antibiotic era. However, most research is still far from clinical application.

Active surveillance for carbapenem resistant enterobacteriaceae (CRE) using stool cultures as a method to decrease CRE infections in the pediatric intensive care unit (PICU)

BACKGROUND

The incidence of Carbapenem Resistant Enterobacteriaceae (CRE) infections is increasing worldwide. Due to dearth of alternative antibiotics, prevention of infection transmission is a part of CRE infection management strategy. Early detection of CRE by active surveillance coupled with contact isolation is much more appropriate compared to contact isolation upon receipt of routine cultures dictated by the patient's clinical condition.

OBJECTIVES

To determine whether active CRE surveillance will decrease CRE infection rates in the Pediatric Intensive Care Unit (PICU).

METHODS

Retrospective observational study done in the 10-bed PICU of a tertiary care teaching children's hospital from July 2013 to June 2015. Rectal swabs for CRE were sent from all PICU patients except stable post-operative patients. Contact isolation precautions were followed for rectal swab positive patients. CRE colonization and infection rates were calculated and compared.

RESULTS

Total of 1262 rectal swabs were sent from 1022 patients. CRE colonization rate was 19.5%. Post intervention, ICU acquired CRE colonization decreased by 36% and ICU acquired CRE infection rates decreased by 100%, both showed significant decrease (p ​< ​0.0001).

CONCLUSION

Active CRE surveillance and institution of contact isolation in appropriate situations is helpful in decreasing CRE colonization and infection rates in the PICU.

The crisis of carbapenemase-mediated carbapenem resistance across the human-animal-environmental interface in India

Carbapenems are the decision-making antimicrobials used to combat severe Gram-negative bacterial infections in humans. Carbapenem resistance poses a potential public health emergency, especially in developing countries such as India, accounting for high morbidity, mortality, and healthcare cost. Emergence and transmission of plasmid-mediated "big five" carbapenemase genes including KPC, NDM, IMP, VIM and OXA-48-type among Gram-negative bacteria is spiralling the issue. Carbapenemase-producing carbapenem-resistant organisms (CP-CRO) cause multi- or pan-drug resistance by co-harboring several antibiotic resistance determinants. In addition of human origin, animals and even environmental sites are also the reservoir of CROs. Spillage in food-chains compromises food safety and security and increases the chance of cross-border transmission of these superbugs. Metallo-β-lactamases, mainly NDM-1 producing CROs, are commonly shared between human, animal and environmental interfaces worldwide, including in India. Antimicrobial resistance (AMR) surveillance using the One Health approach has been implemented in Europe, the United-Kingdom and the United-States to mitigate the crisis. This concept is still not implemented in most developing countries, including India, where the burden of antibiotic-resistant bacteria is high. Lack of AMR surveillance in animal and environmental sectors underestimates the cumulative burden of carbapenem resistance resulting in the silent spread of these superbugs. In-depth indiscriminate AMR surveillance focusing on carbapenem resistance is urgently required to develop and deploy effective national policies for preserving the efficacy of carbapenems as last-resort antibiotics in India. Tracking and mapping of international high-risk clones are pivotal for containing the global spread of CP-CRO.

Comparison of Lateral Flow Immunochromatography and Phenotypic Assays to PCR for the Detection of Carbapenemase-Producing Gram-Negative Bacteria, a Multicenter Experience in Mexico

The identification of carbapenemase-producing Enterobacterales and Pseudomonas aeruginosa is important for treating and controlling hospital infections. The recommended methods for their identification require a long waiting time, technical training, and expertise. Lateral flow immunoassays such as NG-Test CARBA 5^® overcome these needs. We analyzed 84 clinical isolates of carbapenem-resistant Enterobacterales and P. aeruginosa from four different hospitals in a two-year period. Antimicrobial resistance patterns were confirmed with the broth dilution method. Evaluation of KPC, VIM, NDM, IMP, and OXA-48-like enzymes was performed and compared to NG-Test CARBA 5 and phenotypic assays. Enterobacterales represented 69% of isolates and P. aeruginosa represented 31%. Carbapenemase-producing strains were 51 (88%) of Enterobacterales and 23 (88.4%) of P. aeruginosa; 20 (34%) and 23 (88%) were Class B ß-lactamases, respectively. The NG-Test CARBA 5^® assay for Enterobacterales showed high sensitivity (98%), specificity (100%), and PPV (100%); however, it did not for P. aeruginosa. The Kappa concordance coefficient was 0.92 for Enterobacterales and 0.52 for P. aeruginosa. NG-Test CARBA 5^® is a fast and easy-to-use assay. In Enterobacterales, we found excellent agreement in our comparison with molecular tests. Despite the low agreement in P. aeruginosa, we suggest that this test could be used as a complementary tool.

A systematic scoping review of faropenem and other oral penems: treatment of Enterobacterales infections, development of resistance and cross-resistance to carbapenems

Background

Antimicrobial resistance is an urgent global healthcare concern. Beyond carbapenems as broad-spectrum, often 'last resort' antibiotics, oral penem antibiotics currently are approved only in Japan and India, used for the treatment of indications including urinary tract infections (UTIs). Exploring oral penem use to better understand the impact of antibiotic resistance on public health would help inform the management of infectious diseases, including UTIs.

Scoping Review Methodology

This scoping review investigated the impact of faropenem and other oral penems on Enterobacterales infection treatment and evaluated evidence for faropenem resistance and cross-resistance to carbapenems. PubMed, Embase, J-STAGE and CiNii were searched for relevant English- or Japanese-language articles published between 1 January 1996 and 6 August 2021.

Key Findings

From 705 unique publications, 29 eligible articles were included (16 in vitro studies; 10 clinical trials; 2 in vitro and in vivo studies; and 1 retrospective medical chart review). Limited evidence described faropenem to treat infectious disease; only four randomized clinical trials were identified. Faropenem dosing regimens varied broadly within and between indications. One study indicated potential dependence of penem efficacy on underlying antibiotic resistance mechanisms, while several studies reported UTI persistence or recurrence after faropenem treatment. In vitro MIC data suggested some potential bacterial resistance to faropenem, while limited clinical data showed resistance emergence after faropenem treatment. Preliminary in vitro evidence suggested faropenem resistance might foster cross-resistance to carbapenems. Overall, very limited clinical evidence describes faropenem for treating infectious diseases. Preclinical and clinical research investment and dedicated community surveillance monitoring is crucial for understanding faropenem treatment patterns, resistance and potential cross-resistance to carbapenems.

An Escherichia coli isolate from hospital sewage carries blaNDM-1 and blaoxa-10

Carbapenems, as the "last line of defense" against Gram-negative bacteria, are increasingly being challenged by drug-resistant bacteria, especially Enterobacteriaceae. In this study, a carbapenem-resistant Gram-negative bacterium, named AH001, was isolated from hospital sewage, and a modified Hodge test confirmed that this bacterium can produce carbapenemase. Further analysis revealed that this bacterium exhibits multidrug resistance against an additional seven antibiotics. Whole-genome sequencing and analysis showed that AH001 could not be classified by existing MLST, and its serotype could not be distinguished among O9, O89 or O168 according to O antigen prediction. More attention should be given to the role of environmental sources of Escherichia coli in the development and transfer of drug resistance in the hospital environment.

Carbapenem-Resistant Klebsiella pneumoniae Associated with COVID-19

Infections with carbapenem-resistant Enterobacteriaceae are emerging as an important challenge in healthcare settings. Currently, carbapenem-resistant Klebsiella pneumoniae (CRKP) are the species of CRE most commonly encountered in hospitals. CRKP is resistant to almost all available antimicrobial agents, and infections with CRKP have been associated with high rates of morbidity and mortality, particularly among persons with prolonged hospitalization exposed to invasive devices. We report nine patients hospitalized in an intensive care unit (ICU) with severe coronavirus disease 2019 (COVID-19) who developed invasive infections due to carbapenemase-producing Klebsiella pneumoniae (CP-Kp), KPC and OXA-48, strains that have not been previously identified in our hospital. Despite ceftazidime/avibactam therapy, five patients died. Coinfections can contribute to a poor prognosis for patients with COVID-19, especially for high-risk populations such as elderly patients. Therefore, it is crucial to establish a rigorous program of antibiotic administration in intensive care units.

Detection of a New Resistance-Mediating Plasmid Chimera in a blaOXA-48-Positive Klebsiella pneumoniae Strain at a German University Hospital

Mobile genetic elements, such as plasmids, facilitate the spread of antibiotic resistance genes in Enterobacterales. In line with this, we investigated the plasmid-resistome of seven bla_OXA-48 gene-carrying Klebsiella pneumoniae isolates, which were isolated between 2013 and 2014 at the University Medical Center in Göttingen, Germany. All isolates were subjected to complete genome sequencing including the reconstruction of entire plasmid sequences. In addition, phenotypic resistance testing was conducted. The seven isolates comprised both disease-associated isolates and colonizers isolated from five patients. They fell into two clusters of three sequence type (ST)101 and two ST11 isolates, respectively; and ST15 and ST23 singletons. The seven isolates harbored various plasmids of the incompatibility (Inc) groups IncF, IncL/M, IncN, IncR, and a novel plasmid chimera. All bla_OXA-48 genes were encoded on the IncL/M plasmids. Of note, distinct phenotypical resistance patterns associated with different sets of resistance genes encoded by IncL/M and IncR plasmids were observed among isolates of the ST101 cluster in spite of high phylogenetic relatedness of the bacterial chromosomes, suggesting nosocomial transmission. This highlights the importance of plasmid uptake and plasmid recombination events for the fast generation of resistance variability after clonal transmission. In conclusion, this study contributes a piece in the puzzle of molecular epidemiology of resistance gene-carrying plasmids in K. pneumoniae in Germany.

Structure of Bacterial Community with Resistance to Antibiotics in Aquatic Environments. A Systematic Review

Aquatic environments have been affected by the increase in bacterial resistant to antibiotics. The aim of this review is to describe the studies carried out in relation to the bacterial population structure and antibiotic resistance genes in natural and artificial water systems. We performed a systematic review based on the PRISMA guideline (preferred reporting items for systematic reviews and meta-analyzes). Articles were collected from scientific databases between January 2010 and December 2020. Sixty-eight papers meeting the inclusion criteria, i.e., "reporting the water bacterial community composition", "resistance to antibiotics", and "antibiotic resistance genes (ARG)", were evaluated according to pre-defined validity criteria. The results indicate that the predominant phyla were Firmicutes and Bacteroidetes in natural and artificial water systems. Gram-negative bacteria of the family Enterobacteraceae with resistance to antibiotics are commonly reported in drinking water and in natural water systems. The ARGs mainly reported were those that confer resistance to β-lactam antibiotics, aminoglycosides, fluoroquinolones, macrolides and tetracycline. The high influence of anthropogenic activity in the environment is evidenced. The antibiotic resistance genes that are mainly reported in the urban areas of the world are those that confer resistance to the antibiotics that are most used in clinical practice, which constitutes a problem for human and animal health.

Molecular characterization of carbapenem-resistant Enterobacteriaceae and emergence of tigecycline non-susceptible strains in the Henan province in China: a multicentrer study

Introduction

Carbapenem-resistant Enterobacteriaceae (CRE) have been responsible for nosocomial outbreaks worldwide and have become endemic in several countries.

Hypothesis/Gap Statement

To better understand the epidemiological trends and characteristics of CRE in the Henan province.

Aim

We assessed the molecular epidemiological characteristics of 305 CRE strains isolated from patients in 19 secondary or tertiary hospitals in ten areas of the Henan province in China.

Methodology

A total of 305 CRE isolates were subjected to multiple tests, including in vitro antimicrobial susceptibility testing, PCR for carbapenemase genes bla_KPC, bla_NDM, bla_IMP, bla_VIM, bla_OXA-_48-like. Tigecycline-resistant genes ramR, oqxR, acrR, tetA, rpsJ, tetX, tetM, tetL were analysed in five tigecycline non-susceptible carbapenem-resistant Klebsiella pneumoniae isolates (TNSCRKP). Additionally, multilocus sequence typing (MLST) was performed for carbapenem-resistant K. pneumoniae (CRKP).

Results

The most common CRE species were K. pneumoniae (234, 77 %), Escherichia coli (36, 12 %) and Enterobacter cloacae (13, 4 %). All strains exhibited multi-drug resistance. Overall, 97 % (295/305) and 97 % (297/305) of the isolates were susceptible to polymyxin B and tigecycline, respectively. A total of 89 % (271/305) of the CRE isolates were carbapenemase gene-positive, including 70 % bla_KPC, 13 % bla_NDM, 6 % bla_IMP, and 1 % combined bla_KPC/bla_NDM genes. K. pneumoniae carbapenemase (KPC) was the predominant carbapenemase in K. pneumoniae (87 %), whereas NDM and IMP were frequent in E. coli (53 %) and E. cloacae (69 %), respectively. Mutations in the ramR, tetA, and rpsJ genes were detected in five TNSCRKP. Moreover, 15 unique sequence types were detected, with ST11 (74 %), ST15 (9 %) and ST2237 (5 %) being dominant among K. pneumoniae strains.

Conclusion

A high proportion of CRE strains were carbapenemase-positive, and five carbapenem-resistant K. pneumonia isolates were tigecycline non-susceptible, indicating a need for the ongoing surveillance of CRE and effective measures for the prevention of CRE infections.

Does Antimicrobial Therapy Affect Mortality of Patients with Carbapenem-Resistant Klebsiella pneumoniae Bacteriuria? A Nationwide Multicenter Study in Taiwan

Few clinical studies have previously discussed patients with carbapenem-resistant Klebsiella pneumoniae (CRKP) bacteriuria. This study aimed to assess the effect of antimicrobial therapy on the mortality of patients with CRKP bacteriuria. Hospitalized adults with CRKP bacteriuria were enrolled retrospectively from 16 hospitals in Taiwan during 2013 and 2014. Critically ill patients were defined as those with an Acute Physiology and Chronic Health Evaluation (APACHE) II score ≥ 20. Multivariate Cox regression analysis was used to determine independent risk factors for 14- and 28-day mortality. Of 107 patients with CRKP bacteriuria, the 14-day and 28-day mortality was 14.0% and 25.2%, respectively. Thirty-three patients received appropriate antimicrobial therapy. In the multivariate Cox regression analysis, the APACHE II score ≥ 20 was the only independent risk factor for 14-day mortality (hazard ratio [HR]: 6.15, p = 0.024). APACHE II score ≥ 20 (HR: 3.05, p = 0.018) and male sex (HR: 2.57, p = 0.037) were associated with 28-day mortality. Among critically ill patients with CRKP bacteriuria, appropriate antimicrobial therapy was not associated with 14-day or 28-day survival. In conclusion, in patients with CRKP bacteriuria, the use of appropriate antimicrobial therapy was not an independent factor associated with reduced mortality. Our findings may inform future antibiotic stewardship interventions for bacteriuria caused by multidrug resistant pathogens.

Prevalence of antibiotic resistance in the tropical rivers of Sri Lanka and India

We evaluate the imprints of urbanization, landuse and lifestyle on the prevalence and provenance of antibiotic resistance in the tropical rivers of Sri Lanka (Kelani and Gin) and India (Sabarmati, and Brahmaputra River). The prevalence of E. coli in the Kelani, Sabarmati, and Brahmaputra Rivers was in the range of 10-27, 267-76,600, and <50 CFU ml^-1 respectively. Isolated E. coli colonies were subjected to six antibiotics to assess their resistance. We found higher resistance to old generation antibiotics like tetracycline (TC), and sulfamethoxazole (ST) transcends the resistance for fluoroquinolones like norfloxacin (NFX), ciprofloxacin (CIP), and levofloxacin (LVX). Interestingly, both Indian rivers had exhibited relatively higher resistance to TC and ST than the Kelani river or Gin River, implying that the Sri Lankan situation is relatively less critical. At genetic level the resistance for β-lactams, fluoroquinolones and sulphonamides, were detected in many samples, as reported globally. While the resistance genes for aac-(6')-1b-cr, qnrS and sul1 were detected in both Sri Lankan and Indian Rivers, bla_TEM and ampC were specific to the Indian Rivers only. Decoupling of the prevalence of metal contamination and antibiotic resistance has been noticed in India and Sri Lanka. Study implies that urbanization, landuse, and lifestyle (ULL) are the three most critical factors governing multidrug resistance (MDR) and fecal contamination.

Urban and agricultural soils in Southern California are a reservoir of carbapenem-resistant bacteria

Carbapenems are last‐resort β‐lactam antibiotics used in healthcare facilities to treat multidrug‐resistant infections. Thus, most studies on identifying and characterizing carbapenem‐resistant bacteria (CRB) have focused on clinical settings. Relatively, little is still known about the distribution and characteristics of CRBs in the environment, and the role of soil as a potential reservoir of CRB in the United States remains unknown. Here, we have surveyed 11 soil samples from 9 different urban or agricultural locations in the Los Angeles–Southern California area to determine the prevalence and characteristics of CRB in these soils. All samples tested contained CRB with a frequency of <10 to 1.3 × 10⁴ cfu per gram of soil, with most agricultural soil samples having a much higher relative frequency of CRB than urban soil samples. Identification and characterization of 40 CRB from these soil samples revealed that most of them were members of the genera Cupriavidus, Pseudomonas, and Stenotrophomonas. Other less prevalent genera identified among our isolated CRB, especially from agricultural soils, included the genera Enterococcus, Bradyrhizobium, Achromobacter, and Planomicrobium. Interestingly, all of these carbapenem‐resistant isolates were also intermediate or resistant to at least 1 noncarbapenem antibiotic. Further characterization of our isolated CRB revealed that 11 Stenotrophomonas, 3 Pseudomonas, 1 Enterococcus, and 1 Bradyrhizobium isolates were carbapenemase producers. Our findings show for the first time that both urban and agricultural soils in Southern California are an underappreciated reservoir of bacteria resistant to carbapenems and other antibiotics, including carbapenemase‐producing CRB.

The Prevalence and Characterization of Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Bacteria from Hospital Sewage, Treated Effluents and Receiving Rivers

Hospital sewage plays a key role in the dissemination of antibiotic-resistant genes (ARGs) by serving as an environmental antimicrobial resistance reservoir. In this study, we aimed to characterize the cephalosporin- and carbapenem-resistant isolates from hospital sewage and receiving rivers. The results showed that ESBL (bla_CTX-M) and carbapenemase genes (bla_NDM and bla_KPC) were widely detected in a number of different bacterial species. These resistance genes were mainly harbored in Enterobacteriaceae, followed by Acinetobacter and Aeromonas isolates. More attention should be given to these bacteria as important vectors of ARGs in the environment. Furthermore, we showed that the multidrug resistance phenotype was highly prevalent, which was found in 85.5% Enterobacteriaceae and 75% Acinetobacter strains. Notably, the presence of carbapenemase genes in isolates from treated effluents and receiving rivers indicates that the discharges of wastewater treatment plants could be an important source for high-risk resistance genes propagation to the environment. In conclusion, this study shows a high prevalence of ESBL- and carbapenemase-producing bacteria in hospital sewage and receiving rivers in China. These findings have serious implications for human health, and also suggest the need for more efforts to control the dissemination of resistant bacteria from hospital sewage into the environment.