Limited Transmission of Klebsiella pneumoniae among Humans, Animals, and the Environment in a Caribbean Island, Guadeloupe (French West Indies)

Subtle genomic differences in Klebsiella pneumoniae sensu stricto isolates indicate host adaptation

Klebsiella pneumoniae sensu stricto (KpI) is an opportunistic pathogen capable of residing as a commensal in both human and bovine intestinal tracts and can cause serious systemic infections in humans and severe clinical mastitis in dairy cattle. It is unclear what role zoonotic and anthroponotic transmission play in the dissemination of KpI. In this study, we use a comparative genomic approach to identify differences between KpI associated with disease in humans and cattle and aimed to identify any potential genetic barriers limiting transmission of KpI between these two hosts. A total of 128 KpI strains (bovine n = 65; human n = 63) were whole genome sequenced and human and bovine strains were compared based on phylogenomics, the pangenome, mobile genetic elements, and differential gene abundance. No obvious phylogenomic differentiation was observed between isolates from these hosts. However, subtle genetic differences exist between bovine and human KpI which likely reflect environmental adaptation to different host niches, including a higher representation of gene clusters encoding ferric citrate uptake transporters, as well as histidine, arginine, and lactose utilization pathways in bovine isolates. These gene clusters may be positively selected due to the unique metabolic environment of the mammary gland, where lactose, citrate-bound iron, and amino acids like histidine and arginine provide growth advantages for KpI during mastitis. Overall, our study identified no obvious genetic barriers to zoonotic transmission of KpI within the dairy environment and provides insight into the development of host-specific therapeutic options for KpI infections in humans and bovine.

High proportions of multidrug-resistant Klebsiella pneumoniae isolates in community-acquired infections, Brazil

Klebsiella pneumoniae is one of the leading causes of bloodstream (BSI) and urinary tract infections (UTI), but limited data is available regarding community-acquired (CA) infections. This study characterized the clinical aspects of CA-BSI and CA-UTI caused by K. pneumoniae and the molecular features of isolates, including their resistance profiles. Sixty-five isolates (CA-BSI, n = 24; CA-UTI, n = 41) underwent antimicrobial susceptibility testing, β-lactamase and virulence gene assessment, capsular genotyping, and molecular typing. Older age, male gender, and comorbidities, particularly kidney disease, were significantly associated with CA-BSI. The MDR and carbapenem resistance rates for K. pneumoniae from CA infections were 24.6% and 4.6%, respectively. CA-BSI isolates were more antibiotic-resistant and had a higher proportion of ESBL-producing (37.5% versus 9.8%) and MDR isolates (45.8% versus 12.2%) than CA-UTI. The blaCTX-M-like or blaKPC-like genes was found in all ESBL-producing isolates, while blaKPC-like and blaNDM-like were detected exclusively in CA-BSI strains. The isolates' virulence profiles were similar between the groups, although one CA-BSI and two CA-UTI isolates presented hypervirulence biomarkers. A high clonal diversity was observed, with a majority of MDR (81.3%) (ST11, ST15, ST101, ST258, ST307, and ST6852) and hypervirulent (2/3) (ST23 and ST65) isolates being high-risk pandemic clones in humans. Our data highlight the high prevalence of MDR K. pneumoniae in CA infections in Brazil, with CA-BSI showing significant differences in resistance profiles compared to CA-UTI.

Tackling Infectious Diseases in the Caribbean and South America: Epidemiological Insights, Antibiotic Resistance, Associated Infectious Diseases in Immunological Disorders, Global Infection Response, and Experimental Anti-Idiotypic Vaccine Candidates Against Microorganisms of Public Health Importance

This paper explores various aspects of microbiology and immunology, with a particular focus on the epidemiology and molecular characterisation of infectious diseases in the Caribbean and South America. Key areas of investigation include tuberculosis (TB), experimental vaccines, and bloodborne pathogens. A retrospective study conducted in Jamaica highlights the significance of early HIV screening, timely diagnosis, and inte-grated care. The paper also examines the challenges posed by nosocomial infections, particularly those caused by antibiotic-resistant Gram-negative bacteria and methicillin-resistant Staphylococcus aureus (MRSA), emphasising the critical importance of infection control measures. Additionally, it explores the regional microbiome, the global response to infectious diseases, and immune responses in patients with immunodeficiency disorders such as severe combined immunodeficiency (SCID) and chronic granulomatous disease (CGD), underscoring their heightened susceptibility to a wide range of infections.

Limited Evidence of Spillover of Antimicrobial-Resistant Klebsiella pneumoniae from Animal/Environmental Reservoirs to Humans in Vellore, India

BACKGROUND

Klebsiella pneumoniae is a common opportunistic pathogen in humans, often associated with both virulence and antimicrobial resistance (AMR) phenotypes. K. pneumoniae have a highly plastic genome and can act as a vehicle for disseminating genetic information. Aiming to assess the impact of the human-animal-environment interface on AMR dissemination in K. pneumoniae we sampled and genome sequenced organisms from a range of environments and compared their genetic composition.

METHODS

Representative K. pneumoniae isolated from clinical specimens (n = 59), livestock samples (n = 71), and hospital sewage samples (n = 16) during a two-year surveillance study were subjected to whole genome sequencing. We compared the taxonomic and genomic distribution of K. pneumoniae, AMR gene abundance, virulence gene composition, and mobile genetic elements between the three sources.

RESULTS

The K. pneumoniae isolates originating from livestock were clonally distinct from those derived from clinical/hospital effluent samples. Notably, the clinical and hospital sewage isolates typically possessed a greater number of resistance/virulence genes than those from animals. Overall, we observed a limited overlap of K. pneumoniae clones, AMR genes, virulence determinants, and plasmids between the different settings.

CONCLUSION

In this setting, the spread of XDR and hypervirulent clones of K. pneumoniae appears to be restricted to humans with no obvious association with non-clinical sources. Emergent clones of K. pneumoniae carrying both resistance and virulence determinants are likely to have emerged in hospital settings rather than in animal or natural environments. These data challenge the current view of AMR transmission in K. pneumoniae in a One-Health context.

Recovery of clinically relevant multidrug-resistant Klebsiella pneumoniae lineages from wastewater in Kumasi Metropolis, Ghana

Antimicrobial resistance (AMR) is under-monitored in Africa, with few reports characterizing resistant bacteria from the environment. This study examined physicochemical parameters, chemical contaminants and antibiotic-resistant bacteria in waste stabilization pond effluents, hospital wastewater and domestic wastewater from four sewerage sites in Kumasi. The bacteria isolates were sequenced. Three sites exceeded national guidelines for total suspended solids, biochemical oxygen demand, chemical oxygen demand and electrical conductivity. Although sulfamethoxazole levels were low, the antibiotic was detected at all sites. Multi-drug-resistant Klebsiella pneumoniae and Pseudomonas aeruginosa were isolated with multi-locus sequence typing identifying K. pneumoniae strains as ST18 and ST147, and P. aeruginosa as ST235, all of clinical relevance. A comparison of ST147 genomes with isolates from human infections in Africa showed remarkable similarity and shared AMR profiles. Thirteen of the twenty-one plasmids from ST147 harbored at least one AMR gene, including blaCTX-M-15 linked to copper-resistance genes. Our study demonstrated high bacterial counts and organic matter in the analysed wastewater. The recovery of clinically significant isolates with multiple antibiotic and heavy metal resistance genes from the wastewater samples raises public health concerns.

Multidrug-resistant ESBL-producing Klebsiella pneumoniae complex in Czech hospitals, wastewaters and surface waters

BACKGROUND

Multidrug-resistant (MDR) bacteria pose a significant challenge to the treatment of infectious diseases. Of particular concern are members of the Klebsiella pneumoniae species complex (KpSC), which are frequently associated with hospital-acquired infections and have the potential to spread outside hospitals via wastewaters. In this study, we aimed to investigate the occurrence and phylogenetic relatedness of MDR KpSC from patients with urinary tract infections (UTIs), hospital sewage, municipal wastewater treatment plants (mWWTPs) and surface waters and to evaluate the clinical relevance of the KpSC subspecies.

METHODS

A total of 372 KpSC isolates resistant to third-generation cephalosporins and/or meropenem were collected from patients (n = 130), hospital sewage (n = 95), inflow (n = 54) and outflow from the mWWTPs (n = 63), river upstream (n = 13) and downstream mWWTPs (n = 17) from three cities in the Czech Republic. The isolates were characterized by antimicrobial susceptibility testing and whole-genome sequencing (Illumina). The presence of antibiotic resistance genes, plasmid replicons and virulence-associated factors was determined. A phylogenetic tree and single nucleotide polymorphism matrix were created to reveal the relatedness between isolates.

RESULTS

The presence of MDR KpSC isolates (95%) was identified in all water sources and locations. Most isolates (99.7%) produced extended-spectrum beta-lactamases encoded by blaCTX-M-15. Resistance to carbapenems (5%) was observed mostly in wastewaters, but carbapenemase genes, such as blaGES-51 (n = 10), blaOXA-48 (n = 4), blaNDM-1 (n = 4) and blaKPC-3 (n = 1), were found in isolates from all tested locations and different sources except rivers. Among the 73 different sequence types (STs), phylogenetically related isolates were observed only among the ST307 lineage. Phylogenetic analysis revealed the transmission of this lineage from patients to the mWWTP and from the mWWTP to the adjacent river and the presence of the ST307 clone in the mWWTP over eight months. We confirmed the frequent abundance of K. pneumoniae (K. pneumoniae sensu stricto and K. pneumoniae subsp. ozaenae) in patients suffering from UTIs. K. variicola isolates formed only a minor proportion of UTIs, and K. quasipneumoniae was not found among UTIs isolates; however, these subspecies were frequently observed in hospital sewage communities during the first sampling period.

CONCLUSION

This study provides evidence of the transmission and persistence of the ST307 lineage from UTIs isolates via mWWTPs to surface waters. Isolates from UTIs consisted mostly of K. pneumoniae. Other isolates of KpSC were observed in hospital wastewaters, which implies the impact of sources other than UTIs. This study highlights the influence of urban wastewaters on the spread of MDR KpSC to receiving environments.

Genetic characterization and clonal analysis of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae from canine and human origins

Introduction

Carbapenem-resistant Enterobacterales (CRE), particularly carbapenemase-producing Escherichia coli and Klebsiella pneumoniae, pose a significant global health challenge due to their resistance to last-resort antibiotics. This study investigates the genetic characteristics and clonal relationships of CRE isolated from canine and human clinical samples in Bangkok to understand potential interspecies transmission.

Methods

Fifty-two CRE isolates were collected from 477 clinical samples from dogs and humans at Chulalongkorn University between 2017-2021. Bacterial species were identified using MALDI-TOF, and antimicrobial resistance was confirmed through broth microdilution testing. Genetic analyses included plasmid replicon typing, multilocus sequence typing (MLST), whole genome sequencing (WGS), and pulsed-field gel electrophoresis (PFGE) to assess resistance genes and clonal relatedness.

Results

CRE isolates from both species exhibited genetic variability with high ARG counts, particularly in human isolates. MLST identified ST410 in most E. coli isolates from both dogs and humans, and IncFIA/IncFIB plasmids were predominant among blaNDM-positive isolates. PFGE patterns and SNP analysis showed no clonal relationship between canine and human isolates, suggesting independent acquisition pathways for CRE in the two hosts.

Discussion

The study highlights the absence of direct clonal transmission between canine and human isolates but reveals overlapping sequence types and plasmid types. The findings underscore the potential for interspecies transmission under certain conditions, emphasizing the importance of a One Health approach for monitoring CRE in both human and animal populations.

Klebsiella in Wildlife: Clonal Dynamics and Antibiotic Resistance Profiles, a Systematic Review

Klebsiella spp. are a genus of Gram-negative, opportunistic bacteria frequently found in the flora of the mucosal membranes of healthy animals and humans, and in the environment. Species of this group can cause serious infections (meningitis, sepsis, bacteraemia, urinary tract infections, liver damage) and possible death in immunocompromised organisms (and even in immunocompetent ones in the case of hypervirulent K. pneumoniae) that are exposed to them. K. pneumoniae is part of the ESKAPE organisms, and so it is important to understand this genus in terms of multidrug-resistant bacteria and as a carrier of antibiotic resistance mechanisms. As it is a durable bacterium, it survives well even in hostile environments, making it possible to colonize all kinds of habitats, even the mucosal flora of wildlife. This systematic review explores the prevalence of Klebsiella spp. bacteria in wild animals, and the possibility of transmission to humans according to the One Health perspective. The isolates found in this review proved to be resistant to betalactams (blaTEM, blaOXA-48…), aminoglycosides (strAB, aadA2…), fosfomycin, tetracyclines, sulphonamides, trimethoprim, phenicols (catB4), and polymyxins (mcr4).

Triplex real-time PCR ZKIR-T assay for simultaneous detection of the Klebsiella pneumoniae species complex and identification of K. pneumoniae sensu stricto

Klebsiella pneumoniae species complex (KpSC) members, including the most important species K. pneumoniae (phylogroup Kp1 of the KpSC), are important opportunistic pathogens that display increasing rates of antimicrobial resistance worldwide. As they are widespread in food and the environment, there is a need for fast, sensitive, and reliable methods to detect KpSC members in complex matrices. Previously, the ZKIR real-time PCR assay was developed to detect all KpSC members without distinction. Given that Kp1 is the clinically most significant phylogroup of the KpSC, here, we aimed to simultaneously identify Kp1 while detecting all KpSC members. Three TaqMan probes were developed and used: the Kp1 probe to specifically identify this phylogroup; the zkir P1 probe to detect phylogroups Kp1-Kp5 and Kp7; and the zkir P2 probe to detect phylogroup Kp6. The new triplex assay was tested on a total of 95 KpSC and 19 non-KpSC strains from various sources, representing the different phylogroups as defined by whole genome sequencing. The results showed almost complete specificity, as the expected PCR results were obtained for 112 (98%) strains. The new triplex real-time PCR assay, called ZKIR-T, enables the detection of all KpSC taxa while discriminating Kp1, which will be useful for rapid screening and to focus downstream analyses on chosen phylogroups of the KpSC.

IMPORTANCE

The pathogens of the Klebsiella pneumoniae species complex are widespread in food and animals and are among the main pathogens responsible for multidrug resistant infections in humans. In this study, we developed a highly sensitive detection assay that enables detection of this group of bacteria, with the simultaneous identification of the most common and clinically important species. This triplex one-reaction assay was shown to be highly sensitive and precise, enabling fast screening of varied samples for the presence of KpSC and K. pneumoniae sensu stricto.

Vaccine value profile for Klebsiella pneumoniae

Klebsiella pneumoniae causes community- and healthcare-associated infections in children and adults. Globally in 2019, an estimated 1.27 million (95% Uncertainty Interval [UI]: 0.91-1.71) and 4.95 million (95% UI: 3.62-6.57) deaths were attributed to and associated with bacterial antimicrobial resistance (AMR), respectively. K. pneumoniae was the second leading pathogen in deaths attributed to AMR resistant bacteria. Furthermore, the rise of antimicrobial resistance in both community- and hospital-acquired infections is a concern for neonates and infants who are at high risk for invasive bacterial disease. There is a limited antibiotic pipeline for new antibiotics to treat multidrug resistant infections, and vaccines targeted against K. pneumoniae are considered to be of priority by the World Health Organization. Vaccination of pregnant women against K. pneumoniae could reduce the risk of invasive K.pneumoniae disease in their young offspring. In addition, vulnerable children, adolescents and adult populations at risk of K. pneumoniae disease with underlying diseases such as immunosuppression from underlying hematologic malignancy, chemotherapy, patients undergoing abdominal and/or urinary surgical procedures, or prolonged intensive care management are also potential target groups for a K. pneumoniae vaccine. A 'Vaccine Value Profile' (VVP) for K.pneumoniae, which contemplates vaccination of pregnant women to protect their babies from birth through to at least three months of age and other high-risk populations, provides a high-level, holistic assessment of the available information to inform the potential public health, economic and societal value of a pipeline of K. pneumoniae vaccines and other preventatives and therapeutics. This VVP was developed by a working group of subject matter experts from academia, non-profit organizations, public-private partnerships, and multi-lateral organizations, and in collaboration with stakeholders from the WHO. All contributors have extensive expertise on various elements of the K.pneumoniae VVP and collectively aimed to identify current research and knowledge gaps. The VVP was developed using only existing and publicly available information.

Idiosyncratic invasion trajectories of human bacterial pathogens facing temperature disturbances in soil microbial communities

Current knowledge about effects of disturbance on the fate of invaders in complex microbial ecosystems is still in its infancy. In order to investigate this issue, we compared the fate of Klebsiella pneumoniae (Kp) and Listeria monocytogenes (Lm) in soil microcosms. We then used environmental disturbances (freeze-thaw or heat cycles) to compare the fate of both invaders and manipulate soil microbial diversity. Population dynamics of the two pathogens was assessed over 50 days of invasion while microbial diversity was measured at times 0, 20 and 40 days. The outcome of invasion was strain-dependent and the response of the two invaders to disturbance differed. Resistance to Kp invasion was higher under the conditions where resident microbial diversity was the highest while a significant drop of diversity was linked to a higher persistence. In contrast, Lm faced stronger resistance to invasion in heat-treated microcosms where diversity was the lowest. Our results show that diversity is not a universal proxy of resistance to microbial invasion, indicating the need to properly assess other intrinsic properties of the invader, such as its metabolic repertoire, or the array of interactions between the invader and resident communities.

Genomic insights unveil the plasmid transfer mechanism and epidemiology of hypervirulent Klebsiella pneumoniae in Vietnam

Hypervirulent Klebsiella pneumoniae (hvKp) is a significant cause of severe invasive infections in Vietnam, yet data on its epidemiology, population structure and dynamics are scarce. We screened hvKp isolates from patients with bloodstream infections (BSIs) at a tertiary infectious diseases hospital in Vietnam and healthy individuals, followed by whole genome sequencing and plasmid analysis. Among 700 BSI-causing Kp strains, 100 (14.3%) were hvKp. Thirteen hvKp isolates were identified from 350 rectal swabs of healthy adults; none from 500 rectal swabs of healthy children. The hvKp isolates were genetically diverse, encompassing 17 sequence types (STs), predominantly ST23, ST86 and ST65. Among the 113 hvKp isolates, 14 (12.6%) carried at least one antimicrobial resistance (AMR) gene, largely mediated by IncFII, IncR, and IncA/C plasmids. Notably, the acquisition of AMR conjugative plasmids facilitated horizontal transfer of the non-conjugative virulence plasmid between K. pneumoniae strains. Phylogenetic analysis demonstrated hvKp isolates from BSIs and human carriage clustered together, suggesting a significant role of intestinal carriage in hvKp transmission. Enhanced surveillance is crucial to understand the factors driving intestinal carriage and hvKp transmission dynamics for informing preventive measures. Furthermore, we advocate the clinical use of our molecular assay for diagnosing hvKp infections to guide effective management.

Do Microorganisms in Bathing Water in Guadeloupe (French West Indies) Have Resistance Genes?

Waterborne faecal contamination is a major public health concern. The main objectives of this study were to investigate faecal contamination and Escherichia coli (E. coli) antibiotic resistance in recreational fresh water from Guadeloupe and to characterise the microbiome and resistome composition in biofilms from submerged rocks. Significant faecal contamination was observed at 14 freshwater sites. E. coli predominated (62%), followed by Enterobacter cloacae (11%) and Acinetobacter spp. (11%). Of 152 E. coli isolated, none produced extended-spectrum beta-lactamases (ESBLs), but 7% showed resistance to streptomycin and 4% to tetracycline. Biofilm resistome analysis revealed clinically significant antibiotic-resistance genes (ARGs), including those coding for resistance to sulfonamides (sul1), carbapenems (blaKPC), and third-generation cephalosporins (blaCTX-M). Mobile genetic elements (MGEs) (intI1, intI2, intI3) linked to resistance to aminoglycosides, beta-lactams, tetracycline, as well as heavy metal resistance determinants (copA, cusF, czcA, merA) conferring resistance to copper, silver, cadmium, and mercury were also detected. Diverse bacterial phyla were found in biofilm samples, of which Proteobacteria, Bacteroidetes, Planctonomycetes, and Cyanobacteria were predominant. Despite the frequent presence of E. coli exceeding regulatory standards, the low levels of antibiotic-resistant bacteria in freshwater and of ARGs and MGEs in associated biofilms suggest limited antibiotic resistance in Guadeloupean recreational waters.

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.

Population structure and antimicrobial resistance among Klebsiella isolates sampled from human, animal, and environmental sources in Ghana: a cross-sectional genomic One Health study

BACKGROUND

One Health approaches to address the increasing threat of antimicrobial resistance (AMR) are gaining attention. However, data on the distribution and movement of bacteria and their AMR-associated genes between clinical and non-clinical sources are scarce, especially from low-income and middle-income countries. We aimed to analyse Klebsiella isolates from various sources in Ghana and compare the prevalence of AMR with datasets from two other countries.

METHODS

We conducted a cross-sectional genomic One Health study. Multiple clinical, environmental, and animal sources were sampled from 78 locations (eg, hospitals, residential areas, and farms) in and around Tamale, Ghana. Clinical samples were collected through routine screening and in cases of suspected infection between March 15 and Sept 15, 2019, and samples from the wider environment were collected during a dedicated sampling effort between the dates of Aug 19, 2018, and Sept 26, 2019. Sampling locations were approximately evenly distributed from the centre of the city and steadily outwards to capture both rural and urban locations. Samples with positive growth for Klebsiella were included. Isolates of Klebsiella were obtained from the samples using Simmons citrate agar medium and characterised by antimicrobial susceptibility testing and whole-genome sequencing. A comparative analysis with Klebsiella population surveys from Pavia, Italy, and Tromsø, Norway, was performed. AMR-associated and virulence genes were detected, and the population distribution of these genes was studied.

FINDINGS

Of 957 samples collected around Tamale, Ghana, 620 were positive for Klebsiella spp. 573 Klebsiella isolates were successfully sequenced, of which 370 were Klebsiella pneumoniae. Only two hospital isolates were carbapenem-resistant. Extended-spectrum β-lactamase (ESBL) genes were relatively common among the Ghanaian clinical isolates but rare in the environmental samples. Prevalence of ESBL genes in human-hospital disease samples was 64% (14 of 22 isolates) in Ghana and 44% (four of nine isolates) in Italy, and prevalence in human-hospital carriage samples was 7% (eight of 107) in Ghana and 13% (54 of 428) in Italy; the prevalence was higher in human-hospital disease samples than in human-hospital carriage samples in both countries, and prevalence across both samples in both countries was higher than in Norway. Ghanaian isolates showed evidence of high recombination rates (recombination events compared with point mutations [r/m] 9·455) and a considerable accessory gene overlap with isolates from Italy and Norway.

INTERPRETATION

Although several AMR-associated gene classes were observed relatively frequently in non-clinical sources, ESBL, carbapenemase, and virulence genes were predominantly present only in hospital samples. These results suggest that interventions should be focused on clinical settings to have the greatest effect on the prevalence and dissemination of AMR-associated genes.

FUNDING

European Research Council (742158), Academy of Finland EuroHPC grant, Trond Mohn Foundation (BATTALION grant), and Wellcome Trust.

Genomic features of Klebsiella isolates from artisanal ready-to-eat food production facilities

Increasing reports on K. pneumoniae strains with antimicrobial resistance and virulence traits from food and farm animals are raising concerns about the potential role of Klebsiella spp. as a foodborne pathogen. This study aimed to report and characterize Klebsiella spp. isolates from two artisanal ready-to-eat food (soft cheese and salami) producing facilities, and to track similar genotypes in different ecological niches. Over 1170 samples were collected during the whole production chain of different food batches. The overall Klebsiella prevalence was 6%. Strains were classified into the three Klebsiella species complexes: K. pneumoniae (KpSC, n = 17), K. oxytoca (KoSC, n = 38) and K. planticola (KplaSC, n = 18). Despite high genetic diversity we found in terms of known and new sequence types (STs), core genome phylogeny revealed clonal strains persisting in the same processing setting for over 14 months, isolated from the environment, raw materials and end-products. Strains showed a natural antimicrobial resistance phenotype-genotype. K. pneumoniae strains showed the highest virulence potential, with sequence types ST4242 and ST107 strains carrying yersiniabactin ybt16 and aerobactin iuc3. The latter was detected in all K. pneumoniae from salami and was located on a large conjugative plasmid highly similar (97% identity) to iuc3+ plasmids from human and pig strains circulating in nearby regions of Italy. While identical genotypes may persist along the whole food production process, different genotypes from distinct sources in the same facility shared an iuc3-plasmid. Surveillance in the food chain will be crucial to obtain a more comprehensive picture of the circulation of Klebsiella strains with pathogenic potential.