Genetic background of CTX-M-15-producing Enterobacter hormaechei ST114 and Citrobacter freundii ST265 co-infecting a free-living green turtle (Chelonia mydas)

Gut colonization of semi-aquatic turtles inhabiting the Brazilian Amazon by international clones of CTX-M-8-producing Escherichia coli

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli poses a significant threat to public health due to its ability to confer resistance to broad-spectrum antimicrobials, especially third-generation cephalosporins. Herein, we report gut colonization by international clones of CTX-M-8-producing E. coli in scorpion mud turtles (Kinosternon scorpioides) from a captive breeding program in the Brazilian Amazon. The E. coli strains exhibited multidrug resistance to clinically relevant antimicrobials, and genomic analyses revealed broad resistomes to antimicrobials, heavy metals, pesticides, and disinfectants. Detecting these medically important bacteria in captive wildlife underscores the potential risks associated with reintroduction programs, as ESBL-producing bacteria may spill over into the natural ecosystem and threaten wildlife. Our findings highlight the need for enhanced surveillance and control measures in wildlife conservation programs to mitigate the risks of antimicrobial resistance transmission between captive and wild populations.

Phenotypic and Genomic Characterization of ESBL- and AmpC-β-Lactamase-Producing Enterobacterales Isolates from Imported Healthy Reptiles

BACKGROUND/OBJECTIVES

Reptiles are known reservoirs for members of the Enterobacterales. We investigated antimicrobial resistance (AMR) patterns, the diversity of extended-spectrum-/AmpC-β-lactamases (ESBL/AmpC) genes and the genomic organization of the ESBL/AmpC producers.

METHODS

A total of 92 shipments with 184 feces, skin, and urinate samples of live healthy reptiles were obtained during border inspections at Europe's most important airport for animal trade and screened for AMR bacteria by culture, antimicrobial susceptibility testing, and whole genome sequencing (WGS) of selected isolates.

RESULTS

In total, 668 Enterobacterales isolates with phenotypic evidence for extended-spectrum-/AmpC-β-lactamases (ESBL/AmpC) were obtained, from which Klebsiella (n = 181), Citrobacter (n = 131), Escherichia coli (n = 116), Salmonella (n = 69), and Enterobacter (n = 52) represented the most common groups (other genera (n = 119)). Seventy-nine isolates grew also on cefotaxime agar and were confirmed as ESBL (n = 39) or AmpC (n = 39) producers based on WGS data with respective genes localized on chromosomes or plasmids. Isolates of E. coli contained the most diverse set of ESBL genes (n = 29), followed by Klebsiella (n = 9), Citrobacter, and Enterobacter (each n = 1). Contrarily, AmpC genes were detected in E. coli and Citrobacter (n = 13 each), followed by Enterobacter (n = 12) and Klebsiella (n = 4). Isolates of Salmonella with ESBL/AmpC genes were not found, but all genera contained a variety of additional AMR phenotypes and/or genotypes. MLST revealed 36, 13, 10, and nine different STs in E. coli, Klebsiella, Citrobacter, and Enterobacter, respectively.

CONCLUSIONS

A significant fraction of the studied Enterobacterales isolates possessed acquired AMR genes, including some high-risk clones. All isolates were obtained from selective media and also wild-caught animals carried many AMR genes. Assignment of AMR to harvesting modes was not possible.

Molecular detection of Enterobacter hormaechei in bovine respiratory disease

Bovine respiratory disease (BRD) develops from complex interactions among environmental, host and pathogenic factors. This study aimed to phenotypically identify Enterobacter hormaechei isolated from cattle with BRD and assess antimicrobial susceptibility and determining the molecular phylogeny of local E. hormaechei strains. Between November 2023 and March 2024, nasal swabs were collected from 93 cattle with BRD, before culturing for phenotypic analysis, and performing the polymerase chain reaction (PCR) for molecular characterisation. Of the 93 samples evaluated, 15.79% and 24.56% tested positive for E. hormaechei isolates on culture and PCR, respectively. The local isolates exhibited high resistance to amoxicillin, ampicillin, amikacin, nalidixic acid and ceftazidime; high susceptibility to azithromycin, levofloxacin, gentamicin, ofloxacin, cefepime, ceftriaxone, cefotaxime, nitrofurantoin, ceftazidime and ciprofloxacin; and moderate susceptibility to ciprofloxacin, colistin, imipenem and meropenem. Multiple sequence alignment, phylogenetic tree analysis and homology sequence identification, showed that the five positive isolates were similar to the reference isolate. To the best of our knowledge, this is the first time that E. hormaechei has been isolated in cattle with BRD in Iraq. Because phenotype-based assays show limited accuracy to identify species, we recommend molecular and phylogenetic analysis be included in all similar studies in the future.

The curious case of the rare Citrobacter pasteurii isolated from an endangered primate in Brazil

The genus Citrobacter comprises clinically important human pathogens but has been less frequently associated with wildlife infections. Citrobacter pasteurii was first identified as causing human diarrhea and remains rarely documented. In this study, a Gram-negative bacterial strain, named A318, was identified as causing diarrhea in a black lion tamarin. This strain was biochemically identified as Trabulsiella guamensis, a species of unusual nature, and was submitted to whole-genome characterization. Curiously, phylogenomic analysis showed that A318 strain belonged to the genus Citrobacter, with confirmation of the species C. pasteurii by average nucleotide identity (99.02 %) and digital DNA-DNA hybridization (93.80 %) analyzes. Cases of misidentification of C. pasteurii as Citrobacter youngae were detected and corrected in this study. In addition to the genome sequence of the type strain of C. pasteurii, only two others from the Australian cockle and Portuguese silver gull are publicly available. Single nucleotide polymorphism differences among all C. pasteurii indicated a highly diverse population. No acquired antimicrobial resistance genes and plasmid replicons were found. Therefore, our findings emphasize the importance of gold-standard methods for accurate identification and underscores the importance of continued surveillance and research to mitigate the risks posed by zoonotic and zooanthroponotic pathogens.

High toxicity of agro-industrial wastewater on aquatic fauna of a South American stream: Mortality of aquatic turtles and amphibian tadpoles as bioindicators of environmental health

The aim of this study was to characterize an aquatic system of Santa Fe province (Argentina) receiving wastewater from agro-industrial activities (mainly dairy) by in situ assessment (fauna mortality, physicochemical, microbiological, and pesticide residues measurement), and ecotoxicity bioassays on amphibian tadpoles. Water and sediment samples were obtained from the Los Troncos Stream (LTS), previous to the confluence with the "San Carlos" drainage channel (SCC), and from the SCC. Biological parameters (mortality and sublethal biomarkers) were used to evaluate ecotoxicity during 10-day exposure of Rhinella arenarum tadpoles to LTS and SCC samples. Nine pesticides were detected in both LTS and SCC. Chemical and biochemical oxygen demand, ammonia, and coliform count recorded in SCC greatly exceeded limits for aquatic life protection. At SCC and LTS after the confluence with SCC, numerous dying and dead aquatic turtles (Phrynops hilarii) were recorded. In the ecotoxicity assessment, no mortality of tadpoles was observed in LTS treatment, whereas total mortality (100%) was observed in SCC treatments in dilution higher than 50% of water and sediment. For SCC, median lethal concentration and the 95% confidence limits was 18.30% (14.71-22.77) at 24 h; lowest-observed and no-observed effect concentrations were 12.5% and 6.25%, respectively. Oxidative stress and neurotoxicity were observed in tadpoles exposed to 25% SCC dilution treatment. In addition, there was a large genotoxic effect (micronuclei test) in all sublethal SCC dilution treatments (6.25%, 12.5%, and 25%). These results alert about the high environmental quality deterioration and high ecotoxicity for aquatic fauna of aquatic ecosystems affected by agro-industrial wastewater. PRACTITIONER POINTS: Great mortality of turtles was observed in a basin with a high load of agro-industrial wastewater. San Carlos Channel (SCC), where effluents are spilled, is environmentally deteriorated. The water-sediment matrix of SCC caused 100% lethality in tadpoles. SCC dilutions caused neurotoxicity, oxidative stress, and genotoxicity on tadpoles.

Genomic scan of a healthcare-associated NDM-1-producing Citrobacter freundii ST18 isolated from a green sea turtle impacted by plastic pollution

BACKGROUND

Carbapenemase-producing Citrobacter freundii has been reported as a leading cause of healthcare-associated infections. Particularly, C. freundii belonging to the sequence type (ST) 18 is considered to be an emerging nosocomial clone.

OBJECTIVES

To report the genomic background and phylogenomic analysis of a multidrug-resistant NDM-1-producing C. freundii ST18 (strain CF135931) isolated from an endangered green sea turtle affected by plastic pollution in Brazil.

METHODS

Genomic DNA was extracted and sequenced using the Illumina NextSeq platform. De novo assembly was performed by CLC Workbench, and in silico analysis accomplished by bioinformatics tools. For phylogenomic analysis, publicly available C. freundii (txid:546) genome assemblies were retrieved from the NCBI database.

RESULTS

The genome size was calculated at 5 290 351 bp, comprising 5263 total genes, 4 rRNAs, 77 tRNAs, 11ncRNAs, and 176 pseudogenes. The strain belonged to C. freundii ST18, whereas resistome analysis predicted genes encoding resistance to β-lactams (blaNDM-1, blaOXA-1, blaCMY-117, and blaTEM-1C), aminoglycosides (aph(3'')-Ib, aadA16, aph(3')-VI, aac(6')-Ib-cr, and aph(6)-Id), quinolones (aac(6')-Ib-cr), macrolides (mph(A) and erm(B)), sulphonamides (sul1 and sul2), tetracyclines (tetA and tetD), and trimethoprim (dfrA27). The phylogenomic analysis revealed that CF135931 strain is closely related to international human-associated ST18 clones producing NDM-1.

CONCLUSION

Genomic surveillance efforts are necessary for robust monitoring of the emergence of drug-resistant strains and WHO critical priority pathogens within a One Health framework. In this regard, this draft genome and associated data can improve understanding of dissemination dynamics of nosocomial clones of carbapenemase-producing C. freundii beyond hospital walls. In fact, the emergence of NDM-1-producing C. freundii of global ST18 in wildlife deserves considerable attention.

Citrobacter freundii-associated lesions in stranded loggerhead sea turtles (Caretta caretta)

Citrobacter freundii, an opportunistic bacterial pathogen belonging to the family Enterobacteriaceae, has been sporadically reported in sea turtles. Here, the authors describe 3 unusual lesions associated with C. freundii infection in 3 loggerhead sea turtles stranded on the coast of Gran Canaria Island, Spain. It is possible that these 3 distinct lesions played a major role in the death of these turtles. The first turtle had caseous cholecystitis, a lesion not previously described in sea turtles. The second turtle had large intestinal diverticulitis, a rare condition in loggerheads. The third turtle had bilateral caseous salt gland adenitis. Histologically, numerous gram-negative bacilli were observed at the deepest edge of inflammation in all cases. Pure cultures of C. freundii were obtained from these 3 lesions. Molecular detection of C. freundii DNA in formalin-fixed paraffin-embedded samples from the lesions of the 3 turtles confirmed the microbiological isolation. These cases, in addition to expanding the limited body of knowledge on bacterial infections in sea turtles, highlight the potential pathogenic role of C. freundii in loggerhead turtles.

Successful expansion of hospital-associated clone of vanA-positive vancomycin-resistant Enterococcus faecalis ST9 to an anthropogenically polluted mangrove in Brazil

Mangrove ecosystems are hotspots of biodiversity, but have been threatened by anthropogenic activities. Vancomycin-resistant enterococci (VRE) are nosocomial bacteria classified as high priority by the World Health Organization (WHO). Herein, we describe the identification and genomic characteristics of a vancomycin-resistant Enterococcus faecalis strain isolated from a highly impacted mangrove ecosystem of the northeastern Brazilian, in 2021. Genomic analysis confirmed the existence of the transposon Tn1546-vanA and clinically relevant antimicrobial resistance genes, such as streptogramins, tetracycline, phenicols, and fluoroquinolones. Virulome analysis identified several genes associated to adherence, immune modulation, biofilm, and exoenzymes production. The UFSEfl strain was assigned to sequence type (ST9), whereas phylogenomic analysis with publicly available genomes from a worldwide confirmed clonal relatedness with a hospital-associated Brazilian clone. Our findings highlight the successful expansion of hospital-associated VRE in a mangrove area and shed light on the need for strengthening genomic surveillance of WHO priority pathogens in these vital ecosystems.

New Delhi metallo-β-lactamase-1-producing Citrobacter portucalensis belonging to the novel ST264 causing fatal sepsis in a vulnerable migratory sea turtle

Olive ridley (Lepidochelys olivacea) turtles migrate across tropical regions of the Atlantic, Pacific, and Indian Oceans. Worryingly, olive ridley populations have been declining substantially and is now considered a threatened species. In this regard, habitat degradation, anthropogenic pollution, and infectious diseases have been the most notorious threats for this species. We isolated a metallo-β-lactamase (NDM-1)-producing Citrobacter portucalensis from the blood sample of an infected migratory olive ridley turtle found stranded sick in the coast of Brazil. Genomic analysis of C. portucalensis confirmed a novel sequence type (ST), named ST264, and a wide resistome to broad-spectrum antibiotics. The production of NDM-1 by the strain contributed to treatment failure and death of the animal. Phylogenomic relationship with environmental and human strains from African, European and Asian countries confirmed that critical priority clones of C. portucalensis are spreading beyond hospital settings, representing an emerging ecological threat to marine ecosystems.

Bacterial Infections in Sea Turtles

Sea turtles are important for the maintenance of marine and beach ecosystems, but they are seriously endangered due to factors mainly related to human activities and climate change such as pollution, temperature increase, and predation. Infectious and parasitic diseases may contribute to reducing the number of sea turtles. Bacteria are widespread in marine environments and, depending on the species, may act as primary or opportunistic pathogens. Most of them are able to infect other animal species, including humans, in which they can cause mild or severe diseases. Therefore, direct or indirect contact of humans with sea turtles, their products, and environment where they live represent a One Health threat. Chlamydiae, Mycobacteria, and Salmonellae are known zoonotic agents able to cause mild or severe diseases in sea turtles, other animals, and humans. However, other bacteria that are potentially zoonotic, including those that are antimicrobially resistant, are involved in different pathologies of marine turtles.

Microbial composition of carapace, feces, and water column in captive juvenile green sea turtles with carapacial ulcers

Introduction

Green sea turtles are endangered marine reptiles. Carapacial ulcers will develop on juvenile green sea turtles during artificial rescue, seriously affecting their health and potentially leading to death.

Methods

To determine the pathogens causing ulcerative carapacial disease, we performed 16S and ITS high-throughput sequencing, and microbial diversity analysis on samples from carapacial ulcers, healthy carapaces, feces, and seawater of juvenile green sea turtles.

Results

Our analysis showed that changes in microbial diversity of green sea turtle feces and seawater were not significantly associated with ulcerative carapacial disease.

Discussion

Psychrobacter sp. is the dominant species in the carapacial ulcers of green sea turtles. The bacterium is present in both healthy turtles and seawater where carapacial ulcers did not occur and decreasing seawater temperatures are likely responsible for the infection of juvenile green turtles with Psychrobacter sp. This is the first study on carapacial ulcers in captive juvenile green sea turtles. Our research provides theoretical guidance for the prevention and control of carapacial ulcers in captive juvenile green sea turtles.

Phenotypic and Genotypic Characterization of Multidrug-Resistant Enterobacter hormaechei Carrying qnrS Gene Isolated from Chicken Feed in China

Multidrug resistance (MDR) in Enterobacteriaceae including resistance to quinolones is rising worldwide. The plasmid-mediated quinolone resistance (PMQR) gene qnrS is prevalent in Enterobacteriaceae. However, the qnrS gene is rarely found in Enterobacter hormaechei (E. hormaechei). Here, we reported one multidrug resistant E. hormaechei strain M1 carrying the qnrS1 and blaTEM-1 genes. This study was to analyze the characteristics of MDR E. hormaechei strain M1. The E. hormaechei strain M1 was identified as Enterobacter cloacae complex by biochemical assay and 16S rRNA sequencing. The whole genome was sequenced by the Oxford Nanopore method. Taxonomy of the E. hormaechei was based on multilocus sequence typing (MLST). The qnrS with the other antibiotic resistance genes were coexisted on IncF plasmid (pM1). Besides, the virulence factors associated with pathogenicity were also located on pM1. The qnrS1 gene was located between insertion element IS2A (upstream) and transposition element ISKra4 (downstream). The comparison result of IncF plasmids revealed that they had a common plasmid backbone. Susceptibility experiment revealed that the E. hormaechei M1 showed extensive resistance to the clinical antimicrobials. The conjugation transfer was performed by filter membrane incubation method. The competition and plasmid stability assays suggested the host bacteria carrying qnrS had an energy burden. As far as we know, this is the first report that E. hormaechei carrying qnrS was isolated from chicken feed. The chicken feed and poultry products could serve as a vehicle for these MDR bacteria, which could transfer between animals and humans through the food chain. We need to pay close attention to the epidemiology of E. hormaechei and prevent their further dissemination. IMPORTANCE Enterobacter hormaechei is an opportunistic pathogen. It can cause infections in humans and animals. Plasmid-mediated quinolone resistance (PMQR) gene qnrS can be transferred intergenus, which is leading to increase the quinolone resistance levels in Enterobacteriaceae. Chicken feed could serve as a vehicle for the MDR E. hormaechei. Therefore, antibiotic-resistance genes (ARGs) might be transferred to the intestinal flora after entering the gastrointestinal tract with the feed. Furthermore, antibiotic-resistant bacteria (ARB) were also excreted into environment with feces, posing a huge threat to public health. This requires us to monitor the ARB and antibiotic-resistant plasmids in the feed. Here, we demonstrated the characteristics of one MDR E. hormaechei isolate from chicken feed. The plasmid carrying the qnrS gene is a conjugative plasmid with transferability. The presence of plasmid carrying antibiotic-resistance genes requires the maintenance of antibiotic pressure. In addition, the E. hormaechei M1 belonged to new sequence type (ST). These data show the MDR E. hormaechei M1 is a novel strain that requires our further research.

Genomic Analysis of a Highly Virulent NDM-1-Producing Escherichia coli ST162 Infecting a Pygmy Sperm Whale (Kogia breviceps) in South America

Carbapenemase-producing Enterobacterales are rapidly spreading and adapting to different environments beyond hospital settings. During COVID-19 lockdown, a carbapenem-resistant NDM-1-positive Escherichia coli isolate (BA01 strain) was recovered from a pygmy sperm whale (Kogia breviceps), which was found stranded on the southern coast of Brazil. BA01 strain belonged to the global sequence type (ST) 162 and carried the bla_NDM–1, besides other medically important antimicrobial resistance genes. Additionally, genes associated with resistance to heavy metals, biocides, and glyphosate were also detected. Halophilic behavior (tolerance to > 10% NaCl) of BA01 strain was confirmed by tolerance tests of NaCl minimal inhibitory concentration, whereas halotolerance associated genes katE and nhaA, which encodes for catalase and Na⁺/H⁺ antiporter cytoplasmic membrane, respectively, were in silico confirmed. Phylogenomics clustered BA01 with poultry- and human-associated ST162 lineages circulating in European and Asian countries. Important virulence genes, including the astA (a gene encoding an enterotoxin associated with human and animal infections) were detected, whereas in vivo experiments using the Galleria mellonella infection model confirmed the virulent behavior of the BA01 strain. WHO critical priority carbapenemase-producing pathogens in coastal water are an emerging threat that deserves the urgent need to assess the role of the aquatic environment in its global epidemiology.

Bacterial and fungal pathogens in granulomatous lesions of Chelonia mydas in a significant foraging ground off southern Brazil

The green sea turtle Chelonia mydas inhabit near-shore areas exposed to threatening anthropogenic activities. The granulomatous lesions in these animals may indicate infectious diseases that can be associated with environmental contamination and hazards to human health. This study aimed to characterize the granulomatous inflammation associated with bacterial and fungal infection in C. mydas off Paraná state. From September 2015 to February 2019, systematic monitoring was performed by the Santos Basin Beach Monitoring Project for sea turtles'carcasses recovery, necropsy, and cause of death diagnosis. The tissue samples were fixed in buffered formalin 10% for histochemical analysis and frozen for molecular analysis to fungi detection (Internal Transcribed Spacer region of the nuclear rDNA) and bacteria detection (16S ribosomal gene). From a total of 270 C. mydas, granulomatous lesions were observed in different organs of 63 (23.3%) individuals. The histological analysis indicated lesions in 94 organs, affecting most respiratory and digestive systems. Bacteria were identified in 25 animals, including an acid-fast bacteria detected in one animal, and fungi in 24 C. mydas. The fungi species included the genus Candida (Candida zeylanoides, n = 3), Yarrowia (Yarrowia lipolytica, n = 9; Yarrowia deformans, n = 5; and Yarrowia divulgata, n = 1), and Cladosporium anthropophilum (n = 1). No species of bacteria was identified by molecular testing. All fungi species identified are saprobic, some are important to food and medical industries, but are also pathogens of humans and other animals. Therefore, long-term monitoring of these pathogens and the C. mydas health may indicate changes in environmental quality, possible zoonotic diseases, and their effects.

Phylogeographical Landscape of Citrobacter portucalensis Carrying Clinically Relevant Resistomes

During a surveillance study conducted to assess the occurrence and genomic landscape of critical priority pathogens circulating at the human-animal-environment interface in Brazil, as part of the Grand Challenges Explorations-New Approaches to Characterize the Global Burden of Antimicrobial Resistance program, two multidrug-resistant (MDR) Citrobacter portucalensis carrying bla_CTX-M-15 extended-spectrum β-lactamase (ESBL) genes, isolated from green sea turtles, were characterized. Genomic and phylogeographical analysis of C. portucalensis genomes available in public databases revealed the intercontinental dissemination of clades carrying different arrays of clinically relevant genes conferring resistance to carbapenems, broad-spectrum cephalosporins, cephamycins, aminoglycosides and fluoroquinolones, disinfectants, and heavy metals. Our observations suggest that C. portucalensis could be emerging as critical priority bacteria of both public and One Health importance worldwide.

IMPORTANCE The global spread of antibiotic-resistant priority pathogens beyond the hospital setting is a critical issue within a One Health context that integrates the human-animal-environment interfaces. On the other hand, next-generation sequencing technologies along with user-friendly and high-quality bioinformatics tools have improved the identification of bacterial species, and bacterial resistance surveillance. The novel Citrobacter portucalensis species was proposed in 2017 after taxonomic reclassification and definition of the strain A60^T isolated in 2008. Here, we presented genomic data showing the occurrence of multidrug-resistant C. portucalensis isolates carrying bla_CTX-M-15 ESBL genes in South America. Additionally, we observed the intercontinental dissemination of clades harboring a broad resistome to clinically relevant antibiotics. Therefore, these findings highlight that C. portucalensis is a global MDR bacteria that carries intrinsic bla_CMY- and qnrB-type genes and has become a critical priority pathogen due to the acquisition of clinically relevant resistance determinants, such as ESBL and carbapenemase-encoding genes.

Diversity and Function of Wolf Spider Gut Microbiota Revealed by Shotgun Metagenomics

Wolf spiders (Lycosidae) are crucial component of integrated pest management programs and the characteristics of their gut microbiota are known to play important roles in improving fitness and survival of the host. However, there are only few studies of the gut microbiota among closely related species of wolf spider. Whether wolf spiders gut microbiota vary with habitats remains unknown. Here, we used shotgun metagenomic sequencing to compare the gut microbiota of two wolf spider species, Pardosa agraria and P. laura from farmland and woodland ecosystems, respectively. The results show that the gut microbiota of Pardosa spiders is similar in richness and abundance. Approximately 27.3% of the gut microbiota of P. agraria comprises Proteobacteria, and approximately 34.4% of the gut microbiota of P. laura comprises Firmicutes. We assembled microbial genomes and found that the gut microbiota of P. laura are enriched in genes for carbohydrate metabolism. In contrast, those of P. agraria showed a higher proportion of genes encoding acetyltransferase, an enzyme involved in resistance to antibiotics. We reconstructed three high-quality and species-level microbial genomes: Vulcaniibacterium thermophilum, Anoxybacillus flavithermus and an unknown bacterium belonging to the family Simkaniaceae. Our results contribute to an understanding of the diversity and function of gut microbiota in closely related spiders.

Comparative genomic characterization of multidrug-resistant Citrobacter spp. strains in Fennec fox imported to China

BACKGROUND

To investigate the antimicrobial profiles and genomic characteristics of MDR-Citrobacter spp. strains isolated from Fennec fox imported from Sudan to China.

METHODS

Four Citrobacter spp. strains were isolated from stool samples. Individual fresh stool samples were collected and subsequently diluted in phosphate buffered saline as described previously. The diluted fecal samples were plated on MacConkey agar supplemented with 1 mg/l cefotaxime and incubated for 20 h at 37 °C. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) was used for identification. Antimicrobial susceptibility testing was performed using the broth microdilution method. Whole-genome sequencing was performed on an Illumina Novaseq-6000 platform. Acquired antimicrobial resistance genes and plasmid replicons were detected using ResFinder 4.1 and PlasmidFinder 1.3, respectively. Comparative genomic analysis of 277 Citrobacter genomes was also performed.

RESULTS

Isolate FF141 was identified as Citrobacter cronae while isolate FF371, isolate FF414, and isolate FF423 were identified as Citrobacter braakii. Of these, three C. braakii isolates were further confirmed to be extended-spectrum β-lactamases (ESBL)-producer. All isolates are all multidrug resistance (MDR) with resistance to multiple antimicrobials. Plasmid of pKPC-CAV1321 belong to incompatibility (Inc) group. Comparative genomics analysis of Citrobacter isolates generated a large core-genome. Genetic diversity was observed in our bacterial collection, which clustered into five main clades. Human, environmental and animal Citrobacter isolates were distributed into five clusters.

CONCLUSIONS

To our knowledge, this is the first investigation of MDR-Citrobacter from Fennec Fox. Our phenotypic and genomic data further underscore the threat of increased ESBL prevalence in wildlife and emphasize that increased effort should be committed to monitoring the potentially rapid dissemination of ESBL-producers with one health perspective.

Testudines as Sentinels for Monitoring the Dissemination of Antibiotic Resistance in Marine Environments: An Integrative Review

Dissemination of antibiotic resistance (AR) in marine environments is a global concern with a propensity to affect public health and many ecosystems worldwide. We evaluated the use of sea turtles as sentinel species for monitoring AR in marine environments. In this field, antibiotic-resistant bacteria have been commonly identified by using standard culture and sensitivity tests, leading to an overrepresentation of specific, culturable bacterial classes in the available literature. AR was detected against all major antibiotic classes, but the highest cumulative global frequency of resistance in all represented geographical sites was against the beta-lactam class by a two-fold difference compared to all other antibiotics. Wastewater facilities and turtle rehabilitation centres were associated with higher incidences of multidrug-resistant bacteria (MDRB) accounting for an average of 58% and 49% of resistant isolates, respectively. Furthermore, a relatively similar prevalence of MDRB was seen in all studied locations. These data suggest that anthropogenically driven selection pressures for the development of AR in sea turtles and marine environments are relatively similar worldwide. There is a need, however, to establish direct demonstrable associations between AR in sea turtles in their respective marine environments with wastewater facilities and other anthropogenic activities worldwide.

Wide Distribution and Specific Resistance Pattern to Third-Generation Cephalosporins of Enterobacter cloacae Complex Members in Humans and in the Environment in Guadeloupe (French West Indies)

Species belonging to Enterobacter cloacae complex have been isolated in numerous environments and samples of various origins. They are also involved in opportunistic infections in plants, animals, and humans. Previous prospection in Guadeloupe (French West Indies) indicated a high frequency of E. cloacae complex strains resistant to third-generation cephalosporins (3GCs) in a local lizard population (Anolis marmoratus), but knowledge of the distribution and resistance of these strains in humans and the environment is limited. The aim of this study was to compare the distribution and antibiotic susceptibility pattern of E. cloacae complex members from different sources in a “one health” approach and to find possible explanations for the high level of resistance in non-human samples. E. cloacae complex strains were collected between January 2017 and the end of 2018 from anoles, farm animals, local fresh produce, water, and clinical human samples. Isolates were characterized by the heat-shock protein 60 gene-fragment typing method, and whole-genome sequencing was conducted on the most frequent clusters (i.e., C-VI and C-VIII). The prevalence of resistance to 3GCs was relatively high (56/346, 16.2%) in non-human samples. The associated resistance mechanism was related to an AmpC overproduction; however, in human samples, most of the resistant strains (40/62) produced an extended-spectrum beta-lactamase. No relation was found between resistance in isolates from wild anoles (35/168) and human activities. Specific core-genome phylogenetic analysis highlighted an important diversity in this bacterial population and no wide circulation among the different compartments. In our setting, the mutations responsible for resistance to 3GCs, especially in ampD, were diverse and not compartment specific. In conclusion, high levels of resistance in non-human E. cloacae complex isolates are probably due to environmental factors that favor the selection of these resistant strains, and this will be explored further.

Levofloxacin in veterinary medicine: a literature review

A potent third-generation antimicrobial fluoroquinolone drug, levofloxacin was introduced into human clinical practice in 1993. Levofloxacin is also used in veterinary medicine, however its use is limited: it is completely banned for veterinary use in the EU, and used extralabel in only companion animals in the USA. Since its introduction to clinical practice, many studies have been published on levofloxacin in animal species, including pharmacokinetic studies, tissue drug depletion, efficacy, and animal microbial isolate susceptibility to levofloxacin. This literature overview highlights the most clinically relevant and scientifically important levofloxacin studies linked to the field of veterinary medicine.

Detection of multi-drug resistance and AmpC β-lactamase/extended-spectrum β-lactamase genes in bacterial isolates of loggerhead sea turtles (Caretta caretta) from the Mediterranean Sea

Sea turtles are useful sentinels to monitor the dissemination of antimicrobial resistance (AMR) in the marine coastal ecosystems. Forty Gram negative bacteria were isolated from wounds of 52 injured Caretta caretta, living in the Mediterranean Sea. Bacteria were identified using 16S rRNA gene sequencing and tested for susceptibility to 15 antibiotics. In addition, NGS amplicon sequencing was performed to detect the presence of AmpC β-lactamase genes (bla_AmpC) and extended-spectrum β-lactamase (ESBL) genes (bla_CTX-M,bla_SHV,bla_TEM). Seventy-five percent of the isolates (30/40 isolates) exhibited multidrug resistance (MDR) phenotypes and 32.5% (13/40 isolates) were confirmed to be positive for at least one gene. The variants of ESBLs genes were bla_CTX-M-3,bla_TEM-236 and bla_SHV-12. Variants of the bla_AmpCβ-lactamase gene i.e., bla_ACT-24, bla_ACT-2, bla_ACT-17, bla_DHA-4 and bla_CMY-37, were also detected. In addition, 4 isolates were found simultaneously harboring CTX and AmpC genes while 2 strains harbored 3 genes (bla_{ACT-2+TEM-236+SHV-12}, and bla_{CTX-M-3+ACT-24+TEM-236}).

Dissemination of Extended-Spectrum-β-Lactamase-Producing Enterobacter cloacae Complex from a Hospital to the Nearby Environment in Guadeloupe (French West Indies): ST114 Lineage Coding for a Successful IncHI2/ST1 Plasmid

Wastewater treatment plants are considered hot spots for antibiotic resistance. Most studies have addressed the impact on the aquatic environment, as water is an important source of anthropogenic pollutants.

Wastewater treatment plants are considered hot spots for antibiotic resistance. Most studies have addressed the impact on the aquatic environment, as water is an important source of anthropogenic pollutants. Few investigations have been conducted on terrestrial animals living near treatment ponds. We isolated extended-spectrum-β-lactamase Enterobacter cloacae complex-producing strains from 35 clinical isolates, 29 samples of wastewater, 19 wild animals, and 10 domestic animals living in the hospital sewers and at or near a wastewater treatment plant to study the dissemination of clinically relevant resistance through hospital and urban effluents. After comparison of the antibiotic-resistant profiles of E. cloacae complex strains, a more detailed analysis of 41 whole-genome-sequenced strains demonstrated that the most common sequence type, ST114 (n = 20), was present in human (n = 9) and nonhuman (n = 11) samples, with a close genetic relatedness. Whole-genome sequencing confirmed local circulation of this pathogenic lineage in diverse animal species. In addition, nanopore sequencing and specific synteny of an IncHI2/ST1/bla_CTX-M-15 plasmid recovered on the majority of these ST114 clones (n = 18) indicated successful worldwide diffusion of this mobile genetic element.

Endophytic Lifestyle of Global Clones of Extended-Spectrum β-Lactamase-Producing Priority Pathogens in Fresh Vegetables: a Trojan Horse Strategy Favoring Human Colonization?

The global spread of antibiotic-resistant bacteria and their resistance genes is a critical issue that is no longer restricted to hospital settings, but also represents a growing problem involving environmental and food safety. In this study, we have performed a microbiological and genomic investigation of critical priority pathogens resistant to broad-spectrum cephalosporins and showing endophytic lifestyles in fresh vegetables sold in a country with high endemicity of extended-spectrum β-lactamases (ESBLs). We report the isolation of international high-risk clones of CTX-M-15-producing Escherichia coli, belonging to clonal complexes CC38 and CC648, and Klebsiella pneumoniae of complex CC307 from macerated tissue of surface-sterilized leaves of spinach, cabbage, arugula, and lettuce. Regardless of species, all ESBL-positive isolates were able to endophytically colonize common bean (Phaseolus vulgaris) seedlings, showed resistance to acid pH, and had a multidrug-resistant (MDR) profile to clinically relevant antibiotics (i.e., broad-spectrum cephalosporins, aminoglycosides, and fluoroquinolones). Genomic analysis of CTX-M-producing endophytic Enterobacterales revealed a wide resistome (antibiotics, biocides, disinfectants, and pesticides) and virulome, and genes for endophytic fitness and for withstanding acidic conditions. Transferable IncFIB and IncHI2A plasmids carried bla _CTX-M-15 genes and, additionally, an IncFIB plasmid (named pKP301cro) also harbored genes encoding resistance to heavy metals. These data support the hypothesis that fresh vegetables marketed for consumption can act as a figurative Trojan horse for the hidden spread of international clones of critical WHO priority pathogens producing ESBLs, and/or their resistance genes, to humans and other animals, which is a critical issue within a food safety and broader public and environmental health perspective.IMPORTANCE Extended-spectrum β-lactamases (ESBL)-producing Enterobacterales are a leading cause of human and animal infections, being classified as critical priority pathogens by the World Health Organization. Epidemiological studies have shown that spread of ESBL-producing bacteria is not a problem restricted to hospitals, but also represents a growing problem involving environmental and food safety. In this regard, CTX-M-type β-lactamases have become the most widely distributed and clinically relevant ESBLs worldwide. Here, we have investigated the occurrence and genomic features of ESBL-producing Enterobacterales in surface-sterilized fresh vegetables. We have uncovered that international high-risk clones of CTX-M-15-producing Escherichia coli and Klebsiella pneumoniae harboring a wide resistome and virulome, carry additional genes for endophytic fitness and resistance to acidic conditions. Furthermore, we have demonstrated that these CTX-M-15-positive isolates are able to endophytically colonize plant tissues. Therefore, we believe that fresh vegetables can act as a figurative Trojan horse for the hidden spread of critical priority pathogens exhibiting endophytic lifestyles.

Colistin-resistant Enterobacter kobei carrying mcr-9.1 and blaCTX-M-15 infecting a critically endangered franciscana dolphin (Pontoporia blainvillei), Brazil

The emergence of mobile mcr genes mediating resistance to colistin is a critical public health issue that has hindered the treatment of serious infections caused by multidrug-resistant pathogens in humans and other animals. We report the emergence of the mcr-9.1 gene in a polymyxin-resistant extended-spectrum β-lactamase (ESBL)-producing Enterobacter kobei infecting a free-living franciscana dolphin (Pontoporia blainvillei), threatened with extinction in South America. Genomic analysis confirmed the presence of genes conferring resistance to clinically relevant β-lactam [bla_CTX-M-15 , bla_ACT-9 , bla_OXA-1 and bla_TEM-1B ], aminoglycoside [aac(3)-IIa, aadA1, aph(3'')-Ib and aph(6)-Id], trimethoprim [dfrA14], tetracycline [tetA], quinolone [aac(6')-Ib-cr and qnrB1], fosfomycin [fosA], sulphonamide [sul2] and phenicol [catA1 and catB3] antibiotics. The identification of mcr-9.1 in a CTX-M-15-producing pathogen infecting a critically endangered animal is of serious concern, which should be interpreted as a sign of further spread of critical priority pathogens and their resistance genes in threatened ecosystems.

Macroscopic and Histopathologic Findings From a Mass Stranding of Rough-Toothed Dolphins (Steno bredanensis) in 2005 on Marathon Key, Florida, USA

On March 2, 2005 ~70 rough-toothed dolphins (Steno bredanensis) mass stranded along mud flats and associated canals on the Atlantic Ocean side of Marathon Key, Florida. Forty-six were necropsied and placed into two groups for analysis: Group-1 animals (N = 34; 65%) that died prior to medical intervention and rehabilitative efforts and Group-2 animals (N = 12; 35%) that died in rehabilitation. Thirty-four animals were females (18 adults, 5 juvenile/subadult, 7 calves, and 4 of undetermined age) and 12 were males (6 adults, 4 juvenile/subadults, 1 calf, and 1 of undetermined age). Body condition overall was fair to good in Group-1 and fair to poor in Group-2. Lesions were observed in multiple body systems. Greater than 90% of animals in both groups had respiratory lesions. Verminous sinusitis and bronchopneumonia were 2–3 times more prevalent in Group-2. Capture/exertional rhabdomyolysis was observed in Group-2 (42%). Vacuolar hepatopathies were observed in both groups including hepatic lipidosis (Group-1) and mixed etiologies (Group-2). Pancreatic and gastrointestinal tract pathologies were prevalent in Group-2 animals 56 and 75%, respectively, and included gastritis, gastric ulceration, enterocolitis, pancreatic atrophy, and pancreatitis related to physiologic stress. Group-2 more frequently had evidence of hemorrhagic diathesis present which included increased extramedullary hematopoiesis in various organs, increased hemosiderosis, and hemorrhage and hemorrhagic drainage in various organs. Central nervous system disease, primarily edema, and mild inflammation were equally prevalent. Renal proteinuria, tubular necrosis, and pigmentary deposition were observed in Group-2. Dental attrition was observed in ~40% of the groups. Gammaherpesviral-associated pharyngeal plaques were observed in 46 and 54% of Group-1 and 2 animals, respectively. Other lesions observed were mild and incidental with a frequency rate <20%. The findings from this Steno stranding provide a unique window into baseline individual and population clinical conditions and additional perspective into potential clinical sequelae of rehabilitation efforts.

International clones of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli in peri-urban wild animals, Brazil

CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli clones have been increasingly reported worldwide. In this regard, although discussions of transmission routes of these bacteria are in evidence, molecular data are lacking to elucidate the epidemiological impacts of ESBL producers in wild animals. In this study, we have screened 90 wild animals living in a surrounding area of São Paulo, the largest metropolitan city in South America, to monitor the presence of multidrug-resistant (MDR) Gram-negative bacteria. Using a genomic approach, we have analysed eight ceftriaxone-resistant E. coli. Resistome analyses revealed that all E. coli strains carried blaCTX-M -type genes, prevalent in human infections, besides other clinically relevant resistance genes to aminoglycosides, β-lactams, phenicols, tetracyclines, sulphonamides, trimethoprim, fosfomycin and quinolones. Additionally, E. coli strains belonged to international sequence types (STs) ST38, ST58, ST212, ST744, ST1158 and ST1251, and carried several virulence-associated genes. Our findings suggest spread and adaptation of international clones of CTX-M-producing E. coli beyond urban settings, including wildlife from shared environments.