Occurrence of Carbapenemase-Producing Klebsiella pneumoniae in Bat Guano

Carbapenem-Resistant NDM and OXA-48-like Producing K. pneumoniae: From Menacing Superbug to a Mundane Bacteria; A Retrospective Study in a Romanian Tertiary Hospital

BACKGROUND

Carbapenem-resistant Klebsiella pneumoniae (Cr-Kpn) is becoming a growing public health problem through the failure of adequate treatment. This study's objectives are to describe the sources of Cr-Kpn in our hospital over 22 months, associating factors with the outcome of Cr-Kpn-positive patients, especially those with NDM+OXA-48-like (New Delhi Metallo-β-Lactamase and oxacillinase-48), and the effectiveness of the treatments used.

METHODS

A retrospective observational cohort study including all hospitalized patients with Cr-Kpn isolates. We reported data as percentages and identified independent predictors for mortality over hospital time through multivariate analysis.

RESULTS

The main type of carbapenemases identified were NDM+OXA-48-like (49.4%). The statistical analysis identified that diabetes and co-infections with the Gram-negative, non-urinary sites of infection were factors of unfavorable evolution. The Cox regression model identified factors associated with a poor outcome: ICU admission (HR of 2.38), previous medical wards transition (HR of 4.69), and carbapenemase type NDM (HR of 5.98). We did not find the superiority of an antibiotic regimen, especially in the case of NDM+OXA-48-like.

CONCLUSIONS

The increase in the incidence of Cr-Kpn infections, especially with NDM+OXA-48-like pathogens, requires a paradigm shift in both the treatment of infected patients and the control of the spread of these pathogens, which calls for a change in public health policy regarding the use of antibiotics and the pursuit of a One Health approach.

European Wild Carnivores and Antibiotic Resistant Bacteria: A Review

Antibiotic resistance is a global concern that affects not only human health but also the health of wildlife and the environment. Wildlife can serve as reservoirs for antibiotic-resistant bacteria, and antibiotics in veterinary medicine and agriculture can contribute to the development of resistance in these populations. Several European carnivore species, such as wolves, foxes, otters, and bears, can be exposed to antibiotics by consuming contaminated food, water, or other resources in their habitats. These animals can also be indirectly exposed to antibiotics through interactions with domestic animals and human activities in their environment. Antibiotic resistance in wildlife can harm ecosystem health and also impact human health indirectly through various pathways, including zoonotic disease transmission. Moreover, the spread of resistant bacteria in wildlife can complicate conservation efforts, as it can threaten already endangered species. This review aims to describe the presence of antibiotic-resistant bacteria in wild carnivores in Europe.

An overview of carbapenem-resistant organisms from food-producing animals, seafood, aquaculture, companion animals, and wildlife

Carbapenem resistance (CR) is a major global health concern. CR is a growing challenge in clinical settings due to its rapid dissemination and low treatment options. The characterization of its molecular mechanisms and epidemiology are highly studied. Nevertheless, little is known about the spread of CR in food-producing animals, seafood, aquaculture, wildlife, their environment, or the health risks associated with CR in humans. In this review, we discuss the detection of carbapenem-resistant organisms and their mechanisms of action in pigs, cattle, poultry, seafood products, companion animals, and wildlife. We also pointed out the One Health approach as a strategy to attempt the emergency and dispersion of carbapenem-resistance in this sector and to determine the role of carbapenem-producing bacteria in animals among human public health risk. A higher occurrence of carbapenem enzymes in poultry and swine has been previously reported. Studies related to poultry have highlighted P. mirabilis, E. coli, and K. pneumoniae as NDM-5- and NDM-1-producing bacteria, which lead to carbapenem resistance. OXA-181, IMP-27, and VIM-1 have also been detected in pigs. Carbapenem resistance is rare in cattle. However, OXA- and NDM-producing bacteria, mainly E. coli and A. baumannii, are cattle's leading causes of carbapenem resistance. A high prevalence of carbapenem enzymes has been reported in wildlife and companion animals, suggesting their role in the cross-species transmission of carbapenem-resistant genes. Antibiotic-resistant organisms in aquatic environments should be considered because they may act as reservoirs for carbapenem-resistant genes. It is urgent to implement the One Health approach worldwide to make an effort to contain the dissemination of carbapenem resistance.

Evidence of Antimicrobial Resistance in Bats and Its Planetary Health Impact for Surveillance of Zoonotic Spillover Events: A Scoping Review

As a result of the COVID-19 pandemic, as well as other outbreaks, such as SARS and Ebola, bats are recognized as a critical species for mediating zoonotic infectious disease spillover events. While there is a growing concern of increased antimicrobial resistance (AMR) globally during this pandemic, knowledge of AMR circulating between bats and humans is limited. In this paper, we have reviewed the evidence of AMR in bats and discussed the planetary health aspect of AMR to elucidate how this is associated with the emergence, spread, and persistence of AMR at the human-animal interface. The presence of clinically significant resistant bacteria in bats and wildlife has important implications for zoonotic pandemic surveillance, disease transmission, and treatment modalities. We searched MEDLINE through PubMed and Google Scholar to retrieve relevant studies (n = 38) that provided data on resistant bacteria in bats prior to 30 September 2022. There is substantial variability in the results from studies measuring the prevalence of AMR based on geographic location, bat types, and time. We found all major groups of Gram-positive and Gram-negative bacteria in bats, which are resistant to commonly used antibiotics. The most alarming issue is that recent studies have increasingly identified clinically significant multi-drug resistant bacteria such as Methicillin Resistant Staphylococcus aureus (MRSA), ESBL producing, and Colistin resistant Enterobacterales in samples from bats. This evidence of superbugs abundant in both humans and wild mammals, such as bats, could facilitate a greater understanding of which specific pathways of exposure should be targeted. We believe that these data will also facilitate future pandemic preparedness as well as global AMR containment during pandemic events and beyond.

The Threat of Potentially Pathogenic Bacteria in the Feces of Bats

Bats have attracted global attention because of their zoonotic association with severe acute respiratory syndrome coronavirus (SARS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Previous and ongoing studies have predominantly focused on bat-borne viruses; however, the prevalence or abundance of bat-borne pathogenic bacteria and their potential public health significance have largely been neglected. For the first time, this study used both metataxonomics (16S rRNA marker gene sequencing) and culturomics (traditional culture methods) to systematically evaluate the potential public health significance of bat fecal pathogenic bacteria. To this end, fecal samples were obtained from five bat species across different locations in China, and their microbiota composition was analyzed. The results revealed that the bat microbiome was most commonly dominated by Proteobacteria, while the strictly anaerobic phylum Bacteroidetes occupied 35.3% of the relative abundance in Rousettus spp. and 36.3% in Hipposideros spp., but less than 2.7% in the other three bat species (Taphozous spp., Rhinolophus spp., and Myotis spp.). We detected 480 species-level phylotypes (SLPs) with PacBio sequencing, including 89 known species, 330 potentially new species, and 61 potentially higher taxa. In addition, a total of 325 species were identified by culturomics, and these were classified into 242 named species and 83 potentially novel species. Of note, 32 of the 89 (36.0%) known species revealed by PacBio sequencing were found to be pathogenic bacteria, and 69 of the 242 (28.5%) known species isolated by culturomics were harmful to people, animals, or plants. Additionally, nearly 40 potential novel species which may be potential bacterial pathogens were identified. IMPORTANCE Bats are one of the most diverse and widely distributed groups of mammals living in close proximity to humans. In recent years, bat-borne viruses and the viral zoonotic diseases associated with bats have been studied in great detail. However, the prevalence and abundance of pathogenic bacteria in bats have been largely ignored. This study used high-throughput sequencing techniques (metataxonomics) in combination with traditional culture methods (culturomics) to analyze the bacterial flora in bat feces from different species of bats in China, revealing that bats are natural hosts of pathogenic bacteria and carry many unknown bacteria. The results of this study can be used as guidance for future investigations of bacterial pathogens in bats.

Transmission of Klebsiella strains and plasmids within and between grey-headed flying fox colonies

The grey-headed flying fox (Pteropus poliocephalus) is an endemic Australian fruit bat, known to carry zoonotic pathogens. We recently showed they harbour bacterial pathogen Klebsiella pneumoniae and closely related species in the K. pneumoniae species complex (KpSC); however, the dynamics of KpSC transmission and gene flow within flying fox colonies are poorly understood. High-resolution genome comparisons of 39 KpSC isolates from grey-headed flying foxes identified five putative strain transmission clusters (four intra- and one inter-colony). The instance of inter-colony strain transmission of K. africana was found between two flying fox populations within flying distance, indicating either direct or indirect transmission through a common food/water source. All 11 plasmids identified within the KpSC isolates showed 73% coverage (mean) and ≥95% identity to human-associated KpSC plasmids, indicating gene flow between human clinical and grey-headed flying fox isolates. Along with strain transmission, inter-species horizontal plasmid transmission between K. pneumoniae and Klebsiella africana was also identified within a flying fox colony. Finally, genome-scale metabolic models were generated to predict and compare substrate usage to previously published KpSC models, from human and environmental sources. These models indicated no distinction on the basis of metabolic capabilities. Instead, metabolic capabilities were consistent with population structure and ST/lineage.

Microbial isolates with Anti-Pseudogymnoascus destructans activities from Western Canadian bat wings

Pseudogymnoascus destructans (Pd) is the causative agent of white-nose syndrome, which has resulted in the death of millions of bats in North America (NA) since 2006. Based on mortalities in eastern NA, the westward spread of infections likely poses a significant threat to western NA bats. To help prevent/reduce Pd infections in bats in western NA, we isolated bacteria from the wings of wild bats and screened for inhibitory activity against Pd. In total, we obtained 1,362 bacterial isolates from 265 wild bats of 13 species in western Canada. Among the 1,362 isolates, 96 showed inhibitory activity against Pd based on a coculture assay. The inhibitory activities varied widely among these isolates, ranging from slowing fungal growth to complete inhibition. Interestingly, host bats containing isolates with anti-Pd activities were widely distributed, with no apparent geographic or species-specific pattern. However, characteristics of roosting sites and host demography showed significant associations with the isolation of anti-Pd bacteria. Specifically, anthropogenic roosts and swabs from young males had higher frequencies of anti-Pd bacteria than those from natural roosts and those from other sex and age-groups, respectively. These anti-Pd bacteria could be potentially used to help mitigate the impact of WNS. Field trials using these as well as additional microbes from future screenings are needed in order to determine their effectiveness for the prevention and treatment against WNS.

First Report of CC5-MRSA-IV-SCCfus "Maltese Clone" in Bat Guano

Methicillin-resistant Staphylococcus aureus (MRSA) is a widespread pathogen that could cause different illnesses in both human and animals. Presence of MRSA in animals raises concerns of their capacity to act as reservoirs, particularly in wild animals. This study aimed to characterize the resistance and virulence patterns of S. aureus strains isolated from bat guano in Algeria. From March to May 2016, 98 bat guano samples from Aokas’s cave (Bejaia, Algeria) were collected. Swabs were taken for microbiological studies. Isolates were identified by Vitek^® MS system, and antibiotic susceptibility was determined by disk diffusion method. The clonal origin, virulence and antibiotic resistance profiles of S. aureus isolates were characterized by whole genome sequencing. Eleven S. aureus strains were obtained from the 98 guano samples. Seven isolates were sensitive to all antibiotics tested and four (36.3%) were resistant to penicillin G, cefoxitin and fusidic acid. The four MRSA isolates were assigned to the sequence type ST149 and related to spa type t010. These isolates harbored a SCCmecIV element and the fusidic acid resistance element Q6GD50 (fusC). They carried different virulence genes including several enterotoxins (sea, egc enterotoxin locus, sec, sel), and the toxic shock syndrome toxin (tst). Our results highlight that bat guano may constitute an important reservoir of MRSA strains.

Novel strains of Klebsiella africana and Klebsiella pneumoniae in Australian fruit bats (Pteropus poliocephalus)

Over the past decade human associated multidrug resistant (MDR) and hypervirulent Klebsiella pneumoniae lineages have been increasingly detected in wildlife. This study investigated the occurrence of K. pneumoniae species complex (KpSC) in grey-headed flying foxes (GHFF), an Australian fruit bat. Thirty-nine KpSC isolates were cultured from 275 GHFF faecal samples (14.2%), comprising K. pneumoniae (n = 30), Klebsiella africana (n = 8) and Klebsiella variicola subsp. variicola (n = 1). The majority (79.5%) of isolates belonged to novel sequence types (ST), including two novel K. africana STs. This is the first report of K. africana outside of Africa and in a non-human host. A minority (15.4%) of GHFF KpSC isolates shared STs with human clinical K. pneumoniae strains, of which, none belonged to MDR clonal lineages that cause frequent nosocomial outbreaks, and no isolates were characterised as hypervirulent. The occurrence of KpSC isolates carrying acquired antimicrobial resistance genes in GHFF was low (1.1%), with three K. pneumoniae isolates harbouring both fluoroquinolone and trimethoprim resistance genes. This study indicates that GHFF are not reservoirs for MDR and hypervirulent KpSC strains, but they do carry novel K. africana lineages. Health risks associated with KpSC carriage by GHFF are deemed low for the public and GHFF.

Characterization of beta-lactam-resistant Escherichia coli from Australian fruit bats indicates anthropogenic origins

Antimicrobial-resistant Escherichia coli, particularly those resistant to critically important antimicrobials, are increasingly reported in wildlife. The dissemination of antimicrobial-resistant bacteria to wildlife indicates the far-reaching impact of selective pressures imposed by humans on bacteria through misuse of antimicrobials. The grey-headed flying fox (GHFF; Pteropus poliocephalus), a fruit bat endemic to eastern Australia, commonly inhabits urban environments and encounters human microbial pollution. To determine if GHFF have acquired human-associated bacteria, faecal samples from wild GHFF (n=287) and captive GHFF undergoing rehabilitation following illness or injury (n=31) were cultured to detect beta-lactam-resistant E. coli. Antimicrobial susceptibility testing, PCR and whole genome sequencing were used to determine phenotypic and genotypic antimicrobial resistance profiles, strain type and virulence factor profiles. Overall, 3.8 % of GHFF carried amoxicillin-resistant E. coli (wild 3.5 % and captive 6.5 %), with 38.5 % of the 13 GHFF E. coli isolates exhibiting multidrug resistance. Carbapenem (bla_NDM-5) and fluoroquinolone resistance were detected in one E. coli isolate, and two isolates were resistant to third-generation cephalosporins (bla_CTX-M-27 and ampC). Resistance to tetracycline and trimethoprim plus sulfamethoxazole were detected in 69.2% and 30.8 % of isolates respectively. Class 1 integrons, a genetic determinant of resistance, were detected in 38.5 % of isolates. Nine of the GHFF isolates (69.2 %) harboured extraintestinal virulence factors. Phylogenetic analysis placed the 13 GHFF isolates in lineages associated with humans and/or domestic animals. Three isolates were human-associated extraintestinal pathogenic E. coli (ST10 O89:H9, ST73 and ST394) and seven isolates belonged to lineages associated with extraintestinal disease in both humans and domestic animals (ST88, ST117, ST131, ST155 complex, ST398 and ST1850). This study provides evidence of anthropogenic multidrug-resistant and pathogenic E. coli transmission to wildlife, further demonstrating the necessity for incorporating wildlife surveillance within the One Health approach to managing antimicrobial resistance.

The microbiome of bat guano: for what is this knowledge important?

Bats as flying mammals are potent vectors and natural reservoir hosts for many infectious viruses, bacteria, and fungi, also detected in their excreta such as guano. Accelerated deforestation, urbanization, and anthropization hastily lead to overpopulation of the bats in urban areas allowing easy interaction with other animals, expansion, and emergence of new zoonotic disease outbreaks potentially harmful to humans. Therefore, getting new insights in the microbiome of bat guano from different places represents an imperative for the future. Furthermore, the use of novel high-throughput sequencing technologies allows better insight in guano microbiome and potentially indicated that some species could be typical guano-dwelling members. Bats are well known as a natural reservoir of many zoonotic viruses such as Ebola, Nipah, Marburg, lyssaviruses, rabies, henipaviruses, and many coronaviruses which caused a high number of outbreaks including ongoing COVID-19 pandemic. Additionally, many bacterial and fungal pathogens were identified as common guano residents. Thus, the presence of multi-drug-resistant bacteria as environmental reservoirs of extended spectrum β-lactamases and carbapenemase-producing strains has been confirmed. Bat guano is the most suitable substrate for fungal reproduction and dissemination, including pathogenic yeasts and keratinophilic and dimorphic human pathogenic fungi known as notorious causative agents of severe endemic mycoses like histoplasmosis and fatal cryptococcosis, especially deadly in immunocompromised individuals. This review provides an overview of bat guano microbiota diversity and the significance of autochthonous and pathogenic taxa for humans and the environment, highlighting better understanding in preventing emerging diseases. KEY POINTS: Bat guano as reservoir and source for spreading of autochthonous and pathogenic microbiota Bat guano vs. novel zoonotic disease outbreaks Destruction of bat natural habitats urgently demands increased human awareness.

First Clinical Cases of KPC-2-Producing Klebsiella pneumoniae ST258 in Algeria and Outbreak of Klebsiella pneumoniae ST101 Harboring blaOXA-48 Gene in the Urology Department of Annaba Hospital

Objectives: The aim of this study was to characterize the molecular mechanisms of carbapenem resistance in Klebsiella pneumoniae isolated from the urology department of Annaba hospital, Algeria. Methods: Between January 2015 and September 2017, 14 carbapenem-resistant K. pneumoniae strains were isolated during routine surveillance work at Ibn Roched hospital of Annaba, Algeria, from the urology department. Theses strains were recovered, and carbapenem resistance mechanisms were investigated. The strains were identified by using matrix-assisted laser desorption and ionization time-of-flight mass spectrometry. Antibiotic susceptibility was assessed by using the Kirby-Bauer method, whereas minimum inhibitory concentration of imipenem/ertapenem and colistin was determined by Etest and broth microdilution methods, respectively. Carbapenem resistance determinants were studied by using PCR and sequencing methods and analyzed by BLAST against the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT) database. Clonal relationship of strains was performed by using multilocus sequence typing (MLST). Transferability of carbapenem resistance genes was assessed by conjugation and transformation experiments. Results: Fourteen carbapenem-resistant K. pneumoniae isolates were found to be resistant to the eight β-lactam antibiotics tested (except to imipenem for two isolates). Carbapenemase production was positive for all isolates. Molecular characterization revealed that bla_KPC-2 and bla_OXA-48 genes were detected in 3 (21.4%) and 11 isolates (78.6%), respectively. Other β-lactamases genes were identified, including bla_CTX-M-15, bla_{SHV-1-or 12}, and bla_TEM-1. MLST revealed that the 14 isolates belonged to 2 different sequence types (STs), including ST101 (11 OXA-48-producing K. pneumoniae) and ST258 (3 KPC-2-producing K. pneumoniae). PCR amplifications for bla_KPC-2 and bla_OXA-48 carbapenemases genes performed on extracted plasmids, showed positive results, suggesting that both carbapenemase genes were probably borne by plasmids. Conclusion: We report here the first identification of KPC-2-producing K. pneumoniae ST258 in Algerian hospitals and an outbreak of OXA-48-producing K. pneumoniae isolates ST101 in the urology department of Ibn Roched hospital located in Annaba, Algeria.

The Faecal Microbiome of Building-Dwelling Insectivorous Bats (Myotis myotis and Rhinolophus hipposideros) also Contains Antibiotic-Resistant Bacterial Representatives

The bacteriome of bat faeces and bat guano is still not well known, despite the increasing knowledge of it as a potential source of pathogenic and/or antibiotic-resistant species. In this study, the faecal microbiome composition of two building-dwelling insectivorous bat species (Myotis myotis and Rhinolophus hipposideros) was analysed using cultivation-based and non-cultivation-based approaches. The cultivation analyses indicate the dominance of Gram-positive bacteria, represented by the genera Enterococcus, Lactococcus and Lactobacillus. Non-cultivation analysis based on 16S rRNA DGGE assays provided a different pattern, with the genus Rahnella found to predominate in the faecal microbiome. The analyses showed bat species to be the most important factor influencing the structure of the guano-associated microbial population. The presence of several possible human pathogens (Hafnia alvei, Serratia fonticola, S. liquefaciens) and antibiotic-resistant bacteria (e.g. vancomycin resistant Staphylococcus nepalensis) was detected in faeces samples, indicating possible human health risks associated with bat guano. Although the bat-human transmission of infection caused by pathogenic bacteria has not been reliably confirmed to date, this possibility should not be underestimated. Given the very important ecosystem services of bats, particular those studied herein, it is time to think about appropriate management of bat populations inhabiting man-made buildings and potential conflicts with humans.

Spread of OXA-48 and NDM-1-Producing Klebsiella pneumoniae ST48 and ST101 in Chicken Meat in Western Algeria

Aim: We investigated the prevalence of carbapenemase-producing Enterobacteriaceae (CPE) in chicken meat in Western Algeria in 2017. Results: From February to July 2017, samples of chicken meat from three poultry farms in Western Algeria were screened for the presence of CPE. Strains were characterized with regard to antibiotic resistance, β-lactamase content, Plasmid-mediated quinolone resistance, sulfonamide resistance genes, clonality (repetitive sequence-based profiles and multilocus sequence typing) and virulence traits. Of 181 samples analyzed, 29 (16.0%) carbapenemase-producing Klebsiella pneumoniae were detected. Twenty-three OXA-48-producers (79.3%) and six (20.7%) New Delhi metallo (NDM)-1-producers were observed. Clonality analysis showed three distinct lineages and clonal expansions of the OXA-48-producing K. pneumoniae ST48 and the NDM-1-producing K. pneumoniae ST101. These isolates harbored fimH, ureA, mrkD, entB, uge, and wabG. Neither capsular serotype genes nor hypermucoviscous phenotype were detected. Plasmid analysis confirmed that all these isolates harbored the transferable IncL and IncFIIK plasmids. Conclusions: This study reports the spread of OXA-48 and NDM-1-producing K. pneumoniae ST48 and ST101 in chicken meat in Western Algeria and demonstrates that food represents a reservoir of the carbapenemases encoding genes.