Environment, animals, and food as reservoirs of antibiotic-resistant bacteria for humans: One health or more?

Antimicrobial resistance (AMR) is a major public health challenge. For several years, AMR has been addressed through a One Health approach that links human health, animal health, and environmental quality. In this review, we discuss AMR in different reservoirs with a focus on the environment. Anthropogenic activities produce effluents (sewage, manure, and industrial wastes) that contaminate soils and aquatic environments with antibiotic-resistant bacteria (ARB), antibiotic-resistant genes (ARGs), and selective agents such as antibiotics, biocides, and heavy metals. Livestock treated with antibiotics can also contaminate food with ARB. In high-income countries (HICs), effective sanitation infrastructure and limited pharmaceutical industries result in more controlled discharges associated with human activities. Hence, studies using genome-based typing methods have revealed that, although rare inter-reservoir transmission events have been reported, human acquisition in HICs occurs primarily through person-to-person transmission. The situation is different in low- and middle-income countries (LMICs) where high population density, poorer sanitation and animal farming practices are more conducive to inter-reservoir transmissions. In addition, environmental bacteria can be a source of ARGs that, when transferred to pathogenic species under antibiotic selection pressure in environmental hotspots, produce new antibiotic-resistant strains that can potentially spread in the human community through human-to-human transmission. The keys to reducing AMR in the environment are (i) better treatment of human waste by improving wastewater treatment plants (WWTPs) in HICs and improving sanitation infrastructure in LMICs, (ii) reducing the use of antibiotics by humans and animals, (iii) prioritizing the use of less environmentally harmful antibiotics, and (iv) better control of pharmaceutical industry waste.

Emergence of NDM-producing Enterobacterales infections in companion animals from Argentina

Antimicrobial resistance is considered one of the most critical threat for both human and animal health. Recently, reports of infection or colonization by carbapenemase-producing Enterobacterales in companion animals had been described. This study report the first molecular characterization of NDM-producing Enterobacterales causing infections in companion animals from Argentina. Nineteen out of 3662 Enterobacterales isolates analyzed between October 2021 and July 2022 were resistant to carbapenemes by VITEK2C and disk diffusion method, and suspected to be carbapenemase-producers. Ten isolates were recovered from canine and nine from feline animals. Isolates were identified as K. pneumoniae (n = 9), E. coli (n = 6) and E. cloacae complex (n = 4), and all of them presented positive synergy among EDTA and carbapenems disks, mCIM/eCIM indicative of metallo-carbapenemase production and were also positive by PCR for blaNDM gene. NDM variants were determined by Sanger sequencing method. All 19 isolates were resistant to β-lactams and aminoglycosides but remained susceptible to colistin (100%), tigecycline (95%), fosfomycin (84%), nitrofurantoin (63%), minocycline (58%), chloramphenicol (42%), doxycycline (21%), enrofloxacin (5%), ciprofloxacin (5%) and trimethoprim/sulfamethoxazole (5%). Almost all isolates (17/19) co-harbored blaCTX-M plus blaCMY, one harbored blaCTX-M alone and the remaining blaCMY. E. coli and E. cloacae complex isolates harbored blaCTX-M-1/15 or blaCTX-M-2 groups, while all K. pneumoniae harbored only blaCTX-M-1/15 genes. All E. coli and E. cloacae complex isolates harbored blaNDM-1, while in K. pneumoniae blaNDM-1 (n = 6), blaNDM-5 (n = 2), and blaNDM-1 plus blaNDM-5 (n = 1) were confirmed. MLST analysis revealed the following sequence types by species, K. pneumoniae: ST15 (n = 5), ST273 (n = 2), ST11, and ST29; E. coli: ST162 (n = 3), ST457, ST224, and ST1196; E. cloacae complex: ST171, ST286, ST544 and ST61. To the best of our knowledge, this is the first description of NDM-producing E. cloacae complex isolates recovered from cats. Even though different species and clones were observed, it is remarkable the finding of some major clones among K. pneumoniae and E. coli, as well as the circulation of NDM as the main carbapenemase. Surveillance in companion pets is needed to detect the spread of carbapenem-resistant Enterobacterales and to alert about the dissemination of these pathogens among pets and humans.

Molecular characterization and virulence profile of Klebsiella pneumoniae and Klebsiella oxytoca isolated from ill cats and dogs in Portugal

Klebsiella spp. are important pathogens of humans and companion animals such as cats and dogs, capable of causing severe life-threatening diseases. The aim of this study was to characterize the molecular and phenotypic properties of Klebsiella pneumoniae and Klebsiella oxytoca isolated from ill companion animals by whole genome sequencing, followed by in vitro assessment of biofilm formation and in vivo pathogenicity using the Galleria mellonella model. Two LPS O-types were identified for all the K. pneumoniae isolates tested (O3B and O1/O2v2) and only one for K. oxytoca isolates (OL104), and the most common STs found were ST11 and ST266. Furthermore, a high diversity of K-locus types was found for K. pneumoniae (KL102; KL105; KL31, and KL13). Within K. pneumoniae, one specific O/K/ST-types combination (i.e., KL105-ST11-O1/O2v2) showed results that were of concern, as it exhibited a high inflammatory response at 12 h post-infection in G. mellonella with 80% of the larvae dead at 72 h post-infection. This virulence potential, on the other hand, did not appear to be directly related to the biofilm-forming capacity. Also, virulence and resistance scores obtained for this set of strains did surpass score 1. The present study demonstrated that Klebsiella spp. isolated from companion animals belonging to STs that can cause human infections and present virulence on an invertebrate model. Thus, this study underscores the role of dogs and cats as reservoirs of resistant Klebsiella spp. that could potentially be transmitted to humans.

Emphysematous pyometra and emphysematous hepatitis caused by Klebsiella pneumoniae infection in a diabetic dog

A 14-year-old intact female diabetic dog presented with seizures and hyperglycemic hyperosmolar syndrome. Radiographs revealed gas-filled tubular structures in the right and left caudal abdomen, raising concerns of emphysematous pyometra or small intestinal ileus. Ultrasonography played a pivotal role in confirming emphysematous pyometra, a technique previously documented only once in veterinary practice. This report also presents the first documented case of emphysematous pyometra in a diabetic dog attributed to Klebsiella pneumoniae and complicated by emphysematous hepatitis.

Structural and functional basis of bacteriophage K64-ORF41 depolymerase for capsular polysaccharide degradation of Klebsiella pneumoniae K64

Capsule polysaccharide is an important virulence factor of Klebsiella pneumoniae (K. pneumoniae), which protects bacteria against the host immune response. A promising therapeutic approach is using phage-derived depolymerases to degrade the capsular polysaccharide and expose and sensitize the bacteria to the host immune system. Here we determined the cryo-electron microscopy (cryo-EM) structures of a bacteriophage tail-spike protein against K. pneumoniae K64, ORF41 (K64-ORF41) and ORF41 in EDTA condition (K64-ORF41EDTA), at 2.37 Å and 2.50 Å resolution, respectively, for the first time. K64-ORF41 exists as a trimer and each protomer contains a β-helix domain including a right-handed parallel β-sheet helix fold capped at both ends, an insertion domain, and one β-sheet jellyroll domain. Moreover, our structural comparison with other depolymerases of K. pneumoniae suggests that the catalytic residues (Tyr528, His574 and Arg628) are highly conserved although the substrate of capsule polysaccharide is variable. Besides that, we figured out the important residues involved in the substrate binding pocket including Arg405, Tyr526, Trp550 and Phe669. This study establishes the structural and functional basis for the promising phage-derived broad-spectrum activity depolymerase therapeutics and effective CPS-degrading agents for the treatment of carbapenem-resistant K. pneumoniae K64 infections.

Rapid typing of Klebsiella pneumoniae and Pseudomonas aeruginosa by Fourier-transform Infrared spectroscopy informs infection control in veterinary settings

Introduction

The emergence of multi-drug resistant (MDR) pathogens linked to healthcare-associated infections (HCAIs) is an increasing concern in modern veterinary practice. Thus, rapid bacterial typing for real-time tracking of MDR hospital dissemination is still much needed to inform best infection control practices in a clinically relevant timeframe. To this end, the IR Biotyper using Fourier-Transform InfraRed (FTIR) spectroscopy has the potential to provide fast cluster analysis of potentially related organisms with substantial cost and turnaround time benefits.

Materials and methods

A collection of MDR bacterial isolates (n = 199, comprising 92 Klebsiella pneumoniae and 107 Pseudomonas aeruginosa) obtained from companion animal (i.e., dogs, cats and horses) clinical investigations, faecal and environmental screening from four veterinary facilities between 2012 and 2019 was analysed retrospectively by FTIR spectroscopy. Its performance was compared against MLST extracted from whole genomes of a subset of clustering isolates (proportionally to cluster size) for investigation of potential nosocomial transmission between patients and the surrounding hospital environments.

Results

Concordance between the FTIR and MLST types was overall high for K. pneumoniae (Adjusted Rand Index [ARI] of 0.958) and poor for P. aeruginosa (ARI of 0.313). FTIR K. pneumoniae clusters (n = 7) accurately segregated into their respective veterinary facility with evidence of intra-hospital spread of K. pneumoniae between patients and environmental surfaces. Notably, K. pneumoniae ST147 intensely circulated at one Small Animal Hospital ICU. Conversely, Pseudomonas aeruginosa FTIR clusters (n = 18) commonly contained isolates of diversified hospital source and heterogeneous genetic background (as also genetically related isolates spread across different clusters); nonetheless, dissemination of some clones, such as P. aeruginosa ST2644 in the equine hospital, was apparent. Importantly, FTIR clustering of clinical, colonisation and/or environmental isolates sharing genomically similar backgrounds was seen for both MDR organisms, highlighting likely cross-contamination events that led to clonal dissemination within settings.

Conclusion

FTIR spectroscopy has high discriminatory power for hospital epidemiological surveillance of veterinary K. pneumoniae and could provide sufficient information to support early detection of clonal dissemination, facilitating implementation of appropriate infection control measures. Further work and careful optimisation need to be carried out to improve its performance for typing of P. aeruginosa veterinary isolates.

Occurrence and characteristics of extended-spectrum-β-lactamase- and pAmpC-producing Klebsiella pneumoniae isolated from companion animals with urinary tract infections

This study examined 70 Klebsiella pneumoniae isolates derived from companion animals with urinary tract infections in Taiwan. Overall, 81% (57/70) of the isolates carried extended-spectrum β-lactamase (ESBL) and/or plasmid-encoded AmpC (pAmpC) genes. ESBL genes were detected in 19 samples, with blaCTX-M-1, blaCTX-M-9, and blaSHV being the predominant groups. pAmpC genes were detected in 56 isolates, with blaCIT and blaDHA being the predominant groups. Multilocus sequence typing revealed that sequence types (ST)11, ST15, and ST655 were prevalent. wabG, uge, entB, mrkD, and fimH were identified as primary virulence genes. Two isolates demonstrated a hypermucoviscosity phenotype in the string test. Antimicrobial susceptibility testing exhibited high resistance to β-lactams and fluoroquinolones in ESBL-positive isolates but low resistance to aminoglycosides, sulfonamides, and carbapenems. Isolates carrying pAmpC genes exhibited resistance to penicillin-class β-lactams. These findings provide valuable insights into the role of K. pneumoniae in the context of the concept of One Health.

Antimicrobial activity of phenyllactic acid against Klebsiella pneumoniae and its effect on cell wall membrane and genomic DNA

As Klebsiella pneumoniae (KP) has acquired high levels of resistance to multiple antibiotics, it is considered a worldwide pathogen of concern, and substitutes for traditional antibiotics are urgently needed. 3-Phenyllactic acid (PLA) has been reported to have antimicrobial activity against food-borne bacteria. However, there was no experiment evidence for the exact antibacterial effect and mechanism of PLA kills pathogenic KP. In this study, the Oxford cup method indicated that PLA is effective to KP with a minimum inhibitory concentration of 2.5 mg/mL. Furthermore, PLA inhibited the growth and biofilm formation of in a time- and concentration-dependent manner. In vivo, PLA could significantly increase the survival rate of infected mice and reduce the pathological tissue damage. The antibacterial mode of PLA against KP was further explored. Firstly, scanning electron microscopy illustrated the disruption of cellular ultrastructure caused by PLA. Secondly, measurement of leaked alkaline phosphatase demonstrated that PLA disrupted the cell wall integrity of KP and flow cytometry analysis with propidium iodide staining suggested that PLA damaged the cell membrane integrity. Finally, the results of fluorescence spectroscopy and agarose gel electrophoresis demonstrated that PLA bound to genomic DNA and initiated its degradation. The anti-KP mode of action of PLA was attributed to the destruction of the cell wall, membrane, and genomic DNA binding. These findings suggest that PLA has great potential applications as antibiotic substitutes in feed additives against KP infection in animals.

Serotyping and molecular profiles of virulence-associated genes among Klebsiella pneumoniae isolates from teaching hospitals of Ardabil, Iran: A cross-sectional study

Background and Aims

Klebsiella pneumoniae is a Gram-negative bacterium that colonized various organs. This bacterium is associated with different community-acquired and hospital-acquired infections. The present study aims to assess the capsular serotypes and frequency of virulence-associated genes in K. pneumoniae isolates from teaching hospitals in Ardabil, Iran.

Methods

From October 1, 2019, to November 31, 2021, different clinical samples were collected and K. pneumoniae isolates were diagnosed using conventional biochemical tests. The final identification of K. pneumoniae was performed through the polymerase chain reaction (PCR) method using a specific primer targeting the khe gene. The PCR method was employed to confirm the presence of virulence-associated genes and aerobactin, and the main capsular serotypes based on the specific primers.

Results

Of all 100 K. pneumoniae isolates, 4% and 2% were typeable with K5 and K2 primers, respectively. In addition, entB (94%), fimH (91%), and wcaG (87%) had the highest frequency among the virulence-associated genes. 24% of K. pneumoniae isolates harbored the entB-wcaG-fimH genes simultaneously. Moreover, 50% of capsular serotype 5 harbored the ybts-mrkD-entB-wcaG-fimH genes simultaneously.

Conclusion

The findings revealed that 6% of all K. pneumoniae isolates were typeable, distributed in the two serotypes K5 and K2. Most K. pneumoniae isolates were positive for multiple types of virulence genes. Identifying bacterial virulence genes aids in molecular detection, assay development, and therapeutic pathways.

Antimicrobial resistance patterns of Acinetobacter baumannii and Klebsiella pneumoniae isolated from dogs presented at a veterinary academic hospital in South Africa

Background

Acinetobacter baumannii and Klebsiella pneumoniae are opportunistic bacterial pathogens responsible for hospital-acquired infections in veterinary medicine. Infection with these bacteria always requires urgent antimicrobial therapy. However, there is no evidence of studies that have investigated the antimicrobial drug resistance profile of these organisms in a veterinary setting in South Africa. This study investigated the antimicrobial resistance (AMR) patterns of A. baumannii and K. pneumoniae from clinical specimens obtained from dogs presented at a veterinary academic hospital. The findings of this study contribute to an improved understanding of the AMR profile of these bacteria in veterinary medicine.

Materials and Methods

Retrospective data of clinical samples from dogs that were positive for A. baumannii and K. pneumoniae between 2007 and 2013 were used in this study. The antimicrobial susceptibility of the isolates was determined using the disk diffusion method following the Clinical and Laboratory Standards Institute guidelines. The A. baumannii isolates were subjected to a panel of 20 antibiotics, while K. pneumoniae isolates were subjected to a panel of 22 antibiotics. Data were analyzed using descriptive statistics and presented using tables and figures.

Results

Twenty (n = 20) A. baumannii isolates were isolated from bronchoalveolar lavage, foreign objects, bone, urine, skin, blood, ear, nasal, and oral cavity. Almost all A. baumannii (95%, 19/20) isolates were resistant to at least one antibiotic, and 60% (12/20) were multidrug-resistant (MDR). Klebsiella pneumoniae (n = 56) was isolated from urine, foreign objects, abscesses, ears, eyes, tracheal aspirations, bronchoalveolar lavages, eyes, abdominal aspirates, anal glands, bones, and intestinal and lung biopsies. All K. pneumoniae (100%, 56/56) isolates were resistant to at least one antibiotic, and 98% (55/56) were MDR.

Conclusion

Both A. baumannii and K. pneumoniae were isolated in various clinical tissue samples and exhibited a high prevalence of resistance to multiple antibiotics. In addition, these bacteria exhibited a high prevalence of resistance to β-lactam compared to other classes of antibiotics, which is likely to impact treatment options and patient prognosis.

Do post-surgical multiresistant urinary infections occur in horses? Case of unilateral pyelonephritis caused by extended-spectrum beta-lactamase-producing bacteria as a complication of cystotomy

Pyelonephritis is a serious condition that is rarely described in horses. In contrast, urinary tract infections are common in humans and small animals, and multi-drug-resistant urinary infections are an emerging threat. In this report, we describe a horse with unilateral pyelonephritis caused by extended-spectrum beta-lactamase-producing bacteria belonging to the Enterobacter cloacae complex. [Correction added on 9 August 2023, after first online publication: The preceding sentence was corrected.] An 11-year-old Swedish warmblood gelding was diagnosed with a cystolith and a cystotomy through an open left para-inguinal approach was performed. Seven days after surgery the horse presented with pyrexia, dullness and colic. Diagnostic testing and renal transabdominal ultrasonography confirmed the presence of a right-sided pyelonephritis. Culture and antimicrobial susceptibility testing revealed a pure growth of extended-spectrum beta-lactamases-producing E. cloacae complex bacteria with resistance against beta-lactams, aminoglycoside and trimethoprim-sulphonamide classes. Treatment included prolonged oral antimicrobials according to susceptibility testing results (enrofloxacin), judicious use of non-steroidal anti-inflammatory drugs, fluid therapy and gastric ulcer prophylaxis. The horse recovered successfully and is currently in good health (follow-up of 5 years). Once the infection resolved, unilateral renal scarring occurred. Multidrug-resistant upper-urinary infections occur in horses and should be considered in a post-surgical patient that develops fever. Early diagnosis, urine bacterial culturing and antimicrobial susceptibility testing were crucial in this case to successful management.

Whole-Genome Sequencing and Comparative Genomics Analysis of a Newly Emerged Multidrug-Resistant Klebsiella pneumoniae Isolate of ST967

Klebsiella pneumoniae is a common cause of hospital- and community-acquired infections globally, yet its population structure remains unknown for many regions, particularly in low- and middle-income countries (LMICs). Here, we report for the first-time whole-genome sequencing (WGS) of a multidrug-resistant K. pneumoniae isolate, ARM01, recovered from a patient in Armenia. Antibiotic susceptibility testing revealed that ARM01 was resistant to ampicillin, amoxicillin-clavulanic acid, ceftazidime, cefepime, norfloxacin, levofloxacin, and chloramphenicol. Genome sequencing analysis revealed that ARM01 belonged to sequence type 967 (ST967), capsule type K18, and antigen type O1. ARM01 carried 13 antimicrobial resistance (AMR) genes, including blaSHV-27, dfrA12, tet(A), sul1, sul2, catII.2, mphA, qnrS1, aadA2, aph3-Ia, strA, and strB and the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-15, but only one known virulence factor gene, yagZ/ecpA, and one plasmid replicon, IncFIB(K)(pCAV1099-114), were detected. The plasmid profile, AMR genes, virulence factors, accessory gene profile, and evolutionary analyses of ARM01 showed high similarity to isolates recovered from Qatar (SRR11267909 and SRR11267906). The date of the most recent common ancestor (MRCA) of ARM01 was estimated to be around 2017 (95% confidence interval [CI], 2017 to 2018). Although in this study, we report the comparative genomics analysis of only one isolate, it emphasizes the importance of genomic surveillance for emerging pathogens, urging the need for implementation of more effective infection prevention and control practices. IMPORTANCE Whole-genome sequencing and population genetics analysis of K. pneumoniae are scarce from LMICs, and none has been reported for Armenia. Multilevel comparative analysis revealed that ARM01 (an isolate belonging to a newly emerged K. pneumoniae ST967 lineage) was genetically similar to two isolates recovered from Qatar. ARM01 was resistant to a wide range of antibiotics, reflecting the unregulated usage of antibiotics (in most LMICs, antibiotic use is typically unregulated.) Understanding the genetic makeup of these newly emerging lineages will aid in optimizing antibiotic use for patient treatment and contribute to the worldwide efforts of pathogen and AMR surveillance and implementation of more effective infection prevention and control strategies.

Exploring the prevalence and antibiotic resistance profile of Klebsiella pneumoniae and Klebsiella oxytoca isolated from clinically ill companion animals from North of Portugal

Klebsiella spp. is an important pathogen in humans and animals and due to the indiscriminate use of antibiotics, its prevalence and antibiotic resistance has increased in companion animals. The main goal of this study was to investigate the prevalence and antibiotic resistance of Klebsiella spp. isolated from clinically ill cats and dogs admitted in veterinary clinics in the North of Portugal. A total of 255 clinical specimens were collected and, after isolation, the identification of Klebsiella strains was performed using the BBL Crystal™ identification system and confirmed by PCR-based sequencing with specific primers. Antibiotic resistance profile was determined through the disc diffusion method. Beta-lactam resistance genes were screened through a multiplex PCR assay. Fifty Klebsiella strains were isolated and, 39 were identified as Klebsiella pneumoniae and 11 as Klebsiella oxytoca. Thirty-one were recovered from dogs and 19 from cats. The Klebsiella isolates were recovered mainly from skin wounds, respiratory tract, and from urine. Fifty percent of K. oxytoca and K. pneumoniae isolates revealed to be Multidrug Resistant (MDR) strains, with most of them positive for the presence of blaTEM-like and blaSHV genes. This data shows that MDR Klebsiella are highly disseminated in companion animals and that extended-spectrum beta-lactamases can be easily found among these isolates. This highlights the potential role of dogs and cats as a reservoir of resistant Klebsiella spp. that have the potential to be transmitted to humans.

Synergistic effect and antibiofilm activity of the antimicrobial peptide K11 with conventional antibiotics against multidrug-resistant and extensively drug-resistant Klebsiella pneumoniae

Introduction

Infections caused by drug-resistant Klebsiella pneumoniae are now a serious problem for public health, associated with high morbidity and mortality due to limited treatment options. Therefore, new antibacterial agents or a combination of agents as the first line of treatment are urgently needed. K11 is a novel antimicrobial peptide (AMP) that has demonstrated in vitro antimicrobial activity against several types of bacteria. Additionally, K11 has previously shown no hemolytic activity. Herein, the antibacterial activity, the synergistic action of K11 in combination with different conventional antibiotics and the antibiofilm activity of K11 against multidrug-resistant (MDR) and extensively drug-resistant (XDR) K. pneumoniae were investigated. Meanwhile, the stability and ability to induce the bacterial resistance of K11 were also tested.

Methods

Fifteen clinical isolates of MDR/XDR K. pneumoniae were used in this study. The minimum inhibitory concentration (MIC) of K11 against these isolates was determined by the broth microdilution method. In vitro synergy between K11 and antibiotics was evaluated using the checkerboard methodology. The antibiofilm activity of K11 against K. pneumoniae strong biofilm producers were explored by the crystal violet staining. The stability in different environments and resistance induction of K11 were evaluated by MIC determination.

Results

The MIC values of K11 against MDR/XDR K. pneumoniae isolates were 8-512 μg/mL. Intriguingly, the synergistic effects were clearly observed for K11 in combination with chloramphenicol, meropenem, rifampicin, or ceftazidime, whereas no synergy was observed when K11 was combined with colistin. Besides, K11 effectively prevented biofilm formation against K. pneumoniae strong biofilm producers in a concentration-dependent manner starting at 0.25×MIC and exerted an enhancing effect when administered in combination with meropenem, chloramphenicol, or rifampicin. Additionally, K11 demonstrated high thermal and wide pH stability along with good stability in serum and physiological salts. Significantly, K. pneumoniae showed no induction of resistance even after prolonged exposure to a sub-inhibitory concentration of K11.

Conclusion

These findings indicate that K11 is a promising candidate with potent antibacterial and antibiofilm activities without inducing resistance and acts synergistically with conventional antibiotics against drug-resistant K. pneumoniae.

Prevalence and risk factors of Klebsiella spp. in milk samples from dairy cows with mastitis-A global systematic review

Introduction

The overall prevalence of Klebsiella spp., a group of important zoonotic pathogens, in the global dairy herds and the risk of cross-species transmission between humans and dairy cows remain to be clarified. This systematic review aimed to determine the prevalence of Klebsiella spp. in milk samples from dairy cows with mastitis worldwide and to assess the factors influencing the prevalence of these strains.

Methods

Qualified studies published from 2007 to 2021 were retrieved from ScienceDirect, Web of Science, PubMed, WanFang Database, China National Knowledge Infrastructure (CNKI), and VIP Chinese Journal Database. Calculations of prevalence and their 95% confidence intervals (CIs) were performed for all the studies using the Freeman-Tukey double arcsine transformation (PFT).

Results

A total of 79,852 milk samples from 55 manuscripts were examined in this meta-analysis, and 2,478 samples were found to be positive for Klebsiella spp. The pooled prevalence estimates worldwide were 7.95% (95% CI: 6.07%-10.06%), with significant heterogeneity (I ² = 98.8%, p = 0). The sampling period of 2013-2020 had a higher (p < 0.05) Klebsiella-positive proportion of milk samples (12.16%, 95% CI: 8.08%-16.90%) than that of 2007-2012 (3.85%, 95% CI: 2.67%-5.21%), indicating that bovine mastitis caused by Klebsiella may become increasingly prevalent. The risk factors for the high prevalence of Klebsiella in milk samples mainly included: economic development level (developing countries; 11.76%, 95% CI: 8.25%-15.77%), mastitis type (CM; 11.99%, 95% CI: 8.62%-15.79%), and population density (>500 per sq km; 10.28%, 95% CI: 2.73%-21.58%). Additionally, a bivariate meta-regression analysis revealed that the multidrug-resistance (MDR) rate of the epidemic strains was also closely related to economic development level (R ² = 78.87%) and population density (R ² = 87.51%).

Discussion

Due to the potential risk of cross-species transmission between humans and cows, the prevalence of mastitis milk-derived Klebsiella and its high MDR rate need to be monitored, especially in developing countries with high population densities.

High prevalence of antimicrobial resistance and multidrug resistance among bacterial isolates from diseased pets: Retrospective laboratory data (2015-2017)

Laboratory surveillance and the monitoring of antimicrobial resistance (AMR) trends and patterns among local isolates have been highly effective in providing comprehensive information for public health decision-making. A total of 396 cases along with 449 specimens were received for antibiotic susceptibility testing at a public university veterinary diagnostic laboratory in Malaysia between 2015 and 2017. Escherichia coli was the most frequently isolated (n = 101, 13%) bacteria, followed by Staphylococcus pseudintermedius (n = 97, 12%) and Streptococcus canis (n = 62, 8%). In cats, S. pseudintermedius isolates were highly resistant to azithromycin (90%), while the E. coli isolates were highly resistant to doxycycline (90%), tetracycline (81%), and cephalexin (75%). About 55% of S. pseudintermedius and 82% of E. coli were multi-drug resistant (MDR). In dogs, S. intermedius isolates were highly resistant to aminoglycosides neomycin (90.9%) and gentamicin (84.6%), and tetracycline (75%). Whereas the E. coli isolates were highly resistant to cephalexin (82.1%) and amoxicillin/clavulanic acid (76.5%). MDR was observed in 60% of S. intermedius and 72% of E. coli from dogs. Generally, the bacterial isolates from cats demonstrated higher levels of resistance to multiple antibiotics compared to those from dogs.

Isolation of Escherichia coli and Klebsiella pneumoniae strains producing extended spectrum β-lactamases from dog urine of the Metropolitan Area of the Aburrá Valley Antioquia-Colombia

Escherichia coli and Klebsiella pneumoniae are the most common pathogens causing urinary tract infections in humans and animals. Close contact between humans and companion animals can facilitate the spread of multidrugresistant pathogens between both species. Objective: To characterize extended-spectrum β-lactamases (ESBL) -producing E. coli and K. pneumoniae isolated from dogs with urinary tract infections in the metropolitan area of Valle del Aburrá (Antioquia, Colombia). Methods: Three-hundred seventy-one urine samples collected from March 2018 to March 2019 in a veterinary clinical laboratory were analyzed. E. coli and K. pneumoniae isolates were detected in chromogenic agar and identified by biochemical tests. Susceptibility testing was performed by disc diffusion and ESBL production was evaluated by the double disk test in all isolates. MIC determination of ESBL-positive isolates were performed on the automated VITEK®2 system. Multiple PCR was used for the detection of CTX-M beta-lactamases (group 1, 2, 9 and 8/25), SHV, TEM and AmpC of plasmid origin in ESBL-positive isolates. Results: In total 22 out 371 isolates were positive for ESBL production by double disc test, 11 E. coli (ESBL-Ec) and 11 K. pneumoniae (ESBL-Kp). The multiple PCR detected CTX-M group 1 in the 22 ESBL-positive isolates. Multi-drug resistance was observed in all ESBL-producing isolates Conclusions:  A high frequency of antibiotic multi-resistance was found in ESBL-Ec and ESBL-Kp. The main ESBL detected was CTX-M group 1, which also prevails in human isolates.

mcr-1 colistin resistance gene sharing between Escherichia coli from cohabiting dogs and humans, Lisbon, Portugal, 2018 to 2020

BackgroundThe emergence of colistin resistance is a One Health antimicrobial resistance challenge worldwide. The close contact between companion animals and humans creates opportunities for transmission and dissemination of colistin-resistant bacteria.AimTo detect potential animal reservoirs of colistin-resistant Escherichia coli and investigate the possible sharing of these bacteria between dogs, cats and their cohabiting humans in the community in Lisbon, Portugal.MethodsA prospective longitudinal study was performed from 2018 to 2020. Faecal samples from dogs and cats either healthy or diagnosed with a skin and soft tissue or urinary tract infection, and their cohabiting humans were screened for the presence of colistin-resistant E. coli. All isolates were tested by broth microdilution against colistin and 12 other antimicrobials. Colistin-resistant isolates were screened for 30 resistance genes, including plasmid-mediated colistin resistance genes (mcr-1 to mcr-9), and typed by multilocus sequence typing. Genetic relatedness between animal and human isolates was analysed by whole genome sequencing.ResultsColistin-resistant E. coli strains harbouring the mcr-1 gene were recovered from faecal samples of companion animals (8/102; 7.8%) and humans (4/125; 3.2%). No difference between control and infection group was detected. Indistinguishable multidrug-resistant E. coli ST744 strains harbouring the mcr-1 gene were found in humans and their dogs in two households.ConclusionsThe identification of identical E. coli strains containing the plasmid-mediated mcr-1 gene in companion animals and humans in daily close contact is of concern. These results demonstrate the importance of the animal-human unit as possible disseminators of clinically important resistance genes in the community setting.

Genomic characterization of a new phage BUCT541 against Klebsiella pneumoniae K1-ST23 and efficacy assessment in mouse and Galleria mellonella larvae

Over the past decades, the spread of multi-drug-resistant Klebsiella pneumoniae (MDR-KP) is becoming a new threat and new effective therapies against this pathogen are needed. Bacteriophage (phage) therapy is considered to be a promising alternative treatment for MDR-KP infections compared with antibacterial drug usage. Here, we reported a new phage BUCT541 which can lyse MDR-KP ST23. The genome of BUCT541 is a double-stranded linear 46,100-bp long DNA molecule with 48% GC content through the Next generation sequencing (NGS) data. A total of 81 open reading frames and no virulence or antimicrobial resistance genes are annotated in the BUCT541 genome. BUCT541 was able to lyse 7 of the 30 tested MDR-KP according to the host range analysis. And the seven sensitive strains belonged to the K. pneumoniae K1-ST23. BUCT541 exhibited high thermal stability (4–70°C) and broad pH tolerance (pH 3-11) in the stability test. The in vivo results showed that BUCT541 (4 × 10⁵ plaque-forming units (PFU)/each) significantly increased the survival rate of K. pneumoniae infected Galleria mellonella from 5.3% to 83.3% within 48 h. Moreover, in the mouse lung infection model, high doses of BUCT541 (2 × 10⁷ PFU/each) cured 100% of BALB/c mice that were infected with K. pneumoniae. After 30 h of treatment with phage BUCT541 of the multiplicity of infection (MOI) = 10, the K. pneumoniae in the lungs of mice was lower than 10⁴ CFU/mL, compared to the control group 10⁹ CFU/mL. Together, these findings indicate that phage BUCT541 holds great promise as an alternative therapy with excellent stability and a wide lysis range for the treatment of MDR-KP ST23 infection.

First Belgian Report of Ertapenem Resistance in an ST11 Klebsiella Pneumoniae Strain Isolated from a Dog Carrying blaSCO-1 and blaDHA-1 Combined with Permeability Defects

Klebsiella pneumoniae of sequence type (ST) 11 is a hyper-epidemic nosocomial clone, which is spreading worldwide among humans and emerging in pets. This is the first report, to the best of our knowledge, of multidrug-resistant (MDR) K. pneumoniae ST11 carrying blaSCO-1 and blaDHA-1, isolated from a four-month-old dog in Belgium. Antimicrobial susceptibility testing (AST) of the isolate, performed via broth microdilution following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines, revealed resistance to eight different classes of antimicrobials, including carbapenems, in particular ertapenem, third-generation cephalosporins and fluoroquinolones. A hybrid approach, combining long- and short-read sequencing, was employed for in silico plasmid characterization, multi-locus sequence typing (MLST) and the identification and localization of antimicrobial resistance (AMR) and virulence-associated genes. Three plasmids were reconstructed from the whole-genome sequence (WGS) data: the conjugative IncFIB(K), the non-mobilizable IncR and the mobilizable but unconjugative ColRNAI. The IncFIB(K) plasmid carried the blaSCO-1 gene, whereas IncR carried blaDHA-1, both alongside several other antimicrobial resistance genes (ARGs). No virulence genes could be detected. Here, we suggest that the resistance to ertapenem associated with susceptibility to imipenem and meropenem in K. pneumoniae could be related to the presence of blaSCO-1 and blaDHA-1, combined with permeability defects caused by point mutations in an outer membrane porin (OmpK37). The presence of the blaSCO-1 gene on a conjugative IncFIB(K) plasmid is worrisome as it can increase the risk of transmission to humans, to animals and to the environment.

Zoonotic Bacteria Harboring in Goat Intestine: A One Health Perspective

The risk of zoonosis transmission when handling livestock or animal products is substantial, ‘One Health’ interventions should be an effective strategy for the control of many zoonotic bacteria. In this study, 26 fresh fecal samples from 2 clinically healthy goats were collected at different day ages to survey goat-borne zoonotic bacterial infection, and 19 fresh fecal samples from diarrhetic goats were tested to evaluate the possible role of zoonotic pathogens in goat diarrhea. Following all samples were analyzed by Metagenomic Sequencing, a total of 20 kinds of zoonotic bacteria were screened from healthy goats, and 11 (55%) of them were infection mainly during the preweaned period. Of the 19 fresh fecal samples from diarrhetic goats, all were confirmed to be zoonotic bacterial infection positive (range from 11 to 12 species). After comparison with healthy samples of the same or similar day-age goats, it was found that Lactococcus garvieae, Helicobacter pylori, Klebsiella pneumoniae, Shigella sonnei, Shigella boydii, Campylobacter coli, Salmonella enterica, Acinetobacter baumannii, Shigella flexneri, Shigella dysenteriae and Clostridium perfringens and Campylobacter fetus were highly increased incases in some diarrheic cases, while the remains had no significant change. The results suggest that goats may act as a reservoir for many zoonotic bacteria, and some of them may be associated with goat intestinal inflammation.

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.

A Retrospective Study of Antimicrobial Resistant Bacteria Associated with Feline and Canine Urinary Tract Infection in Hong Kong SAR, China—A Case Study on Implication of First-Line Antibiotics Use

Urinary tract infection (UTI) is a common clinical diagnosis for which empirical antibiotics are used in veterinary medicine. For veterinarians, the description of canine and feline antibiograms can help with making prudent use decisions and guideline formulation. For public health officers and epidemiologists, a urinary antibiogram overview helps track and trend antimicrobial resistance (AMR). There is currently a knowledge gap in AMR prevalence associated with urinary tract infection in feline and canine patients and the resistance percentage of these microbes against some of the over-the-counter antibiotics available to local pet owners. This study has two aims. First, it aims to investigate the frequency of the bacteria and bacterial-resistance pattern in urine samples obtained from feline and canine patients. Second, it aims to determine the resistance of Escherichia coli (E. coli), the most frequently isolated bacteria, to first-line antibiotics. Results: We identified the five most-frequently isolated bacterial species and determined these isolates’ antibiotic sensitivity and resistance. The most-frequently isolated bacteria in feline and canine patients was Escherichia coli (E. coli). E. coli was identified, on average, in 37.2% of canine and 46.5% of feline urine samples. Among feline urinary samples, Enterococcus (14.7%) and Staphylococcus (14.5%) spp. were isolated more frequently, followed by Pseudomonas (4.8%) and Klebsiella (5.2%) spp. (). In canine samples, Proteus (17.9%) and Staphylococcus (13.2%) spp. were isolated more frequently, followed by Enterococcus (10.0%) and Klebsiella (8.59%) spp. Among these isolates, 40 to 70% of Staphylococcus spp. bacterial isolates from feline and canine patients were resistant to amoxicillin and ampicillin. During the three-year study period, among canine patients, 10 to 20% of Staphylococcus spp. bacterial isolates were resistance to fluoroquinolones, other quinolones, and third-generation cephalosporins. Among feline patients, 10% of Staphylococcus spp., 15 to 20% of E. coli, 50 to 60% of Klebsiella spp., and 90% of Pseudomonas spp. were resistant to cefovecin, a commonly used antibiotic.

Common Pathogens and Drug Resistance of Neonatal Pneumonia with New Multichannel Sensor

This study aimed to study the application value of a new multichannel sensor in pathogen detection and drug resistance analysis of neonatal pneumonia. 180 newborns with infectious pneumonia were selected, and a new multichannel piezoelectric sensor was constructed. The traditional Kirby–Bauer (K–B) method and the piezoelectric sensor were adopted to detect the pathogens and drug resistance in newborn samples, respectively. The results showed that the sensitivity and specificity under the K–B method (99.58% and 99.32%) and the multichannel piezoelectric sensor (99.43% and 94.29%) were not statistically different (P > 0.05). The detection time (17.25 h) of the K–B method was significantly longer than that (7.43 h) of the multichannel piezoelectric sensor (P < 0.05). From the results of pathogen detection, it was found that Klebsiella pneumoniae accounted for a relatively high proportion of 25.1%, followed by Staphylococcus aureus and Haemophilus influenzae of 13.4% and 12.33%, respectively. The resistance rate of the Staphylococcus aureus to vancomycin and rifampicin was as high as 100% and that to gentamicin, ciprofloxacin, and erythromycin reached more than 50%. In short, the new multichannel piezoelectric sensor had the high sensitivity and specificity for the pathogens' detection of neonatal pneumonia, and it required a shorter time. The pathogens were mostly Gram-negative bacteria, followed by Gram-positive bacteria and fungi. Klebsiella pneumoniae, Staphylococcus aureus, and Haemophilus influenzae were the main ones. The neonatal pneumonia pathogens had also strong drug resistance against vancomycin, rifampicin, chloramphenicol, meropenem, amikacin sulfate, chloramphenicol, and many other antibacterial drugs.

Pandemic Clones of CTX-M-15 Producing Klebsiella pneumoniae ST15, ST147, and ST307 in Companion Parrots

Psittacine birds are commonly kept as companion birds and the maintenance of these birds in captivity may represent a zoonotic risk and contribute to the propagation of multidrug-resistant and β-lactamase extended-spectrum (ESBLs)-producing pathogens. This study aimed to identify and characterize strains of the Klebsiella pneumoniae complex isolated from diseased psittacine birds, determining virulence and resistance profiles. K. pneumoniae strains were isolated from 16 birds (16/46). All strains carried more than three virulence genes, with a high frequency of fimH and kpn (93.75%), uge (87.52%), and irp-2 (81.25%) genes. The antimicrobial susceptibility revealed that 3/16 strains were ESBL producers. Genomic analysis revealed that CTX-M-15-positive strains belonged to sequence types (STs) ST15, ST147, and ST307, characterized as international clones associated with outbreaks of healthcare-associated infections (HAIs) worldwide.

Human pandemic K27-ST392 CTX-M-15 extended-spectrum-β-lactamase-positive Klebsiella pneumoniae: A one health clone threatening companion animals

Extended spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae is a medically important pathogen that commonly causes human nosocomial infections. Since veterinary emergency and critical care services have also significantly progressed over the last decades, there are increasing reports of ESBL-producing K. pneumoniae causing hospital-associated infections in companion animals. We present microbiological and genomic analysis of a multidrug-resistant ESBL-positive K. pneumoniae (LCKp01) isolated from a fatal infection in a dog admitted to a veterinary intensive care unit. LCKp01 strain belonged to the sequence type ST392 and displays a KL27 (wzi-187) and O-locus 4 (O4). A broad resistome and presence of the bla_CTX-M-15 ESBL gene were predicted. SNP-based phylogenomic analysis, using an international genome database, clustered LCKp01 (60–80 SNPs differences) with K. pneumoniae ST392 from human and animal infections, isolated at 4-year interval, whereas phylogeographical analysis confirmed successful expansion of ST392 as a global clone of One Health concern.

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A fatal infection by a multidrug-resistant K. pneumoniae in dog was investigated.

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Identification of human pandemic K. pneumoniae ST392/CTX-M-15 clone is highlighted.

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Phylogenomic analysis revealed clonal relatedness with nosocomial lineages.

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Phylogeographical analysis confirmed expansion of ST392 as global One Health clone.

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Dissemination of K. pneumoniae ST392 at the human-animal interface is discussed.

Companion Animals—An Overlooked and Misdiagnosed Reservoir of Carbapenem Resistance

The dissemination of antimicrobial-resistance is a major global threat affecting both human and animal health. Carbapenems are human use β-lactams of last resort; thus. the dissemination of carbapenemase-producing (CP) bacteria creates severe limitations for the treatment of multidrug-resistant bacteria in hospitalized patients. Even though carbapenems are not routinely used in veterinary medicine, reports of infection or colonization by carbapenemase-producing Enterobacterales in companion animals are being reported. NDM-5 and OXA-48-like carbapenemases are among the most frequently reported in companion animals. Like in humans, Escherichia coli and Klebsiella pneumoniae are the most represented CP Enterobacterales found in companion animals, alongside with Acinetobacter baumannii. Considering that the detection of carbapenemase-producing Enterobacterales presents several difficulties, misdiagnosis of CP bacteria in companion animals may lead to important animal and public-health consequences. It is of the upmost importance to ensure an adequate monitoring and detection of CP bacteria in veterinary microbiology in order to safeguard animal health and minimise its dissemination to humans and the environment. This review encompasses an overview of the carbapenemase detection methods currently available, aiming to guide veterinary microbiologists on the best practices to improve its detection for clinical or research purposes.

Multidrug-Resistant Klebsiella pneumoniae Complex From Clinical Dogs and Cats in China: Molecular Characteristics, Phylogroups, and Hypervirulence-Associated Determinants

Klebsiella pneumoniae complex is an increasingly important bacterial pathogen that is capable of causing severe organs and life-threatening disease. This study aimed to investigate the multidrug resistance, phylogroups, molecular characterization, and hypervirulence-associated determinants of the complex, which were isolated from clinical diseased dogs and cats. A total of 35 K. pneumoniae complex (2.3%; 95% confidence interval, 1.6–3.2) isolates were identified from 1,500 samples, all of which were collected randomly from veterinary hospitals in the 12 regions across China. Antimicrobial susceptibility testing showed that isolates were extremely resistant to amoxicillin–clavulanate (82.9%) and trimethoprim–sulfamethoxazole (77.1%). The rate of multidrug-resistant reached an astonishing 82.9% and found a carbapenemase-producing strain carrying IncX3-bla_NDM−5 derived a cat from Zhejiang. The prevalence rates of extended-spectrum β-lactamase gene bla_CTX−M and plasmid-mediated quinolone resistance gene aac(6')Ib-cr were 51.4% and 45.7%, respectively. The resistance gene aph(3')-Ia of isolates from cats was more significantly (p < 0.05) prevalent than that from dogs. Likewise, K. pneumoniae complex harbored hypervirulence-associated genes ybt (11.4%), iuc (5.7%), and iroB (2.9%). Three (8.6%) of the 35 isolates were determined as hypermucoviscous by the string test. Lipopolysaccharide serotype O1v2 had the highest percentage of 25.7%, but capsular serotypes presented diversity distribution among the isolates. The core–genome phylogenetic tree demonstrated most of the isolates belonged to the KpI phylogroup (91.4%). Multilocus sequence typing analysis identified 25 different STs; ST15 and ST37 were the most abundant accounting for isolates, followed by ST307, ST656, ST1408, and ST4566. In addition, the prevalence of IncFIB-type plasmid for cat isolates was significantly higher (p < 0.05) than that for dogs. Sequences of IncX3 in bla_NDM−5-positive strain contained regions showing >99% nucleotide sequence identity to the reference plasmid pNDM-MGR194 from the human.

Comparative phylogenomics of ESBL-, AmpC- and carbapenemase-producing Klebsiella pneumoniae originating from companion animals and humans

Background

WHO considers ESBL- and carbapenemase-producing Klebsiella pneumoniae a major global concern. In animals, ESBL- and carbapenemase-producing K. pneumoniae of human-related ST11, ST15 and ST307 have been reported, but not in the context of large WGS-based One Health investigations.

Objectives

To perform comparative phylogenomics on a large collection of multidrug-resistant (MDR) K. pneumoniae recovered from diseased companion animals and humans.

Methods

MDR K. pneumoniae (n = 105) recovered from companion animals in France during 2010–18 were phenotypically characterized. All isolates were whole-genome sequenced using the NovaSeq technology and phylogenomic analysis across animal and human K. pneumoniae was performed using appropriate pipelines.

Results

bla_CTX-M-15, bla_DHA-1 and bla_OXA-48 were strongly associated with IncFIIk, IncR and IncL plasmids, respectively. When compared with human K. pneumoniae genomes, four groups of closely related French human and animal isolates belonging to ST11, ST15 and ST307 were detected, suggesting the circulation of clones between the human and animal sectors at country level. A large cluster of 31 ST11-KL105 animal isolates from France and Switzerland suggested it corresponds to a sub-lineage that is particularly well-adapted to the animal host.

Conclusions

This study demonstrates the spread of bla_CTX-M-15-carrying ST15 and ST307, and bla_DHA-1-carrying ST11 K. pneumoniae clones in animal populations. ST11 was the main vector of bla_OXA-48/IncL, despite the absence of carbapenem use in French animals. Comparative phylogenomics suggests cross-transmission of K. pneumoniae sub-lineages more prone than others to colonize/infect the animal host. Our data also evidenced the emergence of convergent hypervirulent and MDR K. pneumoniae in animals.

Diversity in the Characteristics of Klebsiella pneumoniae ST101 of Human, Environmental, and Animal Origin

Background

Klebsiella pneumoniae ST101 is an emerging high-risk clone which exhibits extensive drug resistance. Bacterial strains residing in multiple hosts show unique signatures related to host adaptation. In this study, we assess the genetic relationship of K. pneumoniae ST101 isolated from hospital samples, the environment, community, and livestock using whole genome sequencing (WGS).

Materials and Methods

We selected ten K. pneumoniae ST101 strains from hospitalized patients in Italy (n = 3) (2014) and Spain (n = 5) (2015–2016) as well as Belgian livestock animals (n = 2) (2017–2018). WGS was performed with 2 × 250 bp paired-end sequencing (Nextera XT) sample preparation kit and MiSeq (Illumina Inc.). Long-read sequencing (Pacbio Sequel I) was used to sequence the two livestock strains and three Italian hospital-associated strains. Furthermore, a public ST101 sequence collection of 586 strains (566 hospital-associated strains, 12 environmental strains, six strains from healthy individuals, one food-associated strain and one pig strain) was obtained. BacPipe and Kleborate were used to conduct genome analysis. ISFinder was used to find IS elements, and PHASTER was utilized to identify prophages. A phylogenetic tree was constructed to illustrate genetic relatedness.

Results

Hospital-associated K. pneumoniae ST101 showed higher resistance scores than non-clinical isolates from healthy individuals, the environment, food and livestock (1.85 ± 0.72 in hospital-associated isolates vs. 1.14 ± 1.13 in non-clinical isolates, p < 0.01). Importantly, the lack of integrative conjugative elements ICEKp bearing iron-scavenging yersiniabactin siderophores (ybt) in livestock-associated strains suggests a lower pathogenicity potential than hospital-associated strains. Mobile genetic elements (MGE) appear to be an important source of diversity in K. pneumoniae ST101 strains from different origins, with a highly stable genome and few recombination events outside the prophage-containing regions. Core genome MLST based analysis revealed a distinct genetic clustering between human and livestock-associated isolates.

Conclusion

The study of K. pneumoniae ST101 hospital-associated and strains from healthy individuals and animals revealed a genetic diversity between these two groups, allowing us to identify the presence of yersiniabactin siderophores in hospital-associated isolates. Resistance and virulence levels in livestock-associated strains were considerably lower than hospital-associated strains, implying that the public health risk remains low. The introduction of an ICEKp into animal strains, on the other hand, might pose a public threat over time.

Cell Membrane Remodeling Mediates Polymyxin B Resistance in Klebsiella pneumoniae: An Integrated Proteomics and Metabolomics Study

Polymyxin B (PB) is introduced into the clinic as the last-line therapy against carbapenem-resistant Klebsiella pneumoniae (CRKP). Unfortunately, increased resistance to PB in Klebsiella pneumoniae (K. pneumoniae) has threatened global health. Resistance of K. pneumoniae to PB was induced by passaging in serial concentrations of PB and determined by microbroth dilution method. Growth characteristics of induced strains including growth curve, reversibility of resistance, and biofilm formation (crystal violet staining method) were measured. This study employed TMT-labeled quantitative proteomics and LC-MS/MS metabolomics analysis to investigate the key biological processes associated with PB resistance in K. pneumoniae. A total of 315 differentially expressed proteins (DEPs) were identified, of which 133 were upregulated and 182 were downregulated in the PB-resistant K. pneumoniae. KEGG enrichment analysis revealed that the DEPs were mainly involved in ATP-binding cassette (ABC) transporters and cationic antimicrobial peptide (CAMP) resistance. Proteins related to central carbon metabolism were inhibited in the PB-resistant K. pneumoniae, but proteins mediating LPS modification were activated. Transcriptional levels of CAMP resistance-related proteins were significantly different between PB-susceptible and -resistant K. pneumoniae. PB treatment led to an increase in reactive oxygen species (ROS) levels of K. pneumoniae. Metabolomics data demonstrated that 23 metabolites were significantly upregulated in PB-resistant K. pneumoniae and 5 were downregulated. The differential metabolites were mainly lipids, including glycerophospholipids, sphingolipids, and fatty acids. Exposure to PB resulted in increased level of phospholipid transport gene mlaF in K. pneumoniae. Our study suggested that membrane remodeling and inhibited central carbon metabolism are conducive to the development of PB resistance in K. pneumoniae.

Third generation cephalosporin-resistant Klebsiella pneumoniae thriving in patients and in wastewater: what do they have in common?

BACKGROUND

Klebsiella pneumoniae are ubiquitous bacteria and recognized multidrug-resistant opportunistic pathogens that can be released into the environment, mainly through sewage, where they can survive even after wastewater treatment. A major question is if once released into wastewater, the selection of lineages missing clinically-relevant traits may occur. Wastewater (n = 25) and clinical (n = 34) 3rd generation cephalosporin-resistant K. pneumoniae isolates were compared based on phenotypic, genotypic and genomic analyses.

RESULTS

Clinical and wastewater isolates were indistinguishable based on phenotypic and genotypic characterization. The analysis of whole genome sequences of 22 isolates showed that antibiotic and metal resistance or virulence genes, were associated with mobile genetic elements, mostly transposons, insertion sequences or integrative and conjugative elements. These features were variable among isolates, according to the respective genetic lineage rather than the origin.

CONCLUSIONS

It is suggested that once acquired, clinically relevant features of K. pneumoniae may be preserved in wastewater, even after treatment. This evidence highlights the high capacity of K. pneumoniae for spreading through wastewater, enhancing the risks of transmission back to humans.

Characterization of ESBL-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Clinical Samples in a Northern Portuguese Hospital: Predominance of CTX-M-15 and High Genetic Diversity

Background: Enterobacteriaceae are major players in the spread of resistance to β-lactam antibiotics through the action of CTX-M β-lactamases. We aimed to analyze the diversity and genetic characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae isolates from patients in a Northern Portuguese hospital. Methods: A total of 62 cefotaxime/ceftazidime-resistant E. coli (n = 38) and K. pneumoniae (n = 24) clinical isolates were studied. Identification was performed by MALDI-TOF MS. Antimicrobial susceptibility testing against 13 antibiotics was performed. Detection of ESBL-encoding genes and other resistance genes, phylogenetic grouping, and molecular typing (for selected isolates) was carried out by PCR/sequencing. Results: ESBL activity was detected in all 62 E. coli and K. pneumoniae isolates. Most of the ESBL-producing E. coli isolates carried a bla_CTX-M gene (37/38 isolates), being bla_CTX-M-15 predominant (n = 32), although bla_CTX-M-27 (n = 1) and bla_CTX-M-1 (n = 1) were also detected. Two E. coli isolates carried the bla_KPC2/3 gene. The lineages ST131-B2 and ST410-A were detected among the ESBL-producing blood E. coli isolates. Regarding the 24 ESBL-producing K. pneumoniae isolates, 18 carried a bla_CTX-M gene (bla_CTX-M-15, 16 isolates; bla_CTX-M-55, 2 isolates). All K. pneumoniae isolates carried bla_SHV genes, including ESBL-variants (bla_SHV-12 and bla_SHV-27, 14 isolates) or non-ESBL-variants (bla_SHV-11 and bla_SHV-28, 10 isolates); ten K. pneumoniae isolates also carried the bla_KPC2/3 gene and showed imipenem-resistance. ESBL-positive E. coli isolates were ascribed to the B₂ phylogenetic group (82%), mostly associated with ST131 lineage and, at a lower rate, to ST410/A. Regarding K. pneumoniae, the three international lineages ST15, ST147, and ST280 were detected among selected isolates. Conclusions: Different ESBL variants of CTX-M (especially CTX-M-15) and SHV-type (specially SHV-12) were detected among CTX/CAZ^RE. coli and K. pneumoniae isolates, in occasions associated with carbapenemase genes (bla_KPC2/3 gene).

Genetic Background and Antibiotic Resistance Profiles of K. pneumoniae NDM-1 Strains Isolated from UTI, ABU, and the GI Tract, from One Hospital in Poland, in Relation to Strains Nationally and Worldwide

In recent years, there has been an observed increase in infections caused by carbapenem-resistant Klebsiella pneumonia (Kp) strains. The aim of this study was the phenotypic and genotypic analysis of eight K. pneumoniae NDM (Kp NDM) isolates, recovered in Poland during the years 2016 and 2018 from seven patients with urinary tract infections (UTIs), asymptomatic bacteriuria (ABU), or colonization of the gut. PCR melting profile genotyping indicated a close relationship between the strains derived from 2018, which were not related to the strain isolated in 2016. WGS results were analyzed in relation to international Kp isolates. Clonal and phylogenetic analyses were performed based on multilocus sequence typing (MLST) and single nucleotide polymorphisms (SNPs) of the core genome. The metallo-β-lactamase was assigned to the NDM-1 type and the sequence was identified as ST11. Eleven antimicrobial resistance genes were detected, mostly from plasmid contigs. Unprecedented profiles of plasmid replicons were described with the IncFII/pKPX-1 dominant replicon. In terms of the KL24 and O2v1 capsular antigen profiles, these isolates corresponded to Greek strains. Strains isolated from UTI, ABU, and colonization GI tract patients were not carrying environment-specific virulence genes. Based on the assessment of strain relationships at the genome level and their direction of evolution, the international character of the sublines was demonstrated, with a documented epidemic potential in Poland and Greece. In conclusion, some groups of patients, e.g., renal transplant recipients or those with complicated UTIs, who are frequently hospitalized and undergoing antibiotic therapy, should be monitored not only for the risk of UTI, but also for colonization by Kp NDM strains.

Resistance Phenotype and Molecular Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Shanghai

Background: The emergence and wide global spread of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates are of great concern, and the aim of this study was to investigate drug resistance, molecular epidemiology, and genetic relationship of CRKP isolates from patients in Shanghai, China. Methods: A retrospective study was conducted from April 2018 to July 2019, and a total of 133 CRKP isolates were collected. Antimicrobial susceptibility was determined by VITEK-2 automated microbiology analyzer platform (bioMérieux, France) and the broth microdilution method. Polymerase chain reaction assays were used to investigate the presence of drug resistance genes. A modified carbapenem inactivation method was performed to detect carbapenemases. Multilocus sequence typing and pulsed-field gel electrophoresis (PFGE) were conducted for genetic relatedness of 50 CRKP isolates selected. Results: Among 670 isolates of K. pneumoniae, 133 (19.9%) strains were identified as CRKP, of which, 76.7% (102/133) strains were isolated from intensive care units (ICUs). All the 133 CRKP isolates were found to be carbapenemase-producers and harbor blaKPC-2 gene. No other carbapenemase genes of blaNDM, blaOXA-48, blaVIM, and blaIMP were detected. Furthermore, β-lactamase genes of blaSHV, blaCTX, and blaTEM were the most common resistance-associated genes among these KPC-2 producing isolates. All the 133 CRKP strains displayed >95% of resistance to cephalosporins and carbapenems, except for gentamicin, trimethoprim-sulfamethoxazole, amikacin, tigecycline and colistin, and ceftazidime-avibactam. The most common sequence type was ST11, accounting for 90.0% of the 50 CRKP selected, followed by ST15 (10.0%). PFGE analysis clustered the 50 KPC-2-producing isolates into seven (A-G) distinct clonal clusters at 85% cutoff. Of which, A and G were the two major clusters, accounting for the majority of the strains collected in emergency ICU and neurosurgical ICU. And all the strains of clusters D and E were collected in cardiothoracic surgery ICU, except for one strain collected in one outpatient. Conclusion: The KPC-2-producing K. pneumoniae belonged to ST11 was widely disseminated in ICUs, and active and effective surveillance of infection control strategies was initiated to limit the spread of CRKP strains.

Multidrug-resistant mcr-1 gene-positive Klebsiella pneumoniae ST307 causing urinary tract infection in a cat

RESUMO

The Klebsiella pneumoniae (K. pneumoniae) bacterium is responsible for many opportunistic infections such as sepsis, and a multidrug-resistant (MDR) clone sequence type (ST) 307 has recently begun to spread. The objective of this study was to report the first occurrence of this virulent genotype, which was found in the context of a urinary infection in a domestic feline in Brazil. The K. pneumoniae isolate was identified from the urine of a 6-month-old male crossbreed cat using 16S rRNA sequencing. It was then subjected to antimicrobial susceptibility testing, followed by multilocus sequence typing analysis, and PCR detection of virulence and resistance genes. The antimicrobial susceptibility profile demonstrated that the isolate was MDR and associated with the presence of the colistin resistance gene (mcr-1). Genotyping allowed us to classify the isolate as K. pneumoniae ST307 with the presence of wabG, uge, and entB genes. MDR K. pneumoniae is important in human and veterinary medicine because it causes many types of infections. Clonal propagation of virulent or MDR genotypes such as K. pneumoniae ST307 is a global concern. This report of ST307 isolation from a urine sample in a domestic feline is the first in Brazil.

Genome-Based Analysis of Klebsiella spp. Isolates from Animals and Food Products in Germany, 2013-2017

The increase in infections with multidrug-resistant and virulent Klebsiella pneumoniae (K. pneumoniae) strains poses a serious threat to public health. However, environmental reservoirs and routes of transmission for Klebsiella spp. that cause infections in humans and in livestock animals are not well understood. In this study, we aimed to analyze the distribution of antibiotic resistance genes and important virulence determinants (ybt, clb, iro, iuc, rmpA/A2) among 94 Klebsiella spp. isolates from different animal and food sources isolated between 2013 and 2017 in Germany. Antibiotic susceptibility testing was performed, and the genomes were sequenced by Illumina and Nanopore technology. Genetic relationships were assessed by conducting core genome multilocus sequence typing (cgMLST). Kleborate was used to predict resistance and virulence genes; Kaptive was used to derive the capsule types. The results revealed that 72 isolates (76.6%) belonged to the K. pneumoniae sensu lato complex. Within this complex, 44 known sequence types (STs), 18 new STs, and 38 capsule types were identified. Extended-spectrum beta-lactamase (ESBL) genes were detected in 16 isolates (17.0%) and colistin resistance in one (1.1%) K. pneumoniae isolate. Virulence genes were found in 22 K. pneumoniae isolates. Overall, nine (9.6%) and 18 (19.1%) isolates possessed the genes ybt and iuc, respectively. Notably, aerobactin (iuc lineage 3) was only detected in K. pneumoniae isolates from domestic pigs and wild boars. This study provides a snapshot of the genetic diversity of Klebsiella spp. in animals and food products in Germany. The siderophore aerobactin was found to be more prevalent in K. pneumoniae strains isolated from pigs than other sources. Further investigations are needed to evaluate if pigs constitute a reservoir for iuc lineage 3.

Multidrug-resistant Klebsiella pneumoniae harboring extended spectrum β-lactamase encoding genes isolated from human septicemias

Klebsiella pneumoniae is a major pathogen implicated in nosocomial infections. Extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae isolates are a public health concern. We aim to characterize the type of β-lactamases and the associated resistance mechanisms in ESBL-producing K. pneumoniae isolates obtained from blood cultures in a Portuguese hospital, as well as to determine the circulating clones. Twenty-two cefotaxime/ceftazidime-resistant (CTX/CAZ^R) K. pneumoniae isolates were included in the study. Identification was performed by MALDI-TOF MS and the antimicrobial susceptibility testing by disk-diffusion. The screening test for ESBL-production was performed and ESBL-producer isolates were further characterized. The presence of different beta-lactamase genes (bla_CTX-M, bla_SHV, bla_TEM, bla_KPC, bla_NDM,bla_VIM,bla_OXA-48,bla_CMY-2, bla_DHA-1,bla_FOX,bla_MOX, and bla_ACC) was analyzed by PCR/sequencing in ESBL-producer isolates, as well as the presence of other resistance genes (aac(6’)-Ib-cr, tetA/B, dfrA, qnrA/B/S, sul1/2/3) or integron-related genes (int1/2/3). Multilocus-sequence-typing (MLST) was performed for selected isolates. ESBL activity was detected in 12 of the 22 CTX/CAZ^RK. pneumoniae isolates and 11 of them carried the bla_CTX-M-15 gene (together with bla_TEM)_, and the remaining isolate carried the bla_SHV-106 gene. All the bla_CTX-M-15 harboring isolates also contained a bla_SHV gene (bla_SHV-1, bla_SHV-11 or bla_SHV-27 variants). Both bla_SHV-27 and bla_SHV-106 genes correspond to ESBL-variants. Two of the CTX-M-15 producing isolates carried a carbapenemase gene (bla_KPC2/3 and bla_OXA-48) and showed imipenem resistance. The majority of the ESBL-producing isolates carried the int1 gene, as well as sulphonamide-resistance genes (sul2 and/or sul3); the tetA gene was detected in all eight tetracycline-resistant isolates. Three different genetic lineages were found in selected isolates: ST348 (one CTX-M-15/TEM/SHV-27/KPC-2/3-producer isolate), ST11 (two CTX-M-15/TEM/SHV-1- and CTX-M-15-TEM-SHV-11-OXA-48-producer isolates) and ST15 (one SHV-106/TEM-producer isolate). ESBL enzymes of CTX-M-15 or SHV-type are detected among blood K. pneumoniae isolates, in some cases in association with carbapenemases of KPC or OXA-48 type.

Mechanisms of Resistance in Gram-Negative Urinary Pathogens: From Country-Specific Molecular Insights to Global Clinical Relevance

Urinary tract infections (UTIs) are the most frequent hospital infections and among the most commonly observed community acquired infections. Alongside their clinical importance, they are notorious because the pathogens that cause them are prone to acquiring various resistance determinants, including extended-spectrum beta-lactamases (ESBL); plasmid-encoded AmpC β-lactamases (p-AmpC); carbapenemases belonging to class A, B, and D; qnr genes encoding reduced susceptibility to fluoroquinolones; as well as genes encoding enzymes that hydrolyse aminoglycosides. In Escherichia coli and Klebsiella pneumoniae, the dominant resistance mechanisms are ESBLs belonging to the CTX-M, TEM, and SHV families; p-AmpC; and (more recently) carbapenemases belonging to classes A, B, and D. Urinary Pseudomonas aeruginosa isolates harbour metallo-beta-lactamases (MBLs) and ESBLs belonging to PER and GES families, while carbapenemases of class D are found in urinary Acinetobacter baumannii isolates. The identification of resistance mechanisms in routine diagnostic practice is primarily based on phenotypic tests for the detection of beta-lactamases, such as the double-disk synergy test or Hodge test, while polymerase chain reaction (PCR) for the detection of resistance genes is mostly pursued in reference laboratories for research purposes. As the emergence of drug-resistant bacterial strains poses serious challenges in the management of UTIs, this review aimed to appraise mechanisms of resistance in relevant Gram-negative urinary pathogens, to provide a detailed map of resistance determinants in Croatia and the world, and to discuss the implications of these resistance traits on diagnostic approaches. We summarized a sundry of different resistance mechanisms among urinary isolates and showed how their prevalence highly depends on the local epidemiological context, highlighting the need for tailored interventions in the field of antimicrobial stewardship.

Effective Photodynamic Therapy with Ir(III) for Virulent Clinical Isolates of Extended-Spectrum Beta-Lactamase Klebsiella pneumoniae

Background: The extended-spectrum beta-lactamase (ESBL) Klebsiella pneumoniae is one of the leading causes of health-associated infections (HAIs), whose antibiotic treatments have been severely reduced. Moreover, HAI bacteria may harbor pathogenic factors such as siderophores, enzymes, or capsules, which increase the virulence of these strains. Thus, new therapies, such as antimicrobial photodynamic inactivation (aPDI), are needed. Method: A collection of 118 clinical isolates of K. pneumoniae was characterized by susceptibility and virulence through the determination of the minimum inhibitory concentration (MIC) of amikacin (Amk), cefotaxime (Cfx), ceftazidime (Cfz), imipenem (Imp), meropenem (Mer), and piperacillin–tazobactam (Pip–Taz); and, by PCR, the frequency of the virulence genes K2, magA, rmpA, entB, ybtS, and allS. Susceptibility to innate immunity, such as human serum, macrophages, and polymorphonuclear cells, was tested. All the strains were tested for sensitivity to the photosensitizer PSIR-3 (4 µg/mL) in a 17 µW/cm² for 30 min aPDI. Results: A significantly higher frequency of virulence genes in ESBL than non-ESBL bacteria was observed. The isolates of the genotype K2+, ybtS+, and allS+ display enhanced virulence, since they showed higher resistance to human serum, as well as to phagocytosis. All strains are susceptible to the aPDI with PSIR-3 decreasing viability in 3log10. The combined treatment with Cfx improved the aPDI to 6log10 for the ESBL strains. The combined treatment is synergistic, as it showed a fractional inhibitory concentration (FIC) index value of 0.15. Conclusions: The aPDI effectively inhibits clinical isolates of K. pneumoniae, including the riskier strains of ESBL-producing bacteria and the K2+, ybtS+, and allS+ genotype. The aPDI with PSIR-3 is synergistic with Cfx.

Molecular Investigation of Klebsiella pneumoniae from Clinical Companion Animals in Beijing, China, 2017-2019

This work is aimed to elucidate the prevalence and characteristics of antimicrobial resistance, virulence, and molecular typing in Klebsiella pneumoniae from clinical companion animals in Beijing, China. In total, 105 K. pneumoniae (2.0%) isolates were recovered from 5359 samples (dogs, n = 3356; cats, n = 2003). All tested isolates exhibited high resistance to amoxicillin-clavulanate (74.3%). Moreover, resistance rates in dog isolates (2.1%) were significantly higher than in cat isolates (0.9%); however, the rate of multidrug-resistance (MDR) was 57.1% and the MDR prevalence in cats was significantly higher than dogs. Whole-genome sequencing demonstrated plasmids IncX4 and IncFIA (HI1)/FII(K) carried mcr-1 (n = 1) and mcr-8 (n = 1), but bla_OXA-181 (n = 1) and bla_NDM-5 (n = 4) were harbored in IncX3-type plasmids, and the above genes were in different isolates. The most prevalent sequence types (STs) in companion animals were ST1 (n = 9) and ST37 (n = 9). Compared to National Center for Biotechnology Information (NCBI) data on human K. pneumoniae, resistance genes bla_CTX-M and bla_TEM were more prevalent in human isolates; however, aac(6′)-Ib-cr and oqxAB showed a higher prevalence in companion animals. Hypermucoviscosity was reported in 9 (8.6%) isolates, whereas 64 isolates (61.0%) were hypervirulent K. pneumoniae (hvKP) via the Galleria mellonella. These findings validate the high risk of K. pneumonia and necessitate its relevant control in pet clinics.

Antimicrobial susceptibility of bacterial isolates from urinary tract infections in companion animals in Spain

BACKGROUND

The increasing emergence of multidrug-resistant bacteria, causing urinary tract infections (UTI) in dogs and cats, represents a great therapeutic challenge and a public health concern.

METHODS

Laboratory records of 4943 urinary microbiological diagnosis results and antimicrobial resistance profiles of suspected UTI cases in dogs and cats were analysed from 2016 to 2018 in Spain.

RESULTS

This study showed a higher percentage of positive microbiological diagnoses in dogs (42%, 1368/3270) than in cats (27%, 457/1673). Although Escherichia coli was the most frequently isolated bacterium, the frequency of antimicrobial susceptibility of E. coli isolates was lower compared to other bacterial species like Enterococcus spp., Staphylococcus spp., Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter (E. cloacae), and Proteus mirabilis. The antimicrobial susceptibility testing of Gram-positive cocci showed higher levels of resistance in cats to common beta-lactams used for the treatment of complicated UTIs, as well as to fluoroquinolones, aminoglycosides, and carbapenems. Moreover, enterobacteria (E. coli, K. pneumoniae, and P. mirabilis) from cats presented high resistance frequencies to beta-lactams, including third- and fourth-generation cephalosporins and fluoroquinolones.

CONCLUSION

This study updates data on the current antimicrobial resistance in UTI bacteria from companion animals in Spain, which may help to guide clinicians for the appropriate use of antimicrobials.

Comparative genomics with a multidrug-resistant Klebsiella pneumoniae isolate reveals the panorama of unexplored diversity in Northeast Brazil

The emergence of community acquired infections increases the public health concern on K. pneumoniae and closely related bacteria among which antimicrobial resistance spreads. We report a multidrug-resistant K. pneumoniae isolate, B31, of a patient infected in the community and admitted to an intensive care unit in Northeast Brazil. Antimicrobial susceptibility and genome information were thoroughly investigated to characterize B31 in front of 172 sequenced strains of different countries. Assigned to the Sequence Type 15, which is globally spread, B31 presented extended spectrum beta-lactamase, tigecycline and ciprofloxacin resistance. Genome sequencing revealed most resistance genes being carried by plasmids with high dissemination potential. The absence of main virulence factors, like yersiniabactin and colibactin, apparently suggests a mild pathogenic strain which, on the contrary, persisted and caused severe infection in a previously healthy patient. The present study contributes to unveil the unclear genomic scenario of virulent and multidrug-resistant K. pneumoniae in Brazil.

Carriage of Extended-Spectrum-Beta-Lactamase- and AmpC Beta-Lactamase-Producing Escherichia coli Strains from Humans and Pets in the Same Households

Extended-spectrum-beta-lactamase (ESBL)- or AmpC beta-lactamase (ACBL)-producing Escherichia coli bacteria are the most common cause of community-acquired multidrug-resistant urinary tract infections (UTIs) in New Zealand. The carriage of antimicrobial-resistant bacteria has been found in both people and pets from the same household; thus, the home environment may be a place where antimicrobial-resistant bacteria are shared between humans and pets. In this study, we sought to determine whether members (pets and people) of the households of human index cases with a UTI caused by an ESBL- or ACBL-producing E. coli strain also carried an ESBL- or ACBL-producing Enterobacteriaceae strain and, if so, whether it was a clonal match to the index case clinical strain. Index cases with a community-acquired UTI were recruited based on antimicrobial susceptibility testing of urine isolates. Fecal samples were collected from 18 non-index case people and 36 pets across 27 households. Eleven of the 27 households screened had non-index case household members (8/18 people and 5/36 animals) positive for ESBL- and/or ACBL-producing E. coli strains. Whole-genome sequence analysis of 125 E. coli isolates (including the clinical urine isolates) from these 11 households showed that within seven households, the same strain of ESBL-/ACBL-producing E. coli was cultured from both the index case and another person (5/11 households) or pet dog (2/11 households). These results suggest that transmission within the household may contribute to the community spread of ESBL- or ACBL-producing E. coliIMPORTANCEEnterobacteriaceae that produce extended-spectrum beta-lactamases (ESBLs) and AmpC beta-lactamases (ACBLs) are important pathogens and can cause community-acquired illnesses, such as urinary tract infections (UTIs). Fecal carriage of these resistant bacteria by companion animals may pose a risk for transmission to humans. Our work evaluated the sharing of ESBL- and ACBL-producing E. coli isolates between humans and companion animals. We found that in some households, dogs carried the same strain of ESBL-producing E. coli as the household member with a UTI. This suggests that transmission events between humans and animals (or vice versa) are likely occurring within the home environment and, therefore, the community as a whole. This is significant from a health perspective, when considering measures to minimize community transmission, and highlights that in order to manage community spread, we need to consider interventions at the household level.

Mapping knowledge and comprehension of antimicrobial stewardship and biosecurity among veterinary students

OBJECTIVES

As an important public health concern, antimicrobial resistance (AMR) is related to lack of knowledge among healthcare professionals. Since the Global Action Plan on AMR highlights the importance of training all healthcare professionals, it is essential to focus our attention on the education related to judicious antimicrobial use. The current study was the first attempt in southeastern Europe to quantify the knowledge about antimicrobial usage and biosecurity measure among veterinary students.

METHODS

This questionnaire-based study was performed between April and May of 2019 on 213 veterinary students of the University of Novi Sad, Serbia and the University of Zagreb, Croatia.

RESULTS

Veterinary students appeared to be little aware of antimicrobial use in veterinary medicine contribution to overall AMR since only 56.8% have chosen strong contribution as the answer. Of the students surveyed, only 22.1%/35.7% of them strongly agreed/agreed that the amount of teaching time for pharmacology was about right. Students who denied having good knowledge of the pharmacology of antimicrobials showed higher knowledge about systemic use of antimicrobials in different clinical scenarios (p = 0.002). High importance of some antimicrobials for human medicine was not recognized by surveyed students. Only 8.5% of them identified gentamicin correctly, as first-line therapy. Students expected to graduate later were more likely to identify the importance of rating antimicrobials correctly than those who thought they would graduate earlier (p = 0.002). More than half of students gave correct answer at scenario regarding a dog with recurrent pyoderma by choosing culture and susceptibility (C & S) testing. Our students who think they will graduate sooner have higher knowledge level on C & S testing sample submission for range of clinical scenarios (p = 0.004). Moreover, appropriate use of PPE (personal protective equipment) procedure and biosecurity measure were reported for two thirds of our students in case of only for two clinical scenarios.

CONCLUSION

This study reveals that among veterinary students from Croatia and Serbia improved undergraduate education is needed on the AMR with emphasis on antimicrobial stewardship (AMS) and appropriate biosecurity.

Epidemiology of extended-spectrum β-lactamase-producing Enterobacteriaceae among healthcare students, at the Portuguese Red Cross Health School of Lisbon, Portugal

OBJECTIVE

The aim of the present study was to prospectively evaluate the prevalence of intestinal carriage by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae among Portuguese students attending a Bachelors' course in healthcare, and to determine the molecular features of ESBL-producing isolates.

METHODS

One-hundred and eleven faecal samples recovered from Portuguese healthcare students were screened for either ESBL-producing, carbapenem-resistant, colistin-resistant or pan-aminoglycoside-resistant Enterobacteriaceae, using respective screening media. All recovered isolates were tested for antimicrobial susceptibility and characterised by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).

RESULTS

A total of 17 ESBL-producing Enterobacteriaceae (16 Escherichia coli and a single Klebsiella pneumoniae) were recovered from 16 students, representing a prevalence of 14.5%. The E. coli isolates were distributed into three sequence types (STs) and seven PFGE types. The most common ESBL identified was CTX-M-1 (n=13; 76%), followed by CTX-M-15 (n=3; 18%) and CTX-M-8 (n=1; 6%). The majority of the strains were resistant to sulfonamides (88%) and fosfomycin (71%). Resistance to aminoglycosides was observed at a low rate, that is 12% for both tobramycin and kanamycin. No colistin-, carbapenem- or pan-aminoglycoside-resistant isolates were recovered. A major clone, ST10-bla_CTX-M-1, included 12 E. coli isolates. The bla_CTX-M-1 gene was always located on an IncFIA/FIB plasmid type, co-harbouring genes encoding resistance to tetracycline, sulfonamides, trimethoprim-sulfamethoxazole and fosfomycin.

CONCLUSION

The most commonly identified ESBL gene in E. coli was bla_CTX-M-1, usually identified among ESBL-producing isolates recovered from animals. A high prevalence of faecal carriage of ESBL-producing E. coli was found among healthy healthcare students, underlying this population as an important reservoir.

Genomic features of a polymyxin-resistant Klebsiella pneumoniae ST491 isolate co-harbouring blaCTX-M-8 and qnrE1 genes from a hospitalised cat in São Paulo, Brazil

OBJECTIVES

Klebsiella pneumoniae has emerged as one of the major pathogens of humans and companion animals. Moreover, polymyxin resistance in K. pneumoniae is increasingly reported worldwide, mainly among extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing isolates. The aim of this study was to report the draft genome sequence of a polymyxin-resistant, ESBL-producing K. pneumoniae isolate (14CSI) from a hospitalised domestic cat in Brazil.

METHODS

Whole-genome sequencing of strain 14CSI was performed on an Illumina NextSeq platform and the genome was de novo assembled using Velvet v.1.2.10. Data analysis was performed using bioinformatics tools available from the Center for Genomic Epidemiology and the Institut Pasteur database.

RESULTS

The genome size of strain 14CSI was calculated at 5 260 459 bp, with a GC content of 57.3% and comprising 5294 total genes, 28 tRNAs, 7 rRNAs, 8 ncRNAs and 237 pseudogenes. Klebsiella pneumoniae strain 14CSI belongs to sequence type 491 (ST491), presents a mutation (A14S) in the mgrB gene and co-harbours bla_CTX-M-8 and qnrE1 genes. Genes conferring resistance to heavy metals were further identified.

CONCLUSION

This draft genome could be used as a reference sequence for comparative analysis of polymyxin-resistant and/or CTX-M-8-producing K. pneumoniae strains circulating at the human-animal interface.