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Fu B, Xu J, Yin D, Sun C, Liu D, Zhai W, Bai R, Cao Y, Zhang Q, Ma S, Walsh TR, Hu F, Wang Y, Wu C, Shen J. Transmission of blaNDM in Enterobacteriaceae among animals, food and human. Emerg Microbes Infect 2024; 13:2337678. [PMID: 38629492 PMCID: PMC11034458 DOI: 10.1080/22221751.2024.2337678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
Despite carbapenems not being used in animals, carbapenem-resistant Enterobacterales (CRE), particularly New Delhi metallo-β-lactamase-producing CRE (NDM-CRE), are prevalent in livestock. Concurrently, the incidence of human infections caused by NDM-CRE is rising, particularly in children. Although a positive association between livestock production and human NDM-CRE infections at the national level was identified, the evidence of direct transmission of NDM originating from livestock to humans remains largely unknown. Here, we conducted a cross-sectional study in Chengdu, Sichuan Province, to examine the prevalence of NDM-CRE in chickens and pigs along the breeding-slaughtering-retail chains, in pork in cafeterias of schools, and in colonizations and infections from children's hospital and examined the correlation of NDM-CRE among animals, foods and humans. Overall, the blaNDM increases gradually along the chicken and pig breeding (4.70%/2.0%) -slaughtering (7.60%/22.40%) -retail (65.56%/34.26%) chains. The slaughterhouse has become a hotspot for cross-contamination and amplifier of blaNDM. Notably, 63.11% of pork from the school cafeteria was positive for blaNDM. The prevalence of blaNDM in intestinal and infection samples from children's hospitals was 21.68% and 19.80%, respectively. whole genome sequencing (WGS) analysis revealed the sporadic, not large-scale, clonal spread of NDM-CRE along the chicken and pig breeding-slaughtering-retail chain, with further spreading via IncX3-blaNDM plasmid within each stage of whole chains. Clonal transmission of NDM-CRE is predominant in children's hospitals. The IncX3-blaNDM plasmid was highly prevalent among animals and humans and accounted for 57.7% of Escherichia coli and 91.3% of Klebsiella pneumoniae. Attention should be directed towards the IncX3 plasmid to control the transmission of blaNDM between animals and humans.
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Affiliation(s)
- Bo Fu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jian Xu
- Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People’s Republic of China
| | - Dandan Yin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics (MoH), Shanghai, People’s Republic of China
| | - Chengtao Sun
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Dejun Liu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Weishuai Zhai
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Rina Bai
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yue Cao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Qin Zhang
- Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People’s Republic of China
| | - Shizhen Ma
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Timothy R. Walsh
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Department of Zoology, Ineos-Oxford Institute of Antimicrobial Research, University of Oxford, Oxford, UK
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics (MoH), Shanghai, People’s Republic of China
| | - Yang Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Congming Wu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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Bray AS, Zafar MA. Deciphering the gastrointestinal carriage of Klebsiella pneumoniae. Infect Immun 2024:e0048223. [PMID: 38597634 DOI: 10.1128/iai.00482-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
Bacterial infections pose a significant global health threat, accounting for an estimated 7.7 million deaths. Hospital outbreaks driven by multi-drug-resistant pathogens, notably Klebsiella pneumoniae (K. pneumoniae), are of grave concern. This opportunistic pathogen causes pneumonia, urinary tract infections, and bacteremia, particularly in immunocompromised individuals. The rise of hypervirulent K. pneumoniae adds complexity, as it increasingly infects healthy individuals. Recent epidemiological data suggest that asymptomatic gastrointestinal carriage serves as a reservoir for infections in the same individual and allows for host-to-host transmission via the fecal-oral route. This review focuses on K. pneumoniae's gastrointestinal colonization, delving into epidemiological evidence, current animal models, molecular colonization mechanisms, and the protective role of the resident gut microbiota. Moreover, the review sheds light on in vivo high-throughput approaches that have been crucial for identifying K. pneumoniae factors in gut colonization. This comprehensive exploration aims to enhance our understanding of K. pneumoniae gut pathogenesis, guiding future intervention and prevention strategies.
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Affiliation(s)
- Andrew S Bray
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - M Ammar Zafar
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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Blaikie JM, Sapula SA, Siderius NL, Hart BJ, Amsalu A, Leong LE, Warner MS, Venter H. Resistome Analysis of Klebsiella pneumoniae Complex from Residential Aged Care Facilities Demonstrates Intra-facility Clonal Spread of Multidrug-Resistant Isolates. Microorganisms 2024; 12:751. [PMID: 38674695 PMCID: PMC11051875 DOI: 10.3390/microorganisms12040751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Antimicrobial-resistant Klebsiella pneumoniae is one of the predominant pathogens in healthcare settings. However, the prevalence and resistome of this organism within residential aged care facilities (RACFs), which are potential hotspots for antimicrobial resistance, remain unexplored. Here, we provide a phenotypic and molecular characterization of antimicrobial-resistant K. pneumoniae isolated from RACFs. K. pneumoniae was isolated from urine, faecal and wastewater samples and facility swabs. The antimicrobial susceptibility profiles of all the isolates were determined and the genomic basis for resistance was explored with whole-genome sequencing on a subset of isolates. A total of 147 K. pneumoniae were isolated, displaying resistance against multiple antimicrobials. Genotypic analysis revealed the presence of beta-lactamases and the ciprofloxacin-resistance determinant QnrB4 but failed to confirm the basis for the observed cephalosporin resistance. Clonal spread of the multidrug-resistant, widely disseminated sequence types 323 and 661 was observed. This study was the first to examine the resistome of K. pneumoniae isolates from RACFs and demonstrated a complexity between genotypic and phenotypic antimicrobial resistance. The intra-facility dissemination and persistence of multidrug-resistant clones is concerning, given that residents are particularly vulnerable to antimicrobial resistant infections, and it highlights the need for continued surveillance and interventions to reduce the risk of outbreaks.
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Affiliation(s)
- Jack M. Blaikie
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Sylvia A. Sapula
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Naomi L. Siderius
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Bradley J. Hart
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Anteneh Amsalu
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
- Department of Medical Microbiology, University of Gondar, Gondar 196, Ethiopia
| | - Lex E.X. Leong
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
- Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA 5000, Australia;
| | - Morgyn S. Warner
- Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA 5000, Australia;
- School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
- Infectious Diseases Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Henrietta Venter
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
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Cooper HB, Vezina B, Hawkey J, Passet V, López-Fernández S, Monk JM, Brisse S, Holt KE, Wyres KL. A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex. Microb Genom 2024; 10:001206. [PMID: 38376382 PMCID: PMC10926698 DOI: 10.1099/mgen.0.001206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
The Klebsiella pneumoniae species complex (KpSC) is a major source of nosocomial infections globally with high rates of resistance to antimicrobials. Consequently, there is growing interest in understanding virulence factors and their association with cellular metabolic processes for developing novel anti-KpSC therapeutics. Phenotypic assays have revealed metabolic diversity within the KpSC, but metabolism research has been neglected due to experiments being difficult and cost-intensive. Genome-scale metabolic models (GSMMs) represent a rapid and scalable in silico approach for exploring metabolic diversity, which compile genomic and biochemical data to reconstruct the metabolic network of an organism. Here we use a diverse collection of 507 KpSC isolates, including representatives of globally distributed clinically relevant lineages, to construct the most comprehensive KpSC pan-metabolic model to date, KpSC pan v2. Candidate metabolic reactions were identified using gene orthology to known metabolic genes, prior to manual curation via extensive literature and database searches. The final model comprised a total of 3550 reactions, 2403 genes and can simulate growth on 360 unique substrates. We used KpSC pan v2 as a reference to derive strain-specific GSMMs for all 507 KpSC isolates, and compared these to GSMMs generated using a prior KpSC pan-reference (KpSC pan v1) and two single-strain references. We show that KpSC pan v2 includes a greater proportion of accessory reactions (8.8 %) than KpSC pan v1 (2.5 %). GSMMs derived from KpSC pan v2 also generate more accurate growth predictions, with high median accuracies of 95.4 % (aerobic, n=37 isolates) and 78.8 % (anaerobic, n=36 isolates) for 124 matched carbon substrates. KpSC pan v2 is freely available at https://github.com/kelwyres/KpSC-pan-metabolic-model, representing a valuable resource for the scientific community, both as a source of curated metabolic information and as a reference to derive accurate strain-specific GSMMs. The latter can be used to investigate the relationship between KpSC metabolism and traits of interest, such as reservoirs, epidemiology, drug resistance or virulence, and ultimately to inform novel KpSC control strategies.
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Affiliation(s)
- Helena B. Cooper
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria 3800, Australia
| | - Ben Vezina
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria 3800, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Virginie Passet
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France
| | - Sebastián López-Fernández
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France
| | - Jonathan M. Monk
- Department of Bioengineering, University of California, San Diego, California 92093, USA
| | - Sylvain Brisse
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Kelly L. Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria 3800, Australia
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Wang T, Wang X, Chen S, Zhu J, Zhu Z, Qu F, Chen L, Du H. Emergence of colistin-heteroresistant and carbapenem-resistant hypervirulent Klebsiella pneumoniae. J Glob Antimicrob Resist 2023; 35:237-243. [PMID: 37858865 DOI: 10.1016/j.jgar.2023.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 09/28/2023] [Accepted: 09/30/2023] [Indexed: 10/21/2023] Open
Abstract
OBJECTIVES To investigate the clinical emergence of colistin-heteroresistant, hypervirulent, and multidrug-resistant Klebsiella pneumoniae, and characterize the underlying molecular mechanisms. METHODS The population analysis profiles (PAPs) method was used to detect colistin heteroresistance. The time-killing assay was used to examine the effect of colistin on carbapenem-resistant Klebsiella pneumoniae (CRKP) in vitro. Galleria mellonella larvae infection model was used to test the potential virulence. qRT-PCR assay was conducted to compare the expression levels of efflux pump genes. Next and third-generation sequencing were conducted to analyse the genomic features. RESULTS Two colistin-heteroresistant isolates were detected from a multi-center carbapenem-resistant Enterobacterales (CRE) surveillance study in China, which exhibited similar survival rates as the K2 hypervirulent reference strain ATCC 43816 in a G. mellonella larvae model. The two isolates belonged to ST11, harbouring the iucABCD, iutA, iroBCD, and rpmA2 hypervirulent genes and pLVPK-like virulence plasmids. Colistin showed a weak effect on the heteroresistant strains in vitro. The efflux pump genes acrA, acrB, tolC, oqxA, and oqxB were upregulated in this subpopulation compared to the parental strains. CONCLUSIONS This study showed the clinical emergence of colistin-heteroresistant, hypervirulent, and multidrug-resistant Klebsiella pneumoniae. AcrAB-TolC and OqxAB efflux overexpression were involved in mediating colistin heteroresistance.
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Affiliation(s)
- Tao Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, PR China; Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaojun Wang
- Department of Clinical Laboratory, Suzhou Wuzhong People's Hospital, Suzhou, Jiangsu, PR China
| | - Suming Chen
- The Clinical Laboratory, Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Jie Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, PR China
| | - Zhichen Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, PR China
| | - Fen Qu
- Laboratory Medicine Center Aviation General Hospital, Beijing, 100012, China
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey; Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, PR China.
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