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Tang F, Chen Z, Zhu H, Xi L, Li C, Luo W. Genetic relatedness, antibiotic resistance, and virulence of Klebsiella pneumoniae isolated from healthcare and food sources in Wuhan, China. Am J Infect Control 2024:S0196-6553(24)00504-2. [PMID: 38782211 DOI: 10.1016/j.ajic.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
OBJECTIVE To investigate genetic relatedness and antibiotic resistance of Klebsiella pneumoniae from retail meat samples, clinical source samples, and hospital environmental samples in Wuhan, China. METHODS The hypermucoviscosity phenotypes and biofilm formation ability of K. pneumoniae were determined by string test and crystalline violet staining. The minimal inhibitory concentrations of 18 antimicrobial agents were determined by the broth microdilution test, and PCR assays were performed to detect 14 genes associated with antibiotic resistance. Pulsed-field gel electrophoresis (PFGE) analysis was used to assess the genetic relatedness and clonal dissemination. RESULTS Among the 5730 samples analyzed, 46 tested positive for K. pneumoniae, with higher rates observed in meat (23.4%, CI: 12.8-38.4%) than in clinical samples (0.6%, CI: 0.4-0.8%) and hospital environmental samples (8.0%, CI: 2.6-20.1%). Meat-derived isolates showed high resistance to tetracycline (36.4%, 4/11, CI: 12.4-68.4%), sulphonamide (27.3%, 3/11, CI: 7.3-60.7%), and gentamicin (27.3%, 3/11, CI: 7.3-60.7%), whereas clinical isolates exhibited significant resistance to ampicillin-sulbactam (32.3%, 10/31, CI: 17.3-51.5%). Multidrug resistance was observed in 17.4% (8/46, CI:8.3-32.0%) of the isolates, particularly in hospital environmental samples (3/4, CI: 21.9-98.7%). Biofilm production was observed in 88.1% (37/42, CI: 73.6-95.6%) of K. pneumoniae, with varying degrees of strength. PFGE analysis revealed patient-to-patient K. pneumoniae transmission, transmission between patients and hospital environment, as well as cross-contamination between markets. CONCLUSION The findings underscore the importance of comprehensive surveillance, infection control and judicious antibiotic use in mitigating the impact of K. pneumoniae on public health, especially in food chain and healthcare settings.
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Affiliation(s)
- Feng Tang
- Department of Laboratory Medicine, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China
| | - Zhi Chen
- Microbiological Laboratory, Wuhan Center for Disease Control and Prevention, Wuhan 430024, People's Republic of China
| | - Hanjue Zhu
- Plastic Surgery, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China
| | - Lei Xi
- Department of Laboratory Medicine, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China.
| | - Changzhen Li
- Department of Laboratory Medicine, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China.
| | - Wanjun Luo
- Hospital-Acquired Infection Control Department, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China.
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Denissen J, Havenga B, Reyneke B, Khan S, Khan W. Comparing antibiotic resistance and virulence profiles of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa from environmental and clinical settings. Heliyon 2024; 10:e30215. [PMID: 38720709 PMCID: PMC11076977 DOI: 10.1016/j.heliyon.2024.e30215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Antibiotic resistance and virulence profiles of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa, isolated from water sources collected in informal settlements, were compared to clinical counterparts. Cluster analysis using repetitive extragenic palindromic sequence-based polymerase chain reaction (REP-PCR) indicated that, for each respective species, low genetic relatedness was observed between most of the clinical and environmental isolates, with only one clinical P. aeruginosa (PAO1) and one clinical K. pneumoniae (P2) exhibiting high genetic similarity to the environmental strains. Based on the antibiograms, the clinical E. faecium Ef CD1 was extensively drug resistant (XDR); all K. pneumoniae isolates (n = 12) (except K. pneumoniae ATCC 13883) were multidrug resistant (MDR), while the P. aeruginosa (n = 16) isolates exhibited higher susceptibility profiles. The tetM gene (tetracycline resistance) was identified in 47.4 % (n = 6 environmental; n = 3 clinical) of the E. faecium isolates, while the blaKPC gene (carbapenem resistance) was detected in 52.6 % (n = 7 environmental; n = 3 clinical) and 15.4 % (n = 2 environmental) of the E. faecium and K. pneumoniae isolates, respectively. The E. faecium isolates were predominantly poor biofilm formers, the K. pneumoniae isolates were moderate biofilm formers, while the P. aeruginosa isolates were strong biofilm formers. All E. faecium and K. pneumoniae isolates were gamma (γ)-haemolytic, non-gelatinase producing (E. faecium only), and non-hypermucoviscous (K. pneumoniae only), while the P. aeruginosa isolates exhibited beta (β)-haemolysis and produced gelatinase. The fimH (type 1 fimbriae adhesion) and ugE (uridine diphosphate galacturonate 4-epimerase synthesis) virulence genes were detected in the K. pneumoniae isolates, while the P. aeruginosa isolates possessed the phzM (phenazine production) and algD (alginate biosynthesis) genes. Similarities in antibiotic resistance and virulence profiles of environmental and clinical E. faecium, K. pneumoniae, and P. aeruginosa, thus highlights the potential health risks posed by using environmental water sources for daily water needs in low-and-middle-income countries.
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Affiliation(s)
- Julia Denissen
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Benjamin Havenga
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Brandon Reyneke
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Sehaam Khan
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
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Dangor Z, Benson N, Berkley JA, Bielicki J, Bijsma MW, Broad J, Buurman ET, Cross A, Duffy EM, Holt KE, Iroh Tam PY, Jit M, Karampatsas K, Katwere M, Kwatra G, Laxminarayan R, Le Doare K, Mboizi R, Micoli F, Moore CE, Nakabembe E, Naylor NR, O'Brien S, Olwagen C, Reddy D, Rodrigues C, Rosen DA, Sadarangani M, Srikantiah P, Tennant SM, Hasso-Agopsowicz M, Madhi SA. Vaccine value profile for Klebsiella pneumoniae. Vaccine 2024:S0264-410X(24)00248-2. [PMID: 38503661 DOI: 10.1016/j.vaccine.2024.02.072] [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: 12/21/2023] [Revised: 02/07/2024] [Accepted: 02/24/2024] [Indexed: 03/21/2024]
Abstract
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.
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Affiliation(s)
- Ziyaad Dangor
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa.
| | - Nicole Benson
- Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - James A Berkley
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, UK
| | - Julia Bielicki
- Centre for Neonatal and Paediatric Infection, St George's, University of London, UK; Paediatric Research Centre (PRC), University of Basel Children's Hospital, Basel, Switzerland
| | - Merijn W Bijsma
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef, Amsterdam, the Netherlands; Amsterdam UMC, University of Amsterdam, Department of Pediatrics, Amsterdam Neuroscience, Meibergdreef, Amsterdam, the Netherlands
| | | | - Ed T Buurman
- CARB-X, Boston University, Boston, MA 02215, USA
| | - Alan Cross
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Erin M Duffy
- CARB-X, Boston University, Boston, MA 02215, USA
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Pui-Ying Iroh Tam
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
| | - Mark Jit
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | | | - Michael Katwere
- Makerere University-Johns Hopkins University Research Collaboration, Kampala, Uganda
| | - Gaurav Kwatra
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH, USA; Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | | | - Kirsty Le Doare
- Centre for Neonatal and Paediatric Infection, St George's, University of London, UK; UK Health Security Agency, Porton Down, UK; World Health Organization, Geneva, Switzerland
| | - Robert Mboizi
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | | | - Catrin E Moore
- Centre for Neonatal and Paediatric Infection, St George's, University of London, UK
| | - Eve Nakabembe
- Department of Obstetrics and Gynaecology, School of Medicine, Makerere University College of Health Sciences, Upper Mulago Hill Road, P.O. Box 7072 Kampala, Uganda
| | - Nichola R Naylor
- UK Health Security Agency, Porton Down, UK; Department of Health Services Research and Policy, London School of Hygiene & Tropical Medicine, London, UK
| | - Seamus O'Brien
- Global Antibiotic Research & Development Partnership (GARDP), Geneva, Switzerland
| | - Courtney Olwagen
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Denasha Reddy
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Charlene Rodrigues
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Dept of Paediatrics, Imperial College Healthcare NHS Trust, London, UK; Pathogen Genomics Programme, UK Health Security Agency, London, UK
| | - David A Rosen
- Department of Pediatrics and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Padmini Srikantiah
- Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mateusz Hasso-Agopsowicz
- Department of Immunization, Vaccines & Biologicals, World Health Organization, Geneva, Switzerland
| | - Shabir A Madhi
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
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Joseph A, Edet U, Asanga E, Udoeyop FA, Ubi BI, Bebia G, Akindele AFI, Odu R, Nwaokorie F. Spice-Induced Metal Contamination and Microbiological Risk Assessment of Instant Noodles Prepared for Human Consumption. Biol Trace Elem Res 2023:10.1007/s12011-023-04018-y. [PMID: 38150117 DOI: 10.1007/s12011-023-04018-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/11/2023] [Indexed: 12/28/2023]
Abstract
With the rising worries of potential metal contamination in cooked noodles, this study aimed at unravelling, for the first time, the possible source of metal contamination in cooked noodles. Noodles cooked with full spices (CWFS), cooked with half spices (CWHS), cooked with quarter spices (CWQS), and cooked with no spices (CWNS: control) and their spices were analysed for metals using inductively coupled plasma-atomic emission spectrometry. The microbiological quality of the noodles was also evaluated. Metal concentrations in cooked noodles varied with spice quantity. Noodles CWFS had the highest significant (p < 0.05) concentration of Pb (0.36 ± 0.12 mg/kg), Ni (1.05 ± 0.01 mg/kg), Cd (0.07 ± 0.04 mg/kg), Co (0.02 ± 0.002 mg/kg), and Na (9.45 ± 0.04 mg/kg), compared to the control (CWNS). The mean Pb and Ni of spice and cooked noodles were above the WHO acceptable limits for food and could be harmful to consumers. Pearson's correlation and PCA showed that packed noodle spices introduced metals into the cooked noodles. Although the hazard indices (adults and children) in all noodle's groups were less than 1, children still had the potential to contract cancer from Ni exposure because the carcinogenic risk values of CWQS (2.87 × 10-4), CWHS (3.03 × 10-4), and CWFS (3.21 × 10-4) were greater than 10-4. Microbiological analysis revealed the presence of potential pathogens that showed multidrug resistance and the ability to elaborate protease and amylase enzymes. Given the impending chronic health risks inherent in processed noodles, consistent consumption should be avoided.
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Affiliation(s)
- Akaninyene Joseph
- Department of Biosciences and Biotechnology, Faculty of Science, University of Medical Sciences, Ondo City, Ondo State, Nigeria.
- Key Laboratory of Integrated Regulation and Resource Development On Shallow Lake, College of Environment, Hohai University, Nanjing, 210098, People's Republic of China.
| | - Uwem Edet
- Department of Biological Sciences, Faculty of Natural and Applied Sciences, Arthur Jarvis University, Akpabuyo, Cross River State, Nigeria
| | - Edet Asanga
- Department of Chemical Sciences, Faculty of Natural and Applied Sciences, Arthur Jarvis University, Akpabuyo, Cross River State, Nigeria
| | - Favor Akpakpan Udoeyop
- Department of Biochemistry, Faculty of Basic Medical Sciences, PAMO University of Medical Science, Port Harcourt, Rivers State, Nigeria
| | - Bassey Ini Ubi
- Department of Microbiology, Faculty of Biological Sciences, University of Calabar, Calabar, Cross River State, Nigeria
| | - Glory Bebia
- Department of Medical Microbiology/Parasitology, Faculty of Medical Laboratory Science, University of Calabar, Calabar, Cross River State, Nigeria
| | - Ajoke F I Akindele
- Department of Biosciences and Biotechnology, Faculty of Science, University of Medical Sciences, Ondo City, Ondo State, Nigeria
| | - Regina Odu
- Department of Biological Sciences, Faculty of Natural and Applied Sciences, Arthur Jarvis University, Akpabuyo, Cross River State, Nigeria
| | - Francisca Nwaokorie
- Department of Medical Laboratory Science, College of Medicine of the University of Lagos, Idi-Araba, Lagos, Nigeria
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5
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Kürekci C, Ünaldı Ö, Şahin S, García-Meniño I, Hammerl JA. Impact and Diversity of ESBL-Producing Klebsiella pneumoniae Recovered from Raw Chicken Meat Samples in Türkiye. Antibiotics (Basel) 2023; 13:14. [PMID: 38275324 PMCID: PMC10812783 DOI: 10.3390/antibiotics13010014] [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: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
The interrelationship between human, animal and environmental sectors leads to the spread of antibiotic resistance due to selective pressures, evolutionary traits and genomic evolution. In particular, the frequent use of antibiotics in livestock inevitably influences the emergence of specific resistance determinants in human strains, associated with reduced treatment options in clinical therapy. In this study, ESBL-producing Klebsiella pneumoniae strains isolated from chicken meat samples were evaluated for public health implications in Türkiye. Whole-genome sequencing was used for genetic dissection and phylogenetic comparison of their genomes. The isolates were assigned to four MLST types (ST147, ST37, ST2747 and ST219); two of them were found to represent the ST147 clone associated with severe human infections worldwide. In addition to cephalosporins, high resistance levels to quinolones/fluoroquinolones were identified phenotypically, caused by acquired resistance genes and chromosomal point variations. One isolate was also found to carry the qacE∆1 efflux transporter gene, which confers tolerance to quaternary ammonium compounds. The detection of virulence genes (i.e., that coding for enterobactin) associated with the pathogenicity of K. pneumoniae suggests a public health impact. Thus, comprehensive information on the occurrence and impact of K. pneumoniae from livestock is needed to derive appropriate management strategies for consumer protection. In this study, it was shown that poultry meat serves as a reservoir of clinically emerging multidrug-resistant high-risk clones.
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Affiliation(s)
- Cemil Kürekci
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Hatay Mustafa Kemal University, Hatay 31060, Türkiye
| | - Özlem Ünaldı
- Department of Microbiology Reference Laboratories, General Directorate of Public Health, Ministry of Health, Ankara 06430, Türkiye;
| | - Seyda Şahin
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Sivas Cumhuriyet University, Sivas 58070, Türkiye;
| | - Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain;
- Department Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany;
| | - Jens Andre Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany;
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Mario E, Hamza D, Abdel-Moein K. Hypervirulent Klebsiella pneumoniae among diarrheic farm animals: A serious public health concern. Comp Immunol Microbiol Infect Dis 2023; 102:102077. [PMID: 37844369 DOI: 10.1016/j.cimid.2023.102077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023]
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) is an emerging pathogen and it has more virulence factors than classical Klebsiella pneumoniae strains. Carbapenem-resistant hvKp (CR-hvKp) is a dangerous bacteria that has both high virulence and antibiotic resistance and poses a global public health problem worldwide. The current study was carried out to investigate the occurrence of hvKp as well as carbapenem-resistant Klebsiella pneumoniae (CRKP) and CR-hvKp among diarrheic farm animals. For this purpose, rectal swabs from 165 farm animals (45 cattle, 66 sheep, and 54 goats) were collected. Samples were processed for the isolation and identification of Klebsiella pneumoniae. Moreover, hvKp was detected using molecular techniques by amplification of biomarker virulence genes (rmpA, rmpA2, iucA, iroB, and peg-344), followed by a string test. On the other hand, all K. pneumoniae isolates were examined for carbapenem resistance by both phenotypic and molecular methods. The phylogenetic analysis of peg-344 sequences was carried out. The overall prevalence rates of K. pneumoniae, hvKp, CRKP, and CR-hvKp were 24.2%, 7.9%, 16.4%, and 6.1% respectively. HvKp and CR-hvKp were detected among all examined farm animal species. On a Molecular basis, all biomarker virulence genes were identified except iroB, but rmpA is the most prevalent one. The phylogenetic analysis of peg-344 sequences obtained from the study points out their genetic relatedness to those circulated among humans. In conclusion, the emergence of hvKp and CR-hvKp among diarrheic farm animals confers a great public health implication and thus, the possible animal reservoirs for such hypervirulent-antimicrobial resistant strains cannot be ruled out.
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Affiliation(s)
- Esiri Mario
- Department of Zoonoses, Faculty of Veterinary Medicine, Cairo University, Egypt
| | - Dalia Hamza
- Department of Zoonoses, Faculty of Veterinary Medicine, Cairo University, Egypt.
| | - Khaled Abdel-Moein
- Department of Zoonoses, Faculty of Veterinary Medicine, Cairo University, Egypt
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Mourão J, Ribeiro-Almeida M, Novais C, Magalhães M, Rebelo A, Ribeiro S, Peixe L, Novais Â, Antunes P. From Farm to Fork: Persistence of Clinically Relevant Multidrug-Resistant and Copper-Tolerant Klebsiella pneumoniae Long after Colistin Withdrawal in Poultry Production. Microbiol Spectr 2023; 11:e0138623. [PMID: 37428073 PMCID: PMC10434174 DOI: 10.1128/spectrum.01386-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Abstract
Concerns about colistin-resistant bacteria in animal food-environmental-human ecosystems prompted the poultry sector to implement colistin restrictions and explore alternative trace metals/copper feed supplementation. The impact of these strategies on the selection and persistence of colistin-resistant Klebsiella pneumoniae in the whole poultry production chain needs clarification. We assessed colistin-resistant and copper-tolerant K. pneumoniae occurrence in chickens raised with inorganic and organic copper formulas from 1-day-old chicks to meat (7 farms from 2019 to 2020), after long-term colistin withdrawal (>2 years). Clonal diversity and K. pneumoniae adaptive features were characterized by cultural, molecular, and whole-genome-sequencing (WGS) approaches. Most chicken flocks (75%) carried K. pneumoniae at early and preslaughter stages, with a significant decrease (P < 0.05) in meat batches (17%) and sporadic water/feed contamination. High rates (>50%) of colistin-resistant/mcr-negative K. pneumoniae were observed among fecal samples, independently of feed. Most samples carried multidrug-resistant (90%) and copper-tolerant (81%; silA and pcoD positive and with a MICCuSO4 of ≥16 mM) isolates. WGS revealed accumulation of colistin resistance-associated mutations and F type multireplicon plasmids carrying antibiotic resistance and metal/copper tolerance genes. The K. pneumoniae population was polyclonal, with various lineages dispersed throughout poultry production. ST15-KL19, ST15-KL146, and ST392-KL27 and IncF plasmids were similar to those from global human clinical isolates, suggesting chicken production as a reservoir/source of clinically relevant K. pneumoniae lineages and genes with potential risk to humans through food and/or environmental exposure. Despite the limited mcr spread due to the long-term colistin ban, this action was ineffective in controlling colistin-resistant/mcr-negative K. pneumoniae, regardless of feed. This study provides crucial insights into the persistence of clinically relevant K. pneumoniae in the poultry production chain and highlights the need for continued surveillance and proactive food safety actions within a One Health perspective. IMPORTANCE The spread of bacteria resistant to last-resort antibiotics such as colistin throughout the food chain is a serious concern for public health. The poultry sector has responded by restricting colistin use and exploring alternative trace metals/copper feed supplements. However, it is unclear how and to which extent these changes impact the selection and persistence of clinically relevant Klebsiella pneumoniae throughout the poultry chain. We found a high occurrence of copper-tolerant and colistin-resistant/mcr-negative K. pneumoniae in chicken flocks, regardless of inorganic and organic copper formulas use and a long-term colistin ban. Despite the high K. pneumoniae isolate diversity, the occurrence of identical lineages and plasmids across samples and/or clinical isolates suggests poultry as a potential source of human K. pneumoniae exposure. This study highlights the need for continued surveillance and proactive farm-to-fork actions to mitigate the risks to public health, relevant for stakeholders involved in the food industry and policymakers tasked with regulating food safety.
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Affiliation(s)
- Joana Mourão
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Marisa Ribeiro-Almeida
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Mafalda Magalhães
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
- ESS, Polytechnic of Porto, Porto, Portugal
| | - Sofia Ribeiro
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ângela Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
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8
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Crippa C, Pasquali F, Rodrigues C, De Cesare A, Lucchi A, Gambi L, Manfreda G, Brisse S, Palma F. Genomic features of Klebsiella isolates from artisanal ready-to-eat food production facilities. Sci Rep 2023; 13:10957. [PMID: 37414963 PMCID: PMC10326032 DOI: 10.1038/s41598-023-37821-7] [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: 02/07/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
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.
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Affiliation(s)
- Cecilia Crippa
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy.
| | - Frédérique Pasquali
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Carla Rodrigues
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Alessandra De Cesare
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Ozzano Dell'Emilia, 40064, Bologna, Italy
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Lucia Gambi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
- Biological Resource Center of Institut Pasteur, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Federica Palma
- Biological Resource Center of Institut Pasteur, Institut Pasteur, Université Paris Cité, 75015, Paris, France
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9
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Williamson CHD, Roe CC, Terriquez J, Hornstra H, Lucero S, Nunnally AE, Vazquez AJ, Vinocur J, Plude C, Nienstadt L, Stone NE, Celona KR, Wagner DM, Keim P, Sahl JW. A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment. Microb Genom 2023; 9. [PMID: 37347682 DOI: 10.1099/mgen.0.001046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023] Open
Abstract
Although infections caused by Clostridioides difficile have historically been attributed to hospital acquisition, growing evidence supports the role of community acquisition in C. difficile infection (CDI). Symptoms of CDI can range from mild, self-resolving diarrhoea to toxic megacolon, pseudomembranous colitis, and death. In this study, we sampled C. difficile from clinical, environmental, and canine reservoirs in Flagstaff, Arizona, USA, to understand the distribution and transmission of the pathogen in a One Health framework; Flagstaff is a medium-sized, geographically isolated city with a single hospital system, making it an ideal site to characterize genomic overlap between sequenced C. difficile isolates across reservoirs. An analysis of 562 genomes from Flagstaff isolates identified 65 sequence types (STs), with eight STs being found across all three reservoirs and another nine found across two reservoirs. A screen of toxin genes in the pathogenicity locus identified nine STs where all isolates lost the toxin genes needed for CDI manifestation (tcdB, tcdA), demonstrating the widespread distribution of non-toxigenic C. difficile (NTCD) isolates in all three reservoirs; 15 NTCD genomes were sequenced from symptomatic, clinical samples, including two from mixed infections that contained both tcdB+ and tcdB- isolates. A comparative single nucleotide polymorphism (SNP) analysis of clinically derived isolates identified 78 genomes falling within clusters separated by ≤2 SNPs, indicating that ~19 % of clinical isolates are associated with potential healthcare-associated transmission clusters; only symptomatic cases were sampled in this study, and we did not sample asymptomatic transmission. Using this same SNP threshold, we identified genomic overlap between canine and soil isolates, as well as putative transmission between environmental and human reservoirs. The core genome of isolates sequenced in this study plus a representative set of public C. difficile genomes (n=136), was 2690 coding region sequences, which constitutes ~70 % of an individual C. difficile genome; this number is significantly higher than has been published in some other studies, suggesting that genome data quality is important in understanding the minimal number of genes needed by C. difficile. This study demonstrates the close genomic overlap among isolates sampled across reservoirs, which was facilitated by maximizing the genomic search space used for comprehensive identification of potential transmission events. Understanding the distribution of toxigenic and non-toxigenic C. difficile across reservoirs has implications for surveillance sampling strategies, characterizing routes of infections, and implementing mitigation measures to limit human infection.
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Affiliation(s)
| | - Chandler C Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Heidie Hornstra
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Samantha Lucero
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Amalee E Nunnally
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Adam J Vazquez
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | | | | | - Nathan E Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Kimberly R Celona
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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10
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Liu CM, Aziz M, Park DE, Wu Z, Stegger M, Li M, Wang Y, Schmidlin K, Johnson TJ, Koch BJ, Hungate BA, Nordstrom L, Gauld L, Weaver B, Rolland D, Statham S, Hall B, Sariya S, Davis GS, Keim PS, Johnson JR, Price LB. Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections. One Health 2023; 16:100518. [PMID: 37363239 PMCID: PMC10288061 DOI: 10.1016/j.onehlt.2023.100518] [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: 09/30/2022] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
A one-health perspective may provide new and actionable information about Escherichia coli transmission. E. coli colonizes a broad range of vertebrates, including humans and food-production animals, and is a leading cause of bladder, kidney, and bloodstream infections in humans. Substantial evidence supports foodborne transmission of pathogenic E. coli strains from food animals to humans. However, the relative contribution of foodborne zoonotic E. coli (FZEC) to the human extraintestinal disease burden and the distinguishing characteristics of such strains remain undefined. Using a comparative genomic analysis of a large collection of contemporaneous, geographically-matched clinical and meat-source E. coli isolates (n = 3111), we identified 17 source-associated mobile genetic elements - predominantly plasmids and bacteriophages - and integrated them into a novel Bayesian latent class model to predict the origins of clinical E. coli isolates. We estimated that approximately 8 % of human extraintestinal E. coli infections (mostly urinary tract infections) in our study population were caused by FZEC. FZEC strains were equally likely to cause symptomatic disease as non-FZEC strains. Two FZEC lineages, ST131-H22 and ST58, appeared to have particularly high virulence potential. Our findings imply that FZEC strains collectively cause more urinary tract infections than does any single non-E. coli uropathogenic species (e.g., Klebsiella pneumoniae). Our novel approach can be applied in other settings to identify the highest-risk FZEC strains, determine their sources, and inform new one-health strategies to decrease the heavy public health burden imposed by extraintestinal E. coli infections.
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Affiliation(s)
- Cindy M. Liu
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
- The Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Room 210 Building 56, Applied Research & Development, 1395 S Knoles Drive, Flagstaff, AZ 86011, USA
| | - Maliha Aziz
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Daniel E. Park
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Zhenke Wu
- Department of Biostatistics, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
- Michigan Institute for Data Science (MIDAS), University of Michigan, 500 Church Street, Suite 600, Ann Arbor, MI 48109, USA
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
| | - Mengbing Li
- Department of Biostatistics, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Yashan Wang
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Kara Schmidlin
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1365 Gortner Ave, St Paul, MN 55108, USA
| | - Benjamin J. Koch
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Lora Nordstrom
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Lori Gauld
- Flagstaff Medical Center, 1200 N. Beaver St. Flagstaff, AZ 86001, USA
| | - Brett Weaver
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Diana Rolland
- Flagstaff Medical Center, 1200 N. Beaver St. Flagstaff, AZ 86001, USA
| | - Sally Statham
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - Brantley Hall
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sanjeev Sariya
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Gregg S. Davis
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Paul S. Keim
- The Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Room 210 Building 56, Applied Research & Development, 1395 S Knoles Drive, Flagstaff, AZ 86011, USA
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
| | - James R. Johnson
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN 55417, USA
| | - Lance B. Price
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), 3051 W Shamrell Blvd, Flagstaff, AZ 86005, USA
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11
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Florea A, Casey JA, Nachman K, Price LB, Pomichowski ME, Takhar HS, Quinlivan V, Childs LD, Davis MF, Wei R, Hong V, Ku JH, Liu CM, Pressman A, Robinson S, Bruxvoort KJ, Salas SB, Tartof SY. Impact of California's Senate Bill 27 on Antimicrobial-Resistant Escherichia coli Urinary Tract Infection in Humans: Protocol for a Study of Methods and Baseline Data. JMIR Res Protoc 2023; 12:e45109. [PMID: 37145842 PMCID: PMC10199382 DOI: 10.2196/45109] [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: 01/17/2023] [Revised: 03/17/2023] [Accepted: 04/04/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Overuse of antibiotics contributes to antimicrobial resistance (AMR) and is a growing threat to human health worldwide. Previous work suggests a link between antimicrobial use in poultry and human AMR extraintestinal pathogenic Escherichia coli (E coli) urinary tract infections (UTIs). However, few US-based studies exist, and none have comprehensively assessed both foodborne and environmental pathways using advanced molecular and spatial epidemiologic methods in a quasi-experimental design. Recently, California enacted Senate Bill 27 (SB27), which changed previous policy to require a veterinarian's prescription for the use of antibiotic drugs, and which banned antibiotic use for disease prevention in livestock. This provided an opportunity to evaluate whether SB27 will result in a reduction in antimicrobial-resistant infections in humans. OBJECTIVE We describe in detail the methods implemented to achieve the overarching objective of this study to evaluate the impact of SB27 on downstream antibiotic resistance rates in human UTIs. METHODS A summary of the overall approach and the partnerships between Columbia University, George Washington University (GWU), Johns Hopkins Bloomberg School of Public Health, Kaiser Permanente Southern California (KPSC) Research and Evaluation, the Natural Resources Defense Council, Sanger Institute at Stanford University, Sutter Health Center for Health Systems Research, the University of Cambridge, and the University of Oxford is presented. The collection, quality control testing, and shipment of retail meat and clinical samples are described. Retail meat (chicken, beef, turkey, and pork) was purchased from stores throughout Southern California from 2017 to 2021. After processing at KPSC, it was shipped to GWU for testing. From 2016 to 2021, after clinical specimens were processed for routine clinical purposes and immediately before discarding, those with isolated colonies of E coli, Campylobacter, and Salmonella from KPSC members were collected and processed to be shipped for testing at GWU. Detailed methods of the isolation and testing as well as the whole-genome sequencing of the meat and clinical samples at GWU are described. KPSC electronic health record data were used to track UTI cases and AMR patterns among the cultured specimens. Similarly, Sutter Health electronic health record data were used to track UTI cases in its Northern California patient population. RESULTS From 2017 to 2021, overall, 12,616 retail meat samples were purchased from 472 unique stores across Southern California. In addition, 31,643 positive clinical cultures were collected from KPSC members during the same study period. CONCLUSIONS Here, we presented data collection methods for the study, which was conducted to evaluate the impact of SB27 on downstream antibiotic resistance rates in human UTI. To date, it is one of the largest studies of its kind to be conducted. The data collected during this study will be used as the foundation for future analyses specific to the various objectives of this large body of work. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/45109.
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Affiliation(s)
- Ana Florea
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Joan A Casey
- Columbia University Mailman School of Public Health, New York City, NY, United States
| | - Keeve Nachman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Lance B Price
- Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Magdalena E Pomichowski
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Harpreet S Takhar
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Vanessa Quinlivan
- Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Lee D Childs
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Meghan F Davis
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Rong Wei
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Vennis Hong
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Jennifer H Ku
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Cindy M Liu
- Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Alice Pressman
- Center for Health Systems Research, Sutter Health, Walnut Creek, CA, United States
| | - Sarah Robinson
- Center for Health Systems Research, Sutter Health, Walnut Creek, CA, United States
| | - Katia J Bruxvoort
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - S Bianca Salas
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Sara Y Tartof
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
- Department of Health Systems Science, Kaiser Permanente Bernard J Tyson School of Medicine, Pasadena, CA, United States
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12
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Lavin LE, Maki LC. Antimicrobial use in the surgical treatment of canine pyometra: A questionnaire survey of Arizona-licensed veterinarians. Vet Med Sci 2023; 9:1124-1133. [PMID: 37051761 DOI: 10.1002/vms3.1130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 02/06/2023] [Accepted: 03/03/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND Recent studies and consensus statements in veterinary and human medicine recommend more judicious use of antimicrobials. While guidelines have been provided for some veterinary diseases, others have poorly elucidated guidelines. Postoperative treatment of canine pyometra is a condition with minimal guidelines regarding antimicrobial use. OBJECTIVE To identify and investigate patterns of antimicrobial use following surgically treated canine pyometra. METHODS A 23-question survey, sent to 863 small and mixed animal practitioners, investigated demographics, patterns of antibiotic use, rate of culture submission and participant's recollection of outcomes of surgically treated pyometra cases. Responses were analysed for relationships between demographics, patterns of antibiotic use and culture results to better understand reasoning for antibiotic protocols. RESULTS One hundred and fifty-two responses were received. Overall, 76% of veterinarians stated they always use preoperative and perioperative antibiotics, and 74% stated they always use postoperative antibiotics. A total of 16 different antibiotics were reported. Twelve per cent of respondents regularly submitted a culture. Culture submission was impacted by cost, prior experience, poor owner compliance, result turnaround time and anticipated results. CONCLUSIONS Most respondents always used antibiotics and rarely or never submitted a culture. To optimise patient care, future clinical studies are needed to determine specific guidelines for the use of culture and antibiotics in the treatment of canine pyometra following ovariohysterectomy.
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Affiliation(s)
- Lindsey E Lavin
- Department of Small Animal Surgery, Ocean State Veterinary Specialists, East Greenwich, Rhode Island
| | - Lynn C Maki
- Department of Small Animal Surgery, VetMED Emergency and Specialty Veterinary Hospital, Phoenix, Arizona, United States
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13
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Shen C, Lv T, Huang G, Zhang X, Zheng L, Chen Y. Genomic Insights Into Molecular Characteristics and Phylogenetic Linkage Between the Cases of Carbapenem-Resistant Klebsiella pneumoniae From a Non-tertiary Hospital in China: A Cohort Study. Jundishapur J Microbiol 2023. [DOI: 10.5812/jjm-133210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) strains have been listed as one of the major clinical concerns. Objectives: We investigated CPKP isolates from non-tertiary hospitals to find disseminated clones and analyze extensive phenotypic and genetic diversity in this study. Methods: In this cohort study, a total of 49 CRKP isolates from 3 hospitals in the same region were collected in 2021. The prevalence and antimicrobial susceptibility patterns were analyzed. Clinical data were retrieved from electronic medical record systems. The molecular types, antimicrobial resistance (AMR) profiles, plasmid replicons, and virulence factors were analyzed. The maximum-likelihood phylogenetic tree and transmission networks were constructed using single-nucleotide polymorphisms (SNPs). Results: The median age of patients (N = 49) was 66.0 years, and 85.7% were male. The most common CRKP infection was nosocomial pneumonia (75.5%), followed by bacteremia (10.2%). More than 53% of isolates were resistant to ceftazidime-avibactam (CAZ/AVI). Forty-five isolates were successfully sequenced; the predominant carbapenem-resistant gene was blaKPC-2 (93.3%). The 30-day mortality in our cohort was 24.5%. The most dominant sequence type (ST) was ST11 (60.0%), followed by ST15 (13.3%). Whole genome sequencing (WGS) analysis exhibited dissemination of ST11 strain clones, ST420, and ST15 clones, both within and outside the given hospital. Conclusions: In this surveillance study, several dissemination chains of CRKP were discovered in the hospital and the region, as ST11 was the main epidemic clone. Our findings suggest that effective infection control practices and antimicrobial stewardship are needed in non-tertiary hospitals in China.
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14
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Casey JA, Tartof SY, Davis MF, Nachman KE, Price L, Liu C, Yu K, Gupta V, Innes GK, Tseng HF, Do V, Pressman AR, Rudolph KE. Impact of a Statewide Livestock Antibiotic Use Policy on Resistance in Human Urine Escherichia coli Isolates: A Synthetic Control Analysis. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:27007. [PMID: 36821707 PMCID: PMC9945560 DOI: 10.1289/ehp11221] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND On 1 January 2018, California implemented Senate Bill 27 (SB27), banning, for the first time in the United States, routine preventive use of antibiotics in food-animal production and any antibiotic use without a veterinarian's prescription. OBJECTIVES Our objective was to assess whether SB27 was associated with decreased antimicrobial resistance among E. coli isolated from human urine. METHODS We used U.S. nationwide monthly state-level data from BD Insights Research Database (Becton, Dickinson, and Co.) spanning 1 January 2013 to 30 June 2021 on antibiotic-resistance patterns of 30-d nonduplicate E. coli isolated from urine. Tested antibiotic classes included aminoglycosides, extended-spectrum cephalosporins (ESC), fluoroquinolones, and tetracyclines. Counts of tested and not-susceptible (resistant and intermediate, hereafter resistant) urine isolates were available by sex, age group (<65, 65+ year), month, and state. We applied a synthetic control approach to estimate the causal effect of SB27 on resistance patterns. Our approach created a synthetic California based on a composite of other states without the policy change and contrasted its counterfactual postpolicy trends with the observed postpolicy trends in California. FINDINGS We included 7.1 million E. coli urine isolates, 90% among women, across 33 states. From 2013 to 2017, the median (interquartile range) resistance percentages in California were 11.9% (7.4, 17.6), 13.8% (5.8, 20.0), 24.6% (9.6, 36.4), 7.9% (2.1, 13.1), for aminoglycosides, ESC, fluoroquinolones, and tetracyclines, respectively. SB27 was associated with a 7.1% reduction in ESC resistance (p-value for joint null: <0.01), but no change in resistance to aminoglycosides, fluoroquinolones, or tetracyclines. DISCUSSION Further research is needed to determine the role of SB27 in the observed reduction in ESC resistance E. coli in human populations, particularly as additional states implement similar legislation. https://doi.org/10.1289/EHP11221.
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Affiliation(s)
- Joan A. Casey
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Sara Y. Tartof
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, California, USA
| | - Meghan F. Davis
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Molecular and Comparative Pathobiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Keeve E. Nachman
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Johns Hopkins Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Lance Price
- Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, USA
| | - Cindy Liu
- Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, USA
| | - Kalvin Yu
- Medical and Scientific Affairs, Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Vikas Gupta
- Medical and Scientific Affairs, Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Gabriel K. Innes
- Yuma Center of Excellence for Desert Agriculture (YCEDA), University of Arizona, Yuma, Arizona, USA
| | - Hung Fu Tseng
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Vivian Do
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Alice R. Pressman
- Center for Health Systems Research, Sutter Health, Walnut Creek, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Kara E. Rudolph
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, USA
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15
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Xie ST, Ding LJ, Huang FY, Zhao Y, An XL, Su JQ, Sun GX, Song YQ, Zhu YG. VFG-Chip: A high-throughput qPCR microarray for profiling virulence factor genes from the environment. ENVIRONMENT INTERNATIONAL 2023; 172:107761. [PMID: 36682204 DOI: 10.1016/j.envint.2023.107761] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
As zoonotic pathogens are threatening public health globally, the virulence factor genes (VFGs) they carry underlie latent risk in the environment. However, profiling VFGs in the environment is still in its infancy due to lack of efficient and reliable quantification tools. Here, we developed a novel high-throughput qPCR (HT-qPCR) chip, termed as VFG-Chip, to comprehensively quantify the abundances of targeted VFGs in the environment. A total of 96 VFGs from four bacterial pathogens including Klebsiella pneumoniae, Acinetobacter baumannii, Escherichia coli, and Salmonella enterica were targeted by 120 primer pairs, which were involved in encoding five types of virulence factors (VFs) like toxin, adherence, secretion system, immune evasion/invasion, and iron uptake. The specificity of VFG-Chip was both verified computationally and experimentally, with high identity of amplicon sequencing and melting curves analysis proving its robust capability. The VFG-Chip also displayed high sensitivity (by plasmid serial dilution test) and amplification efficiency averaging 97.7%. We successfully applied the VFG-Chip to profile the distribution of VFGs along a wastewater treatment system with 69 VFGs detected in total. Overall, the VFG-Chip provides a robust tool for comprehensively quantifying VFGs in the environment, and thus provides novel information in assessing the health risks of zoonotic pathogens in the environment.
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Affiliation(s)
- Shu-Ting Xie
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Fu-Yi Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Yi Zhao
- School of Water Resources and Environment, China, University of Geosciences (Beijing), Beijing 100083, China
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Jian-Qiang Su
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Guo-Xin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ya-Qiong Song
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsenvej 40, 1871 Frederiksberg, Denmark
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
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16
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Draft Genomic Sequence for Klebsiella pneumoniae 060517CS3-g, a Bacterium Harboring Multidrug Resistance Genes, Isolated from Retail Ground Chicken Meat. Microbiol Resour Announc 2023; 12:e0094922. [PMID: 36475878 PMCID: PMC9872595 DOI: 10.1128/mra.00949-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Klebsiella pneumoniae is an important foodborne pathogen that can cause human infections. Here, we report the draft genomic sequence for K. pneumoniae 060517CS3-g, isolated from retail ground chicken meat, which has several antibiotic resistance genes, multiple plasmids, and genes that may result in its hypervirulence based on the sequence data.
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17
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Shao S, Pan W, Wang B, Liu Y, Gan H, Li M, Liao T, Yang X, Yang Q, Huang C, Geng M, Pan G, Liu K, Zhu P, Tao F. Association between antibiotic exposure and the risk of infertility in women of childbearing age: A case-control study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114414. [PMID: 36516626 DOI: 10.1016/j.ecoenv.2022.114414] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Based on self-report questionnaires, two previous epidemiological studies investigated the association between the exposure of women to antibiotics and their fertility. However, biomonitoring studies on low-dose antibiotic exposure, mainly from food and water, and its relation to the risk of infertility are missing. METHODS Based on a case-control study design, 302 women with infertility (144 primary infertility, 158 secondary infertility) and 302 women with normal fertility, all aged 20-49 years, were recruited from Anhui Province, China, in 2020 and 2021. A total of 41 common antibiotics and two antibiotic metabolites in urine samples were determined by liquid chromatography-triple quadrupole tandem mass spectrometry (LC-QqQ-MS/MS). RESULTS Twenty-eight antibiotics with detection rates from 10% to 100% in both cases (median concentration: ∼2.294 ng/mL) and controls (∼1.596 ng/mL) were included in the analysis. Logistic regression analysis revealed that after controlling for confounding factors, high concentrations of eight individual antibiotics (sulfamethoxazole, sulfaclozine, sulfamonomethoxine, penicillin G, chlorotetracycline, ofloxacin, norfloxacin, and cyadox) and four antibiotic classes (sulfonamides, tetracyclines, quinoxalines, and veterinary antibiotics) were related to a high risk of female infertility, with odds ratios (ORs) ranging from 1.30 to 2.86, except for chlorotetracycline (OR = 6.34), while another nine individual antibiotics (sulfamethazine, azithromycin, cefaclor, amoxicillin, oxytetracycline, pefloxacin, sarafloxacin, enrofloxacin, and florfenicol) and classes of chloramphenicol analogs and human antibiotics were related to a reduced risk of infertility, with ORs ranging from 0.70 to 0.20. Based on restricted cubic spline models after controlling for confounding factors, we observed that the relationship between all of the above protective antibiotics and infertility was nonlinear: A certain concentration could reduce the risk of female infertility while exceeding a safe dose could increase the risk of infertility. CONCLUSION These results provide preliminary evidence that the effects of antibiotics on female fertility vary based on the active ingredient and usage and imply the importance of exposure dose. Future studies are needed to verify these results by controlling for multiple confounding factors.
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Affiliation(s)
- Shanshan Shao
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, No 81 Meishan Road, Hefei, Anhui, China; Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
| | - Weijun Pan
- Clinical Center of Reproductive Medicine, Ma'anshan Maternal and Child Health Hospital, Ma'anshan, Anhui, China
| | - Baolin Wang
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, No 81 Meishan Road, Hefei, Anhui, China; Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
| | - Yuwei Liu
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, No 81 Meishan Road, Hefei, Anhui, China; Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
| | - Hong Gan
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, No 81 Meishan Road, Hefei, Anhui, China; Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
| | - Mengdie Li
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, No 81 Meishan Road, Hefei, Anhui, China; Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
| | - Tierong Liao
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, No 81 Meishan Road, Hefei, Anhui, China; Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
| | - Xinliu Yang
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, No 81 Meishan Road, Hefei, Anhui, China; Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
| | - Qianhui Yang
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, No 81 Meishan Road, Hefei, Anhui, China; Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
| | - Cun Huang
- Clinical Center of Reproductive Medicine, Ma'anshan Maternal and Child Health Hospital, Ma'anshan, Anhui, China
| | - Menglong Geng
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, No 81 Meishan Road, Hefei, Anhui, China; Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
| | - Guixia Pan
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
| | - Kaiyong Liu
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, No 81 Meishan Road, Hefei, Anhui, China; Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
| | - Peng Zhu
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, No 81 Meishan Road, Hefei, Anhui, China; Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China
| | - Fangbiao Tao
- School of Public Health, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, No 81 Meishan Road, Hefei, Anhui, China; Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, No 81 Meishan Road, Hefei, Anhui, China.
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18
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Huang M, He P, He P, Wu Y, Munir S, He Y. Novel Virulence Factors Deciphering Klebsiella pneumoniae KpC4 Infect Maize as a Crossing-Kingdom Pathogen: An Emerging Environmental Threat. Int J Mol Sci 2022; 23:ijms232416005. [PMID: 36555647 PMCID: PMC9785288 DOI: 10.3390/ijms232416005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Klebsiella pneumoniae is not only a human and animal opportunistic pathogen, but a food-borne pathogen. Cross-kingdom infection has been focused on since K. pneumoniae was identified as the pathogen of maize, banana, and pomegranate. Although the pathogenicity of K. pneumoniae strains (from ditch water, maize, and human) on plant and mice has been confirmed, there are no reports to explain the molecular mechanisms of the pathogen. This study uncovered the K. pneumoniae KpC4 isolated from maize top rot for the determination of various virulence genes and resistance genes. At least thirteen plant disease-causing genes are found to be involved in the disruption of plant defense. Among them, rcsB is responsible for causing disease in both plants and animals. The novel sequence types provide solid evidence that the pathogen invades plant and has robust ecological adaptability. It is imperative to perform further studies on the verification of these KpC4 genes’ functions to understand the molecular mechanisms involved in plant−pathogen interactions.
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Affiliation(s)
- Min Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- College of Agronomy and Life Sciences and Engineering Research Center for Urban Modern Agriculture of Higher Education in Yunnan Province, Kunming University, Kunming 650214, China
| | - Pengfei He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Pengbo He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Yixin Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Shahzad Munir
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Correspondence: (S.M.); (Y.H.)
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Correspondence: (S.M.); (Y.H.)
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19
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Yadav M, Dhyani S, Joshi P, Awasthi S, Tanwar S, Gupta V, Rathore DK, Chaudhuri S. Formic acid, an organic acid food preservative, induces viable-but-non-culturable state, and triggers new Antimicrobial Resistance traits in Acinetobacter baumannii and Klebsiella pneumoniae. Front Microbiol 2022; 13:966207. [PMID: 36504816 PMCID: PMC9730046 DOI: 10.3389/fmicb.2022.966207] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/14/2022] [Indexed: 11/25/2022] Open
Abstract
Numerous human pathogens, especially Gram-negative bacteria, are able to enter the viable-but-non-culturable (VBNC) state when they are exposed to environmental stressors and pose the risk of being resuscitated and causing infection after the removal of the trigger. Widely used food preservatives like weak organic acids are potential VBNC inducers in food processing and packaging facilities but have only been reported for food-borne pathogens. In the present study, it is demonstrated for the first time that one such agent, formic acid (FA), can induce a VBNC state at food processing, storage, and distribution temperatures (4, 25, and 37°C) with a varied time of treatment (days 4-10) in pathogenic Gram-negative bacteria Acinetobacter baumannii and Klebsiella pneumoniae. The use of hospital-associated pathogens is critical based on the earlier reports that demonstrated the presence of these bacteria in hospital kitchens and commonly consumed foods. VBNC induction was validated by multiple parameters, e.g., non-culturability, metabolic activity as energy production, respiratory markers, and membrane integrity. Furthermore, it was demonstrated that the removal of FA was able to resuscitate VBNC with an increased expression of multiple virulence and Antimicrobial Resistance (AMR) genes in both pathogens. Since food additives/preservatives are significantly used in most food manufacturing facilities supplying to hospitals, contamination of these packaged foods with pathogenic bacteria and the consequence of exposure to food additives emerge as pertinent issues for infection control, and control of antimicrobial resistance in the hospital setting.
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Affiliation(s)
| | | | | | | | | | | | | | - Susmita Chaudhuri
- Department of Multidisciplinary Clinical and Translational Research, Translational Health Science and Technology Institute, Faridabad, Haryana, India
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20
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Dereeper A, Gruel G, Pot M, Couvin D, Barbier E, Bastian S, Bambou JC, Gelu-Simeon M, Ferdinand S, Guyomard-Rabenirina S, Passet V, Martino F, Piveteau P, Reynaud Y, Rodrigues C, Roger PM, Roy X, Talarmin A, Tressieres B, Valette M, Brisse S, Breurec S. Limited Transmission of Klebsiella pneumoniae among Humans, Animals, and the Environment in a Caribbean Island, Guadeloupe (French West Indies). Microbiol Spectr 2022; 10:e0124222. [PMID: 36094181 PMCID: PMC9603589 DOI: 10.1128/spectrum.01242-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 08/08/2022] [Indexed: 12/30/2022] Open
Abstract
Guadeloupe (French West Indies), a Caribbean island, is an ideal place to study the reservoirs of the Klebsiella pneumoniae species complex (KpSC) and identify the routes of transmission between human and nonhuman sources due to its insularity, small population size, and small area. Here, we report an analysis of 590 biological samples, 546 KpSC isolates, and 331 genome sequences collected between January 2018 and May 2019. The KpSC appears to be common whatever the source. Extended-spectrum-β-lactamase (ESBL)-producing isolates (21.4%) belonged to K. pneumoniae sensu stricto (phylogroup Kp1), and all but one were recovered from the hospital setting. The distribution of species and phylogroups across the different niches was clearly nonrandom, with a distinct separation of Kp1 and Klebsiella variicola (Kp3). The most frequent sequence types (STs) (≥5 isolates) were previously recognized as high-risk multidrug-resistant (MDR) clones, namely, ST17, ST307, ST11, ST147, ST152, and ST45. Only 8 out of the 63 STs (12.7%) associated with human isolates were also found in nonhuman sources. A total of 22 KpSC isolates were defined as hypervirulent: 15 associated with human infections (9.8% of all human isolates), 4 (8.9%) associated with dogs, and 3 (15%) associated with pigs. Most of the human isolates (33.3%) belonged to the globally successful sublineage CG23-I. ST86 was the only clone shared by a human and a nonhuman (dog) source. Our work shows the limited transmission of KpSC isolates between human and nonhuman sources and points to the hospital setting as a cornerstone of the spread of MDR clones and antibiotic resistance genes. IMPORTANCE In this study, we characterized the presence and genomic features of isolates of the Klebsiella pneumoniae species complex (KpSC) from human and nonhuman sources in Guadeloupe (French West Indies) in order to identify the reservoirs and routes of transmission. This is the first study in an island environment, an ideal setting that limits the contribution of external imports. Our data showed the limited transmission of KpSC isolates between the different compartments. In contrast, we identified the hospital setting as the epicenter of antibiotic resistance due to the nosocomial spread of successful multidrug-resistant (MDR) K. pneumoniae clones and antibiotic resistance genes. Ecological barriers and/or limited exposure may restrict spread from the hospital setting to other reservoirs and vice versa. These results highlight the need for control strategies focused on health care centers, using genomic surveillance to limit the spread, particularly of high-risk clones, of this important group of MDR pathogens.
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Affiliation(s)
- Alexis Dereeper
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Gaëlle Gruel
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Elodie Barbier
- UMR AgroEcologie, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Sylvaine Bastian
- Laboratory of Clinical Microbiology, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | | | - Moana Gelu-Simeon
- Hepato-Gastroenterology Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | | | - Virginie Passet
- Institut Pasteur, University Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Frederic Martino
- Intensive Care Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | | | - Yann Reynaud
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Carla Rodrigues
- Institut Pasteur, University Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Pierre-Marie Roger
- Infectious Disease Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
- Faculty of Medecine Hyacinthe Bastaraud, University of the Antilles, Pointe-à-Pitre, France
| | - Xavier Roy
- Veterinary Clinic, Baie-Mahault, Guadeloupe
| | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Benoit Tressieres
- INSERM Center for Clinical Investigation 1424, Pointe-à-Pitre/Les Abymes, France
| | - Marc Valette
- Intensive Care Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | - Sylvain Brisse
- Institut Pasteur, University Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
- Laboratory of Clinical Microbiology, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
- Faculty of Medecine Hyacinthe Bastaraud, University of the Antilles, Pointe-à-Pitre, France
- INSERM Center for Clinical Investigation 1424, Pointe-à-Pitre/Les Abymes, France
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Sanni AO, Onyango J, Usman A, Abdulkarim LO, Jonker A, Fasina FO. Risk Factors for Persistent Infection of Non-Typhoidal Salmonella in Poultry Farms, North Central Nigeria. Antibiotics (Basel) 2022; 11:antibiotics11081121. [PMID: 36009991 PMCID: PMC9405283 DOI: 10.3390/antibiotics11081121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/13/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022] Open
Abstract
Salmonellosis is a bacterial zoonosis causing an array of health conditions. Non-typhoidal salmonellosis (NTS) has a discrete adaptation to certain animals; in poultry, pullorum and fowl typhoid are its primary disease manifestations. The diseases are prevalent in Nigerian poultry and have been well-studied in Nigeria, but less so in North Central Nigeria (NCN). Using field sampling, laboratory methods and a semi-structured questionnaire for 1000 poultry farms in NCN, we explored the incidence and risk factors for the persistence of NTS infection in poultry. Approximately 41.6% of the farms had experienced NTS over the last 18 months. Farm experience of NTS moderately predicted awareness of salmonellosis. Increasing stock in smallholder farms, self-mixing of concentrate on the farm, usage of stream water, pen odour, non-adherence and partial adherence of farms to recommended poultry vaccination against pullorum and fowl typhoid and lack of and non-adherence to biosecurity were identified risk factors that increased the odds of NTS infection in poultry. Antibiotic use practice may have reduced the isolation rate of NTS, yet NTS continues to challenge poultry farms in Nigeria. Identified risk practices must be mitigated intentionally and biosecurity and hygiene must be improved to reduce the burden of NTS.
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Affiliation(s)
- Abdullahi O. Sanni
- Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, Pretoria 0110, South Africa
- Agro-Processing, Productivity Enhancement and Livelihood Improvement Support (APPEALS) Project, Lokoja 260101, Kogi State, Nigeria
| | - Joshua Onyango
- Harper and Keele Veterinary School, Harper Adams University, Newport TF10 8NB, UK
| | - Abdulkadir Usman
- Department of Animal Production, Federal University of Technology, Minna 920101, Niger, Nigeria
| | - Latifah O. Abdulkarim
- Agro-Processing, Productivity Enhancement and Livelihood Improvement Support (APPEALS) Project, Lokoja 260101, Kogi State, Nigeria
| | - Annelize Jonker
- Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, Pretoria 0110, South Africa
| | - Folorunso O. Fasina
- Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, Pretoria 0110, South Africa
- ECTAD Food and Agriculture Organization of the United Nations, Nairobi 00100, Kenya
- Correspondence: or ; Tel.: +254-111-3232-70
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22
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Parkhill J. Antimicrobial Resistance Exchange Between Humans and Animals: Why We Need to Know More. ENGINEERING (BEIJING, CHINA) 2022; 15:11-12. [PMID: 35910850 PMCID: PMC9325553 DOI: 10.1016/j.eng.2022.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/12/2022] [Accepted: 04/24/2022] [Indexed: 05/22/2023]
Affiliation(s)
- Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
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de Sousa ATHI, Costa MTDS, Cândido SL, Makino H, Morgado TO, Pavelegini LAD, Colodel EM, Nakazato L, Dutra V. Determination of multidrug-resistant populations and molecular characterization of complex Klebsiella spp. in wild animals by multilocus sequence typing. Vet World 2022; 15:1691-1698. [PMID: 36185529 PMCID: PMC9394135 DOI: 10.14202/vetworld.2022.1691-1698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/26/2022] [Indexed: 11/23/2022] Open
Abstract
Background and Aim: One of the most significant public health concerns is multidrug-resistant (MDR) microorganisms. Klebsiella spp. have been at the forefront of causing different types of infections such as bacteremia, urinary tract infections, pneumonia, enteritis, and sepsis in humans as well as animals. This study aimed to determine the genomic similarity between Klebsiella spp. isolated from wild animal samples and those described in the Institut Pasteur genomic database to verify the spread of resistant clones regionally in the state of Mato Grosso, and to compare the epidemiological data in different regions of Brazil and the world. Materials and Methods: Isolates from various sites of injury in wild animals were identified by sequencing the 16S rRNA gene. Antimicrobial susceptibility testing was performed using the disk diffusion method to verify the resistance profile, and then, multilocus sequence typing was performed to verify the population structure and compare the isolates from other regions of Brazil and the world. Results: Twenty-three sequence types (STs) were observed; of these, 11 were new STs, as new alleles were detected. There was no predominant ST among the isolates. All isolates were MDR, with high rates of resistance to sulfonamides, ampicillin, amoxicillin, and nitrofurantoin and low resistance to meropenem, imipenem, and amikacin. Conclusion: Improving our understanding of the population structure of Klebsiella spp. in wild animals may help determine the source of infection during outbreaks in humans or animals, as the One Health concept emphasizes the interlinks between humans, animals, and environmental health.
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Affiliation(s)
| | - Marco Túlio dos Santos Costa
- Microbiology Laboratory of the Veterinary Hospital, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Stefhano Luis Cândido
- Microbiology Laboratory of the Veterinary Hospital, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Herica Makino
- Microbiology Laboratory of the Veterinary Hospital, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Thais Oliveira Morgado
- Center for Medicine and Research of Wild Animals, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | | | - Edson Moleta Colodel
- Pathology Laboratory of the Veterinary Hospital, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Luciano Nakazato
- Microbiology Laboratory of the Veterinary Hospital, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Valéria Dutra
- Microbiology Laboratory of the Veterinary Hospital, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
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Rybak B, Potrykus M, Plenis A, Wolska L. Raw Meat Contaminated with Cephalosporin-Resistant Enterobacterales as a Potential Source of Human Home Exposure to Multidrug-Resistant Bacteria. Molecules 2022; 27:molecules27134151. [PMID: 35807396 PMCID: PMC9267975 DOI: 10.3390/molecules27134151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
The prevalence of cephalosporine-resistant (3GC-R) strains among United States community-related research samples ranged from 5.6 to 10.8%, while, in the European countries, it was 1.2% to 10.1%. Several studies suggest that meat of animal origin could be one of the reservoirs of 3GC-R bacteria. Here, 86 raw meat samples (turkey, pork, chicken and beef) were collected randomly and verified for the presence of 3GC-R bacteria. The 3GC-R bacteria were isolated, identified and characterized phenotypically (antibiotic resistance, motility and biofilm) and genotypically (repetitive-sequence-based rep-PCR) to elucidate any correlations with principal component analysis (PCA). From 28 3GC-R positive samples, 41 strains were isolated, from which the majority belonged to Serratia fonticola (39%), followed by Escherichia coli (19.5%), Enterobacter cloacae (17.1%) and Klebsiella pneumoniae (14.6%). The isolates of E. coli and S. fonticola presented diverse profiles in rep-PCR. Generally, 3GC-R strains were more resistant to antibiotics used in veterinary medicine than in human medicine. PCA derived from antibiotic resistance, motility and biofilm formation of S. fonticola and E. coli strains showed that resistance to beta-lactams was separated from the resistance to other antibiotic classes. Moreover, for the S. fonticola, E. coli and En. cloacae, the type of meat can create a specific tendency towards antibiotic resistance and phenotypic characteristics for S. fonticola, while these relationships were not found for other tested species.
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Affiliation(s)
- Bartosz Rybak
- Department of Environmental Toxicology, Faculty of Health Sciences, Medical University of Gdansk, Debowa Str. 23A, 80-204 Gdansk, Poland; (B.R.); (M.P.); (L.W.)
| | - Marta Potrykus
- Department of Environmental Toxicology, Faculty of Health Sciences, Medical University of Gdansk, Debowa Str. 23A, 80-204 Gdansk, Poland; (B.R.); (M.P.); (L.W.)
| | - Alina Plenis
- Department of Analytical Chemistry, Faculty of Pharmacy, Medical University of Gdansk, Hallera Str. 107, 80-416 Gdansk, Poland
- Correspondence: ; Tel.: +48-58-349-10-96
| | - Lidia Wolska
- Department of Environmental Toxicology, Faculty of Health Sciences, Medical University of Gdansk, Debowa Str. 23A, 80-204 Gdansk, Poland; (B.R.); (M.P.); (L.W.)
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Phenotypic and Genetic Characterization of Klebsiella pneumoniae Isolates from Wild Animals in Central Italy. Animals (Basel) 2022; 12:ani12111347. [PMID: 35681810 PMCID: PMC9179660 DOI: 10.3390/ani12111347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Despite Klebsiella pneumoniae being widely recognized as a nosocomial pathogen, there is a critical lack in defining its reservoirs and sources of infections. Most studies on risk factors have focused on multidrug-resistant (MDR) isolates and clinically-oriented questions. Over a two-year period, we sampled 131 wild animals including mammal and bird species from three regions of Central Italy. All typical colonies isolated from the analytical portions were confirmed by real-time PCR and identified by MALDI-TOF mass spectrometry (MALDI-TOF MS). All confirmed K. pneumoniae isolates were tested for antimicrobial susceptibility to 29 antimicrobials and subjected to whole genome sequencing. Typical colonies were detected in 17 samples (13%), which were identified as K. pneumoniae (n = 16) and as K. quasipneumoniae (n = 1) by MALDI-TOF MS. The antimicrobial susceptibility profile showed that all the isolates were resistant to β-lactams (ceftobiprole, cloxacillin, cefazolin) and tetracycline; resistance to ertapenem and trimethoprim was observed and nine out of 16 K. pneumoniae isolates (56.2%) were classified as MDR. Genomic characterization allowed the detection of fluoroquinolone resistance-associated efflux pumps, fosfomycin and β-lactamase resistance genes, and virulence genes in the overall dataset. The cluster analysis of two isolates detected from wild boar with available clinical genomes showed the closest similarity. This study highlights the link between humans, domestic animals, and wildlife, showing that the current knowledge on this ecological context is lacking and that the potential health risks are underestimated.
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Håkonsholm F, Hetland MA, Svanevik CS, Lunestad BT, Löhr IH, Marathe NP. Insights into the genetic diversity, antibiotic resistance and pathogenic potential of Klebsiella pneumoniae from the Norwegian marine environment using whole-genome analysis. Int J Hyg Environ Health 2022; 242:113967. [DOI: 10.1016/j.ijheh.2022.113967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/25/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023]
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27
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Donner L, Staley ZR, Petali J, Sangster J, Li X, Mathews W, Snow D, Howe A, Soupir M, Bartelt-Hunt S. The Human Health Implications of Antibiotic Resistance in Environmental Isolates from Two Nebraska Watersheds. Microbiol Spectr 2022; 10:e0208221. [PMID: 35311538 PMCID: PMC9045274 DOI: 10.1128/spectrum.02082-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/31/2022] [Indexed: 11/25/2022] Open
Abstract
One Health field-based approaches are needed to connect the occurrence of antibiotics present in the environment with the presence of antibiotic resistance genes (ARGs) in Gram-negative bacteria that confer resistance to antibiotics important in for both veterinary and human health. Water samples from two Nebraska watersheds influenced by wastewater effluent and agricultural runoff were tested for the presence of antibiotics used in veterinary and human medicine. The water samples were also cultured to identify the bacteria present. Of those bacteria isolated, the Gram-negative rods capable of causing human infections had antimicrobial susceptibility testing and whole-genome sequencing (WGS) performed to identify ARGs present. Of the 211 bacterial isolates identified, 37 belonged to pathogenic genera known to cause human infections. Genes conferring resistance to beta-lactams, aminoglycosides, fosfomycins, and quinolones were the most frequently detected ARGs associated with horizontal gene transfer (HGT) in the watersheds. WGS also suggest recent HGT events involving ARGs transferred between watershed isolates and bacteria of human and animal origins. The results of this study demonstrate the linkage of antibiotics and bacterial ARGs present in the environment with potential human and/or veterinary health impacts. IMPORTANCE One health is a transdisciplinary approach to achieve optimal health for humans, animals, plants and their shared environment, recognizing the interconnected nature of health in these domains. Field based research is needed to connect the occurrence of antibiotics used in veterinary medicine and human health with the presence of antibiotic resistance genes (ARGs). In this study, the presence of antibiotics, bacteria and ARGs was determined in two watersheds in Nebraska, one with agricultural inputs and the other with both agricultural and wastewater inputs. The results presented in this study provide evidence of transfer of highly mobile ARG between environment, clinical, and animal-associated bacteria.
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Affiliation(s)
- Linsey Donner
- College of Allied Health Professions, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Zachery R. Staley
- Department of Civil and Environmental Engineering, University of Nebraska – Lincoln, Lincoln, Nebraska, USA
| | - Jonathan Petali
- Environmental Health Program, New Hampshire Department of Environmental Services, Concord, New Hampshire, USA
| | - Jodi Sangster
- Department of Civil and Environmental Engineering, University of Nebraska – Lincoln, Lincoln, Nebraska, USA
| | - Xu Li
- Department of Civil and Environmental Engineering, University of Nebraska – Lincoln, Lincoln, Nebraska, USA
| | - Wayne Mathews
- College of Allied Health Professions, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Daniel Snow
- Nebraska Water Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, USA
| | - Michelle Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, USA
| | - Shannon Bartelt-Hunt
- College of Allied Health Professions, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Department of Civil and Environmental Engineering, University of Nebraska – Lincoln, Lincoln, Nebraska, USA
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Hawkey J, Cottingham H, Tokolyi A, Wick RR, Judd LM, Cerdeira L, de Oliveira Garcia D, Wyres KL, Holt KE. Linear plasmids in Klebsiella and other Enterobacteriaceae. Microb Genom 2022; 8. [PMID: 35416146 PMCID: PMC9453081 DOI: 10.1099/mgen.0.000807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Linear plasmids are extrachromosomal DNA elements that have been found in a small number of bacterial species. To date, the only linear plasmids described in the family Enterobacteriaceae belong to Salmonella, first found in Salmonella enterica Typhi. Here, we describe a collection of 12 isolates of the Klebsiella pneumoniae species complex in which we identified linear plasmids. Screening of assembly graphs assembled from public read sets identified linear plasmid structures in a further 13 K. pneumoniae species complex genomes. We used these 25 linear plasmid sequences to query all bacterial genome assemblies in the National Center for Biotechnology Information database, and discovered an additional 61 linear plasmid sequences in a variety of Enterobacteriaceae species. Gene content analysis divided these plasmids into five distinct phylogroups, with very few genes shared across more than two phylogroups. The majority of linear plasmid-encoded genes are of unknown function; however, each phylogroup carried its own unique toxin–antitoxin system and genes with homology to those encoding the ParAB plasmid stability system. Passage in vitro of the 12 linear plasmid-carrying Klebsiella isolates in our collection (which include representatives of all five phylogroups) indicated that these linear plasmids can be stably maintained, and our data suggest they can transmit between K. pneumoniae strains (including members of globally disseminated multidrug-resistant clones) and also between diverse Enterobacteriaceae species. The linear plasmid sequences, and representative isolates harbouring them, are made available as a resource to facilitate future studies on the evolution and function of these novel plasmids.
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Affiliation(s)
- Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Hugh Cottingham
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Alex Tokolyi
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Ryan R Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | | | | | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - 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
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Factors influencing antimicrobial resistance in the European food system and potential leverage points for intervention: A participatory, One Health study. PLoS One 2022; 17:e0263914. [PMID: 35192666 PMCID: PMC8863257 DOI: 10.1371/journal.pone.0263914] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/29/2022] [Indexed: 11/19/2022] Open
Abstract
Introduction Antimicrobial resistance (AMR) is a global crisis that evolves from a complex system of factors. Understanding what factors interact is key to finding solutions. Our objective was to identify the factors influencing AMR in the European food system and places to intervene. Materials and methods We conducted two workshops involving participants with diverse perspectives to identify the factors influencing AMR and leverage points (places) to target interventions. Transcripts were open coded for factors and connections, then transcribed into Vensim 8.0.4 to develop a causal loop diagram (CLD) and compute the number of feedback loops. Thematic analysis followed to describe AMR dynamics in Europe’s food system and places for intervention. The CLD and themes were confirmed via participant feedback. Results Seventeen participants representing human, animal and agricultural sectors identified 91 CLD factors and 331 connections. Seven themes (e.g., social and economic conditions) describing AMR dynamics in Europe’s food system, five ‘overarching factors’ that impact the entire CLD system (e.g., leadership) and fourteen places for intervention (e.g., consumer demand) emerged from workshop discussions. Most leverage points fell on highly networked feedback loops suggesting that intervening at these places may create unpredictable consequences. Conclusions Our study produced a CLD of factors influencing AMR in Europe’s food system that implicates sectors across the One Health spectrum. The high connectivity between the CLD factors described by participants and our finding that factors are connected with many feedback mechanisms underscores the complexity of the AMR problem and the challenge with finding long-term solutions. Identifying factors and feedbacks helped identify relevant leverage points in the system. Some actions, such as government’s setting AMU standards may be easier to implement. These actions in turn can support multi-pronged actions that can help redefine the vision, values and goals of the system to sustainably tackle AMR.
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30
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Rodrigues C, Hauser K, Cahill N, Ligowska-Marzęta M, Centorotola G, Cornacchia A, Garcia Fierro R, Haenni M, Nielsen EM, Piveteau P, Barbier E, Morris D, Pomilio F, Brisse S. High Prevalence of Klebsiella pneumoniae in European Food Products: a Multicentric Study Comparing Culture and Molecular Detection Methods. Microbiol Spectr 2022; 10:e0237621. [PMID: 35196810 PMCID: PMC8865463 DOI: 10.1128/spectrum.02376-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/20/2022] [Indexed: 12/20/2022] Open
Abstract
The Klebsiella pneumoniae species complex (KpSC) is a leading cause of multidrug-resistant human infections. To better understand the potential contribution of food as a vehicle of KpSC, we conducted a multicentric study to define an optimal culture method for its recovery from food matrices and to characterize food isolates phenotypically and genotypically. Chicken meat (n = 160) and salad (n = 145) samples were collected in five European countries and screened for the presence of KpSC using culture-based and zur-khe intergenic region (ZKIR) quantitative PCR (qPCR) methods. Enrichment using buffered peptone water followed by streaking on Simmons citrate agar with inositol (44°C for 48 h) was defined as the most suitable selective culture method for KpSC recovery. A high prevalence of KpSC was found in chicken meat (60% and 52% by ZKIR qPCR and the culture approach, respectively) and salad (30% and 21%, respectively) samples. Genomic analyses revealed high genetic diversity with the dominance of phylogroups Kp1 (91%) and Kp3 (6%). A total of 82% of isolates presented a natural antimicrobial susceptibility phenotype and genotype, with only four CTX-M-15-producing isolates detected. Notably, identical genotypes were found across samples-same food type and same country (15 cases), different food types and same country (1), and same food type and two countries (1)-suggesting high rates of transmission of KpSC within the food sector. Our study provides a novel isolation strategy for KpSC from food matrices and reinforces the view of food as a potential source of KpSC colonization in humans. IMPORTANCE Bacteria of the Klebsiella pneumoniae species complex (KpSC) are ubiquitous, and K. pneumoniae is a leading cause of antibiotic-resistant infections in humans. Despite the urgent public health threat represented by K. pneumoniae, there is a lack of knowledge of the contribution of food sources to colonization and subsequent infection in humans. This is partly due to the absence of standardized methods for characterizing the presence of KpSC in food matrices. Our multicentric study provides and implements a novel isolation strategy for KpSC from food matrices and shows that KpSC members are highly prevalent in salads and chicken meat, reinforcing the view of food as a potential source of KpSC colonization in humans. Despite the large genetic diversity and the low levels of resistance detected, the occurrence of identical genotypes across samples suggests high rates of transmission of KpSC within the food sector, which need to be further explored to define possible control strategies.
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Affiliation(s)
- Carla Rodrigues
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Kathrin Hauser
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
| | - Niamh Cahill
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | | | - Gabriella Centorotola
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Alessandra Cornacchia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Raquel Garcia Fierro
- Unité Antibiorésistance et Virulence Bactériennes, Université Claude Bernard Lyon 1 - ANSES, Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Université Claude Bernard Lyon 1 - ANSES, Lyon, France
| | | | | | - Elodie Barbier
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Sylvain Brisse
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
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Patil A, Banerji R, Kanojiya P, Saroj SD. Foodborne ESKAPE Biofilms and Antimicrobial Resistance: lessons Learned from Clinical Isolates. Pathog Glob Health 2021; 115:339-356. [PMID: 33851566 PMCID: PMC8592604 DOI: 10.1080/20477724.2021.1916158] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The ESKAPE pathogens (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) are identified to be multidrug-resistant (MDR), extensively drug-resistant (XDR), and pan drug-resistant (PDR); thereby, imposing severe challenges in the treatment of associated infections. ESKAPE pathogens colonize on various biotic and abiotic surfaces; biofilms formed by these pathogens are a potential source for food contamination. Moreover, biofilms play a pivotal role in the development of antimicrobial-resistant (AMR) strains. Hence, the frequent isolation of antimicrobial-resistant ESKAPE pathogens from food products across the globe imposes a threat to public health. A comprehensive understanding of the adhesion signaling involved in the polymicrobial and single-species biofilm will assist in developing alternative preservation techniques and novel therapeutic strategies to combat ESKAPE pathogens. The review provides a comprehensive overview of the signaling mechanisms that prevail in the ESKAPE pathogens for adhesion to abiotic and biotic surfaces and molecular mechanisms associated with poly-microbial biofilm-assisted AMR in ESKAPE.
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Affiliation(s)
- Amrita Patil
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, PuneMaharashtra, India
| | - Rajashri Banerji
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, PuneMaharashtra, India
| | - Poonam Kanojiya
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, PuneMaharashtra, India
| | - Sunil D. Saroj
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, PuneMaharashtra, India
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Abstract
Gram-negative bacteremia is a devastating public health threat, with high mortality in vulnerable populations and significant costs to the global economy. Concerningly, rates of both Gram-negative bacteremia and antimicrobial resistance in the causative species are increasing. Gram-negative bacteremia develops in three phases. First, bacteria invade or colonize initial sites of infection. Second, bacteria overcome host barriers, such as immune responses, and disseminate from initial body sites to the bloodstream. Third, bacteria adapt to survive in the blood and blood-filtering organs. To develop new therapies, it is critical to define species-specific and multispecies fitness factors required for bacteremia in model systems that are relevant to human infection. A small subset of species is responsible for the majority of Gram-negative bacteremia cases, including Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii The few bacteremia fitness factors identified in these prominent Gram-negative species demonstrate shared and unique pathogenic mechanisms at each phase of bacteremia progression. Capsule production, adhesins, and metabolic flexibility are common mediators, whereas only some species utilize toxins. This review provides an overview of Gram-negative bacteremia, compares animal models for bacteremia, and discusses prevalent Gram-negative bacteremia species.
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Affiliation(s)
- Caitlyn L Holmes
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mark T Anderson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Harry L T Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Michael A Bachman
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Hayakawa Ito de Sousa AT, Dos Santos Costa MT, Makino H, Cândido SL, de Godoy Menezes I, Lincopan N, Nakazato L, Dutra V. Multidrug-resistant mcr-1 gene-positive Klebsiella pneumoniae ST307 causing urinary tract infection in a cat. Braz J Microbiol 2021; 52:1043-1046. [PMID: 33713022 PMCID: PMC8105429 DOI: 10.1007/s42770-021-00466-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 02/28/2021] [Indexed: 10/21/2022] Open
Abstract
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.
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Affiliation(s)
- Alessandra Tammy Hayakawa Ito de Sousa
- Laboratory of Microbiology, Veterinary Hospital, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil.
- School of Veterinary Medicine, Federal University of Mato Grosso, Cuiabá, Brazil.
| | | | - Herica Makino
- Laboratory of Microbiology, Veterinary Hospital, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Stéfhano Luis Cândido
- Laboratory of Microbiology, Veterinary Hospital, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Isabela de Godoy Menezes
- Mycology Laboratory, Faculty of Pharmaceutical Sciences (FCF), University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Luciano Nakazato
- Laboratory of Microbiology, Veterinary Hospital, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Valéria Dutra
- Laboratory of Microbiology, Veterinary Hospital, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
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Klaper K, Hammerl JA, Rau J, Pfeifer Y, Werner G. Genome-Based Analysis of Klebsiella spp. Isolates from Animals and Food Products in Germany, 2013-2017. Pathogens 2021; 10:pathogens10050573. [PMID: 34066734 PMCID: PMC8170897 DOI: 10.3390/pathogens10050573] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Kathleen Klaper
- Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855 Wernigerode, Germany; (Y.P.); (G.W.)
- Correspondence:
| | - Jens Andre Hammerl
- Unit Epidemiology, Zoonoses and Antimicrobial Resistance, Department Biological Safety, German Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung [BfR]), 12277 Berlin, Germany;
| | - Jörg Rau
- Chemical and Veterinary Analysis Agency (CVUAS) Stuttgart, 70736 Fellbach, Germany;
| | - Yvonne Pfeifer
- Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855 Wernigerode, Germany; (Y.P.); (G.W.)
| | - Guido Werner
- Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855 Wernigerode, Germany; (Y.P.); (G.W.)
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Elmonir W, Abd El-Aziz NK, Tartor YH, Moustafa SM, Abo Remela EM, Eissa R, Saad HA, Tawab AA. Emergence of Colistin and Carbapenem Resistance in Extended-Spectrum β-Lactamase Producing Klebsiella pneumoniae Isolated from Chickens and Humans in Egypt. BIOLOGY 2021; 10:biology10050373. [PMID: 33926062 PMCID: PMC8146310 DOI: 10.3390/biology10050373] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/26/2022]
Abstract
Simple Summary Carbapenems and colistin are reserved as the last-resort treatments of multidrug-resistant (MDR) infections in humans. Consequently, the emergence of carbapenem and colistin-resistant Klebsiella pneumoniae (K. pneumoniae) in poultry, contact workers and hospitalized patients is of grave concern for therapeutic options, and no data are available supporting this assumption on a regional or countrywide scale. We investigated the frequency and typing of extended-spectrum β-lactamase (ESBL) and carbapenemase-producing K. pneumoniae (ESBLK and CPK) in hospitalized patients, chickens from 10 poultry farms and their environment (water, food and litter) and farm workers in Egypt. All isolates from patients (13/90, 14.4%), workers (5/22, 22.7%), chickens (9/100, 9%) and the environment (10/60, 16.7%) harbored a single or multiple β-lactamase genes, blaSHV, blaTEM, blaCTX-M1 and blaOXA-1, often in combination with carbapenemase genes (blaVIM, blaNDM-1 or blaIMP; 45.9%), the mcr-1 gene (18.9%) or both (13.5%). Enterobacterial repetitive intergenic consensus (ERIC)-PCR genotyping highlighted potential inter and intraspecies clonal dissemination in the study area. The increased frequency and genetic relatedness of ESBLK and CPK from chickens and humans pose a public health threat that urges more prudent use of antimicrobials in chicken farms to avoid the propagation and expansion of both ESBLK and CPK from the chicken sources to humans. Abstract This study investigated the frequency of carbapenem and colistin resistance in ESBL-producing K. pneumoniae (ESBLK) isolates recovered from chickens and their environment, contact farm workers and hospitalized patients in Egypt. Further, the phenotypic and genotypic relationships between the community and hospital-acquired K. pneumoniae isolates in the same geographical area were investigated. From 272 total samples, 37 (13.6%) K. pneumoniae isolates were identified, of which 20 (54.1%) were hypervirulent. All isolates (100%) were multidrug-resistant (MDR) with multiple antibiotic resistance (MAR) indices ranging from 0.19 to 0.94. Colistin-resistant isolates (18.9%) displayed colistin MIC values >2 μg/mL, all harbored the mcr-1 gene. All isolates from patients (13/90, 14.4%), workers (5/22, 22.7%), chickens (9/100, 9%) and the environment (10/60, 16.7%) harbored a single or multiple β-lactamase genes, blaSHV, blaTEM, blaCTX-M1 and blaOXA-1, often in combination with carbapenemase genes (blaVIM, blaNDM-1 or blaIMP; 45.9%), the mcr-1 gene (18.9%) or both (13.5%). Enterobacterial repetitive intergenic consensus (ERIC)–PCR genotyping revealed 24 distinct ERIC types (ETs) with a discrimination index of 0.961. Six ETs showed clusters of identical isolates from chicken and human sources. The increased frequency and genetic relatedness of ESBLK and carbapenemase-producing K. pneumoniae (CPK) from chickens and humans pose a public health threat that urge more prudent use of antimicrobials in chicken farms to avoid the propagation and expansion of both ESBLK and CPK from the chicken sources to humans.
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Affiliation(s)
- Walid Elmonir
- Department of Hygiene and Preventive Medicine (Zoonoses), Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Norhan K Abd El-Aziz
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Yasmine H Tartor
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Samar M Moustafa
- Department of Zoonoses, Faculty of Veterinary Medicine, Benha University, Benha 13518, Egypt
| | - Etab M Abo Remela
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
- Department of Biology, College of Science, Taibah University, Madina 42353, Saudi Arabia
| | - Radwa Eissa
- Department of Microbiology and Immunology, Faculty of Medicine, Tanta University, Tanta 31527, Egypt
| | - Hosam A Saad
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed Abdel Tawab
- Department of Microbiology, Faculty of Medicine, Al Azhar University, Cairo 11884, Egypt
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Antimicrobial Resistance Profile and ExPEC Virulence Potential in Commensal Escherichia coli of Multiple Sources. Antibiotics (Basel) 2021; 10:antibiotics10040351. [PMID: 33810387 PMCID: PMC8067153 DOI: 10.3390/antibiotics10040351] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
We recently described the genetic antimicrobial resistance and virulence profile of a collection of 279 commensal E. coli of food-producing animal (FPA), pet, wildlife and human origin. Phenotypic antimicrobial resistance (AMR) and the role of commensal E. coli as reservoir of extra-intestinal pathogenic Escherichia coli (ExPEC) virulence-associated genes (VAGs) or as potential ExPEC pathogens were evaluated. The most common phenotypic resistance was to tetracycline (76/279, 27.24%), sulfamethoxazole/trimethoprim (73/279, 26.16%), streptomycin and sulfisoxazole (71/279, 25.45% both) among the overall collection. Poultry and rabbit were the sources mostly associated to AMR, with a significant resistance rate (p > 0.01) to quinolones, streptomycin, sulphonamides, tetracycline and, only for poultry, to ampicillin and chloramphenicol. Finally, rabbit was the source mostly associated to colistin resistance. Different pandemic (ST69/69*, ST95, ST131) and emerging (ST10/ST10*, ST23, ST58, ST117, ST405, ST648) ExPEC sequence types (STs) were identified among the collection, especially in poultry source. Both ST groups carried high number of ExPEC VAGs (pandemic ExPEC STs, mean = 8.92; emerging ExPEC STs, mean = 6.43) and showed phenotypic resistance to different antimicrobials (pandemic ExPEC STs, mean = 2.23; emerging ExPEC STs, mean = 2.43), suggesting their role as potential ExPEC pathogens. Variable phenotypic resistance and ExPEC VAG distribution was also observed in uncommon ExPEC lineages, suggesting commensal flora as a potential reservoir of virulence (mean = 3.80) and antimicrobial resistance (mean = 1.69) determinants.
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Imchen M, Moopantakath J, Kumavath R, Barh D, Tiwari S, Ghosh P, Azevedo V. Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance. Front Genet 2020; 11:563975. [PMID: 33240317 PMCID: PMC7677515 DOI: 10.3389/fgene.2020.563975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
A multitude of factors, such as drug misuse, lack of strong regulatory measures, improper sewage disposal, and low-quality medicine and medications, have been attributed to the emergence of drug resistant microbes. The emergence and outbreaks of multidrug resistance to last-line antibiotics has become quite common. This is further fueled by the slow rate of drug development and the lack of effective resistome surveillance systems. In this review, we provide insights into the recent advances made in computational approaches for the surveillance of antibiotic resistomes, as well as experimental formulation of combinatorial drugs. We explore the multiple roles of antibiotics in nature and the current status of combinatorial and adjuvant-based antibiotic treatments with nanoparticles, phytochemical, and other non-antibiotics based on synergetic effects. Furthermore, advancements in machine learning algorithms could also be applied to combat the spread of antibiotic resistance. Development of resistance to new antibiotics is quite rapid. Hence, we review the recent literature on discoveries of novel antibiotic resistant genes though shotgun and expression-based metagenomics. To decelerate the spread of antibiotic resistant genes, surveillance of the resistome is of utmost importance. Therefore, we discuss integrative applications of whole-genome sequencing and metagenomics together with machine learning models as a means for state-of-the-art surveillance of the antibiotic resistome. We further explore the interactions and negative effects between antibiotics and microbiomes upon drug administration.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, India
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Hu Y, Anes J, Devineau S, Fanning S. Klebsiella pneumoniae: Prevalence, Reservoirs, Antimicrobial Resistance, Pathogenicity, and Infection: A Hitherto Unrecognized Zoonotic Bacterium. Foodborne Pathog Dis 2020; 18:63-84. [PMID: 33124929 DOI: 10.1089/fpd.2020.2847] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Klebsiella pneumoniae is considered an opportunistic pathogen, constituting an ongoing health concern for immunocompromised patients, the elderly, and neonates. Reports on the isolation of K. pneumoniae from other sources are increasing, many of which express multidrug-resistant (MDR) phenotypes. Three phylogroups were identified based on nucleotide differences. Niche environments, including plants, animals, and humans appear to be colonized by different phylogroups, among which KpI (K. pneumoniae) is commonly associated with human infection. Infections with K. pneumoniae can be transmitted through contaminated food or water and can be associated with community-acquired infections or between persons and animals involved in hospital-acquired infections. Increasing reports are describing detections along the food chain, suggesting the possibility exists that this could be a hitherto unexplored reservoir for this opportunistic bacterial pathogen. Expression of MDR phenotypes elaborated by these bacteria is due to the nature of various plasmids carrying antimicrobial resistance (AMR)-encoding genes, and is a challenge to animal, environmental, and human health alike. Raman spectroscopy has the potential to provide for the rapid identification and screening of antimicrobial susceptibility of Klebsiella isolates. Moreover, hypervirulent isolates linked with extraintestinal infections express phenotypes that may support their niche adaptation. In this review, the prevalence, reservoirs, AMR, Raman spectroscopy detection, and pathogenicity of K. pneumoniae are summarized and various extraintestinal infection pathways are further narrated to extend our understanding of its adaptation and survival ability in reservoirs, and associated disease risks.
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Affiliation(s)
- Yujie Hu
- UCD-Centre for Food Safety, UCD School of Public Health, Physiotherapy and Sports Science, Science Centre South, College of Health and Agricultural Sciences, University College Dublin (UCD), Dublin, Ireland.,Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, China
| | - João Anes
- UCD-Centre for Food Safety, UCD School of Public Health, Physiotherapy and Sports Science, Science Centre South, College of Health and Agricultural Sciences, University College Dublin (UCD), Dublin, Ireland
| | | | - Séamus Fanning
- UCD-Centre for Food Safety, UCD School of Public Health, Physiotherapy and Sports Science, Science Centre South, College of Health and Agricultural Sciences, University College Dublin (UCD), Dublin, Ireland.,Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, China.,Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
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Chen F, Zhang W, Schwarz S, Zhu Y, Li R, Hua X, Liu S. Genetic characterization of an MDR/virulence genomic element carrying two T6SS gene clusters in a clinical Klebsiella pneumoniae isolate of swine origin. J Antimicrob Chemother 2020; 74:1539-1544. [PMID: 30903161 DOI: 10.1093/jac/dkz093] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/16/2019] [Accepted: 02/11/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES Multiresistant Klebsiella pneumoniae isolates rarely cause infections in pigs. The aim of this study was to investigate a multiresistant porcine K. pneumoniae isolate for plasmidic and chromosomal antimicrobial resistance and virulence genes and their genetic environment. METHODS K. pneumoniae strain ZYST1 originated from a pig with pneumonia. Antimicrobial susceptibility testing was performed using broth microdilution. Conjugation experiments were conducted using Escherichia coli J53 as the recipient. The complete sequences of the chromosomal DNA and the plasmids were generated by WGS and analysed for the presence of resistance and virulence genes. RESULTS The MDR K. pneumoniae ST1 strain ZYST1 contained three plasmids belonging to incompatibility groups IncFIIk5-FIB, IncI1 and IncX4, respectively. The IncFIIk5-FIB plasmid carried the resistance genes aadA2, mph(A), sul1 and aph(3')-Ia, and the IncI1 plasmid carried aadA22 and erm(B). No resistance genes were present on the IncX4 plasmid. Plasmids related to the aforementioned three plasmids were also present in other Enterobacteriaceae species from humans, animals and the environment. Bioinformatic analyses identified a chromosomal 904 kb MDR element flanked by two copies of ISKpn26. This element included virulence factors, such as a type VI secretion system (T6SS) and genes for type 1 fimbriae, the toxin-antitoxin system HipA/HipB, antimicrobial resistance genes, such as blaSHV-187, mdtk, catA and the multiple antibiotic resistance operon marRABC, and heavy metal resistance determinants, such as chrB/chrA and tehA/tehB. CONCLUSIONS This study reports a novel 904 kb MDR/virulence genomic element and three important plasmids coexisting in a clinical K. pneumoniae isolate of animal origin.
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Affiliation(s)
- Fuguang Chen
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, P.R. China
| | - Wanjiang Zhang
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, P.R. China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Yao Zhu
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, P.R. China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China
| | - Xin Hua
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, P.R. China
| | - Siguo Liu
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, P.R. China
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Díaz-Jiménez D, García-Meniño I, Fernández J, García V, Mora A. Chicken and turkey meat: Consumer exposure to multidrug-resistant Enterobacteriaceae including mcr-carriers, uropathogenic E. coli and high-risk lineages such as ST131. Int J Food Microbiol 2020; 331:108750. [PMID: 32559710 DOI: 10.1016/j.ijfoodmicro.2020.108750] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 04/10/2020] [Accepted: 06/06/2020] [Indexed: 12/13/2022]
Abstract
For the first time, this study evaluates consumer exposure via poultry meat to Enterobacteriaceae with capacity to develop severe extraintestinal infections by either bacterial virulence and/or antibiotic resistance traits. The characterization of 256 isolates and the assessment of five parameters, showed that 96 of 100 poultry meat samples from supermarkets of northwest Spain posed ≥ one potential risk: i) 96% carried Enterobacteriaceae resistant to antimicrobials of categories A (64% to monobactams) or B (95% to cephalosporins 3rd and 4rd- generation, quinolones and/or polymixins) of the new categorization of EMA. ii) More than one extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae species were recovered from 28% of poultry meat. iii) High-risk lineages of E. coli, including multidrug-resistant ST131-H22, were present in 62% of samples. iv) E. coli recovered from 25% of samples conformed the ExPEC status. v) E. coli from 17% of samples satisfied the UPEC status. Of note, the recovery from different samples of two E. coli CC10-A (CH11-54) carrying mcr-1.1-bearing IncX4 plasmids, and four E. coli CC10-A (eae-beta1) of the hybrid pathotype aEPEC/ExPEC. (ESBL)-producing K. pneumoniae were isolated from 27% of samples. In summary, poultry meat microbiota is a source of genetically diverse Enterobacteriaceae, resistant to relevant antimicrobials and potentially pathogenic for consumers.
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Affiliation(s)
- Dafne Díaz-Jiménez
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Javier Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA). Instituto de Investigación del Principado de Asturias (ISPA), Oviedo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain.; Department of Veterinary and Animal Sciences, Section of Veterinary Clinical Microbiology, University of Copenhagen, København, Denmark
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain..
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Abstract
In general, foodborne diseases present themselves with gastrointestinal symptoms caused by bacterial, viral, and parasitic pathogens well established to be foodborne. These pathogens are also associated with extraintestinal clinical manifestations. Recent studies have suggested that Escherichia coli and Klebsiella pneumoniae, which both cause common extraintestinal infections such as urinary tract and bloodstream infections, may also be foodborne. The resolution and separation of these organisms into pathotypes versus commensals by modern genotyping methods have led to the identification of key lineages of these organisms causing outbreaks of extraintestinal infections. These epidemiologic observations suggested common- or point-source exposures, such as contaminated food. Here, we describe the spectrum of extraintestinal illnesses caused by recognized enteric pathogens and then review studies that demonstrate the potential role of extraintestinal pathogenic E. coli (ExPEC) and K. pneumoniae as foodborne pathogens. The impact of global food production and distribution systems on the possible foodborne spread of these pathogens is discussed.
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Affiliation(s)
- Lee W. Riley
- School of Public Health, University of California, Berkeley, California 94720, USA
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The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples. Appl Environ Microbiol 2020; 86:AEM.02711-19. [PMID: 32005732 PMCID: PMC7082575 DOI: 10.1128/aem.02711-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/21/2020] [Indexed: 11/20/2022] Open
Abstract
The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources. Klebsiella pneumoniae is of growing public health concern due to the emergence of strains that are multidrug resistant, virulent, or both. Taxonomically, the K. pneumoniae complex (“Kp”) includes seven phylogroups, with Kp1 (K. pneumoniaesensu stricto) being medically prominent. Kp can be present in environmental sources such as soils and vegetation, which could act as reservoirs of animal and human infections. However, the current lack of screening methods to detect Kp in complex matrices limits research on Kp ecology. Here, we analyzed 1,001 genome sequences and found that existing molecular detection targets lack specificity for Kp. A novel real-time PCR method, the ZKIR (zur-khe intergenic region) assay, was developed and used to detect Kp in 96 environmental samples. The results were compared to a culture-based method using Simmons citrate agar with 1% inositol medium coupled to matrix-assisted laser desorption ionization–time of flight mass spectrometry identification. Whole-genome sequencing of environmental Kp was performed. The ZKIR assay was positive for the 48 tested Kp reference strains, whereas 88 non-Kp strains were negative. The limit of detection of Kp in spiked soil microcosms was 1.5 × 10−1 CFU g−1 after enrichment for 24 h in lysogeny broth supplemented with ampicillin, and it was 1.5 × 103 to 1.5 × 104 CFU g−1 directly after soil DNA extraction. The ZKIR assay was more sensitive than the culture method. Kp was detected in 43% of environmental samples. Genomic analysis of the isolates revealed a predominance of phylogroups Kp1 (65%) and Kp3 (32%), a high genetic diversity (23 multilocus sequence types), a quasi-absence of antibiotic resistance or virulence genes, and a high frequency (50%) of O-antigen type 3. This study shows that the ZKIR assay is an accurate, specific, and sensitive novel method to detect the presence of Kp in complex matrices and indicates that Kp isolates from environmental samples differ from clinical isolates. IMPORTANCE The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources.
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Cinar HN, Gopinath G, Murphy HR, Almeria S, Durigan M, Choi D, Jang A, Kim E, Kim R, Choi S, Lee J, Shin Y, Lee J, Qvarnstrom Y, Benedict TK, Bishop HS, da Silva A. Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing. Parasit Vectors 2020; 13:122. [PMID: 32143704 PMCID: PMC7060604 DOI: 10.1186/s13071-020-3997-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/26/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Outbreaks of cyclosporiasis, a diarrheal illness caused by Cyclospora cayetanensis, have been a public health issue in the USA since the mid 1990's. In 2018, 2299 domestically acquired cases of cyclosporiasis were reported in the USA as a result of multiple large outbreaks linked to different fresh produce commodities. Outbreak investigations are hindered by the absence of standardized molecular epidemiological tools for C. cayetanensis. For other apicomplexan coccidian parasites, multicopy organellar DNA such as mitochondrial genomes have been used for detection and molecular typing. METHODS We developed a workflow to obtain complete mitochondrial genome sequences from cilantro samples and clinical samples for typing of C. cayetanensis isolates. The 6.3 kb long C. cayetanensis mitochondrial genome was amplified by PCR in four overlapping amplicons from genomic DNA extracted from cilantro, seeded with oocysts, and from stool samples positive for C. cayetanensis by diagnostic methods. DNA sequence libraries of pooled amplicons were prepared and sequenced via next-generation sequencing (NGS). Sequence reads were assembled using a custom bioinformatics pipeline. RESULTS This approach allowed us to sequence complete mitochondrial genomes from the samples studied. Sequence alterations, such as single nucleotide polymorphism (SNP) profiles and insertion and deletions (InDels), in mitochondrial genomes of 24 stool samples from patients with cyclosporiasis diagnosed in 2014, exhibited discriminatory power. The cluster dendrogram that was created based on distance matrices of the complete mitochondrial genome sequences, indicated distinct strain-level diversity among the 2014 C. cayetanensis outbreak isolates analyzed in this study. CONCLUSIONS Our results suggest that genomic analyses of mitochondrial genome sequences may help to link outbreak cases to the source.
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Affiliation(s)
- Hediye Nese Cinar
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Gopal Gopinath
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Helen R. Murphy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Sonia Almeria
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Mauricio Durigan
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Dajung Choi
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - AhYoung Jang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Eunje Kim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - RaeYoung Kim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Seonju Choi
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Jeongu Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Yurim Shin
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Jieon Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Yvonne Qvarnstrom
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Theresa K. Benedict
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Henry S. Bishop
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Alexandre da Silva
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
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Tarazi YH, Abu-Basha EA, Ismail ZB, Tailony RA. In vitro and in vivo efficacy study of cefepime, doripenem, tigecycline, and tetracycline against extended-spectrum beta-lactamases Escherichia coli in chickens. Vet World 2020; 13:446-451. [PMID: 32367948 PMCID: PMC7183477 DOI: 10.14202/vetworld.2020.446-451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/21/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND AND AIM At present, there are no data about the efficacy of some recent antibiotics on Escherichia coli in broiler chickens in the study area. This study was designed to evaluate the in vitro and in vivo efficacy of cefepime, doripenem, tigecycline, and tetracycline against multidrug-resistant-extended-spectrum beta-lactamases (MDR-ESBLs) producing E. coli in broiler chicks. MATERIALS AND METHODS A total of 34 MDR-ESBLs E. coli isolates were used in this study. In vitro evaluation of the antibacterial efficacy of cefepime, doripenem, tigecycline, and tetracycline were performed using disk diffusion and minimum inhibitory concentration (MIC) assays. In vivo evaluation of the efficacy of the antibiotics was perfumed using 180, 2-week-old chicks challenged with MDR-ESBL-producing E. coli strain O78. Chicks were divided into six groups (30 chicks each) according to the treatment regimen. Treatment was administered to chicks in Groups 3-6 intravenously, twice per day for 1 week using one antibiotic per group at concentration 10 times the determined MIC. Chicks in the positive control (Group 1) were challenged and received 0.2 ml of sterile Tryptone Soy Broth (TSB), while those in the negative control (Group 2) were not challenged and received 0.2 ml of sterile TSB. The severity of clinical signs, gross lesions, and mortality rate was scored and compared between groups. RESULTS All E. coli isolates were sensitive to doripenem and tigecycline, while 88% were sensitive to cefepime and only 23% were sensitive to tetracycline. In vivo antibiotic efficacy evaluation in challenged chicks revealed a significant reduction in the severity of clinical signs, gross lesions, and mortality (3%) in chicks treated with cefepime compared to non-treated chicks (55%). There was no significant effect on the severity of clinical signs, gross lesions, and mortality in chicks treated with doripenem, tigecycline, and tetracycline compared to non-treated chicks. The mortality rates of chicks treated with doripenem, tigecycline, and tetracycline were 57%, 50%, and 90%, respectively. CONCLUSION The results of this study indicate that most MDR-ESBLs producing E. coli isolates were sensitive to doripenem, tigecycline, and cefepime. However, in vivo study indicated that only cefepime was effective and resulted in a significant reduction in clinical signs, gross lesions, and mortality in infected chicks. Therefore, cefepime could be used to treat naturally infected chickens with MDR-ESBLs producing strains of E. coli.
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Affiliation(s)
- Yaser Hamadeh Tarazi
- Department of Basic Medical Veterinary Sciences, Faculty of Veterinary Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Ehab A. Abu-Basha
- Department of Basic Medical Veterinary Sciences, Faculty of Veterinary Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Zuhair Bani Ismail
- Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Rawan A. Tailony
- Department of Basic Medical Veterinary Sciences, Faculty of Veterinary Medicine, Jordan University of Science and Technology, Irbid, Jordan
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Abstract
Klebsiella pneumoniae is a common cause of antimicrobial-resistant opportunistic infections in hospitalized patients. The species is naturally resistant to penicillins, and members of the population often carry acquired resistance to multiple antimicrobials. However, knowledge of K. pneumoniae ecology, population structure or pathogenicity is relatively limited. Over the past decade, K. pneumoniae has emerged as a major clinical and public health threat owing to increasing prevalence of healthcare-associated infections caused by multidrug-resistant strains producing extended-spectrum β-lactamases and/or carbapenemases. A parallel phenomenon of severe community-acquired infections caused by 'hypervirulent' K. pneumoniae has also emerged, associated with strains expressing acquired virulence factors. These distinct clinical concerns have stimulated renewed interest in K. pneumoniae research and particularly the application of genomics. In this Review, we discuss how genomics approaches have advanced our understanding of K. pneumoniae taxonomy, ecology and evolution as well as the diversity and distribution of clinically relevant determinants of pathogenicity and antimicrobial resistance. A deeper understanding of K. pneumoniae population structure and diversity will be important for the proper design and interpretation of experimental studies, for interpreting clinical and public health surveillance data and for the design and implementation of novel control strategies against this important pathogen.
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Laxminarayan R, Van Boeckel T, Frost I, Kariuki S, Khan EA, Limmathurotsakul D, Larsson DGJ, Levy-Hara G, Mendelson M, Outterson K, Peacock SJ, Zhu YG. The Lancet Infectious Diseases Commission on antimicrobial resistance: 6 years later. THE LANCET. INFECTIOUS DISEASES 2020; 20:e51-e60. [PMID: 32059790 DOI: 10.1016/s1473-3099(20)30003-7] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/02/2020] [Accepted: 01/06/2020] [Indexed: 12/21/2022]
Abstract
In 2013, a Lancet Infectious Diseases Commission described the state of antimicrobial resistance worldwide. Since then, greater awareness of the public health ramifications of antimicrobial resistance has led to national actions and global initiatives, including a resolution at the high-level meeting of the UN General Assembly in 2016. Progress in addressing this issue has ranged from a ban on irrational drug combinations in India to commitments to ban colistin as a growth promoter in animals, improve hospital infection control, and implement better antimicrobial stewardship. Funds have been mobilised, and regulatory barriers to new antibiotic development have been relaxed. These efforts have been episodic and uneven across countries, however. Sustained funding for antimicrobial resistance and globally harmonised targets to monitor progress are still urgently needed. Except for in a few leading countries, antimicrobial resistance has not captured the sustained focus of national leaders and country-level actors, including care providers.
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Affiliation(s)
- Ramanan Laxminarayan
- Centre for Disease Dynamics, Economics & Policy, New Delhi, India; Princeton Environmental Institute, Princeton University, Princeton, NJ, USA.
| | - Thomas Van Boeckel
- Institute for Environmental Decisions, Swiss Federal Institute of Technology in Zurich, Zurich, Switzerland
| | - Isabel Frost
- Centre for Disease Dynamics, Economics & Policy, New Delhi, India; Faculty of Medicine, Department of Infectious Disease, Imperial College, London, UK
| | | | - Ejaz Ahmed Khan
- Shifa International Hospital, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | | | - D G Joakim Larsson
- Institute for Biomedicine, Department of Infectious Diseases, Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Gabriel Levy-Hara
- Infectious Disease Unit, Hospital Carlos G Durand, Buenos Aires, Argentina
| | - Marc Mendelson
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | | | | | - Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
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47
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Ludden C, Moradigaravand D, Jamrozy D, Gouliouris T, Blane B, Naydenova P, Hernandez-Garcia J, Wood P, Hadjirin N, Radakovic M, Crawley C, Brown NM, Holmes M, Parkhill J, Peacock SJ. A One Health Study of the Genetic Relatedness of Klebsiella pneumoniae and Their Mobile Elements in the East of England. Clin Infect Dis 2020; 70:219-226. [PMID: 30840764 PMCID: PMC6938978 DOI: 10.1093/cid/ciz174] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 02/27/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a human, animal, and environmental commensal and a leading cause of nosocomial infections, which are often caused by multiresistant strains. We evaluate putative sources of K. pneumoniae that are carried by and infect hospital patients. METHODS We conducted a 6-month survey on 2 hematology wards at Addenbrooke's Hospital, Cambridge, United Kingdom, in 2015 to isolate K. pneumoniae from stool, blood, and the environment. We conducted cross-sectional surveys of K. pneumoniae from 29 livestock farms, 97 meat products, the hospital sewer, and 20 municipal wastewater treatment plants in the East of England between 2014 and 2015. Isolates were sequenced and their genomes compared. RESULTS Klebsiella pneumoniae was isolated from stool of 17/149 (11%) patients and 18/922 swabs of their environment, together with 1 bloodstream infection during the study and 4 others over a 24-month period. Each patient carried 1 or more lineages that was unique to them, but 2 broad environmental contamination events and patient-environment transmission were identified. Klebsiella pneumoniae was isolated from cattle, poultry, hospital sewage, and 12/20 wastewater treatment plants. There was low genetic relatedness between isolates from patients/their hospital environment vs isolates from elsewhere. Identical genes encoding cephalosporin resistance were carried by isolates from humans/environment and elsewhere but were carried on different plasmids. CONCLUSION We identified no patient-to-patient transmission and no evidence for livestock as a source of K. pneumoniae infecting humans. However, our findings reaffirm the importance of the hospital environment as a source of K. pneumoniae associated with serious human infection.
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Affiliation(s)
- Catherine Ludden
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Hinxton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
| | - Danesh Moradigaravand
- Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Cambridge
| | - Dorota Jamrozy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
| | - Theodore Gouliouris
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge
| | - Beth Blane
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge
| | - Plamena Naydenova
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge
| | | | - Paul Wood
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
| | - Nazreen Hadjirin
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - Milorad Radakovic
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - Charles Crawley
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge
| | - Nicholas M Brown
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge
| | - Mark Holmes
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
| | - Sharon J Peacock
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Hinxton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge
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Huang M, He P, Munir S, Wu Y, Li X, He P, He Y. Ecology and etiology of bacterial top rot in maize caused by Klebsiella pneumoniae KpC4. Microb Pathog 2019; 139:103906. [PMID: 31786257 DOI: 10.1016/j.micpath.2019.103906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/28/2019] [Accepted: 11/28/2019] [Indexed: 10/25/2022]
Abstract
Klebsiella pneumoniae is an important opportunistic pathogen in humans and animals. Recently, K. pneumoniae KpC4 was identified as a causative agent of bacterial top rot in maize, which has been observed in many areas of Yunnan province, China. KpC4 is potentially dangerous to humans and livestock due to its cross-kingdom infection ability. Our study revealed the disease cycle of maize bacterial top rot caused by KpC4 and the ecological adaptability and host range of KpC4. We found same pathogenicity in maize between KpC4, the environmental strains E1, E4 (K1 serotype), E5, and the clinical strain K. pneumoniae 138 (Kp138). Alternative hosts of K. pneumoniae include not only humans and animals but also a variety of plants (such as maize, banana and sorghum). One of the survival strategies of K. pneumoniae is ecological adaptability, which is an essential factor for KpC4 to be able to cause bacterial top rot in maize. K. pneumoniae, for example, could survive in large numbers (2.34 ± 0.22 × 103 cfu/g) not only in the maize leaves (2.34 ± 0.22 × 103 cfu/g) under natural light, but persist in dried maize plant debris (1.51 × 104 cfu/g) for at least 6 months. K. pneumoniae strains from different sources can generally induce infection in susceptible hosts. Thus, this study revealed the ecological basis of KpC4 cross-kingdom infections, laying the foundation for the study of the mechanisms underlying cross-kingdom infections involving this type of human/animal opportunistic pathogen.
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Affiliation(s)
- Min Huang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China; College of Agriculture and Life Sciences, Urban Modern Agriculture Engineering Research Center, Kunming University, Kunming, 650214, China
| | - Pengfei He
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Shahzad Munir
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yixin Wu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Xingyu Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Pengbo He
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yueqiu He
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
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Manson AL, Van Tyne D, Straub TJ, Clock S, Crupain M, Rangan U, Gilmore MS, Earl AM. Chicken Meat-Associated Enterococci: Influence of Agricultural Antibiotic Use and Connection to the Clinic. Appl Environ Microbiol 2019; 85:e01559-19. [PMID: 31471308 PMCID: PMC6821970 DOI: 10.1128/aem.01559-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/27/2019] [Indexed: 12/17/2022] Open
Abstract
Industrial farms are unique, human-created ecosystems that provide the perfect setting for the development and dissemination of antibiotic resistance. Agricultural antibiotic use amplifies naturally occurring resistance mechanisms from soil ecologies, promoting their spread and sharing with other bacteria, including those poised to become endemic within hospital environments. To better understand the role of enterococci in the movement of antibiotic resistance from farm to table to clinic, we characterized over 300 isolates of Enterococcus cultured from raw chicken meat purchased at U.S. supermarkets by the Consumers Union in 2013. Enterococcus faecalis and Enterococcus faecium were the predominant species found, and antimicrobial susceptibility testing uncovered striking levels of resistance to medically important antibiotic classes, particularly from classes approved by the FDA for use in animal production. While nearly all isolates were resistant to at least one drug, bacteria from meat labeled as raised without antibiotics had fewer resistances, particularly for E. faecium Whole-genome sequencing of 92 isolates revealed that both commensal- and clinical-isolate-like enterococcal strains were associated with chicken meat, including isolates bearing important resistance-conferring elements and virulence factors. The ability of enterococci to persist in the food system positions them as vehicles to move resistance genes from the industrial farm ecosystem into more human-proximal ecologies.IMPORTANCE Bacteria that contaminate food can serve as a conduit for moving drug resistance genes from farm to table to clinic. Our results show that chicken meat-associated isolates of Enterococcus are often multidrug resistant, closely related to pathogenic lineages, and harbor worrisome virulence factors. These drug-resistant agricultural isolates could thus represent important stepping stones in the evolution of enterococci into drug-resistant human pathogens. Although significant efforts have been made over the past few years to reduce the agricultural use of antibiotics, continued assessment of agricultural practices, including the roles of processing plants, shared breeding flocks, and probiotics as sources for resistance spread, is needed in order to slow the evolution of antibiotic resistance. Because antibiotic resistance is a global problem, global policies are needed to address this threat. Additional measures must be taken to mitigate the development and spread of antibiotic resistance elements from farms to clinics throughout the world.
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Affiliation(s)
- Abigail L Manson
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Daria Van Tyne
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Timothy J Straub
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah Clock
- Food Safety and Sustainability Center, Consumer Reports, Yonkers, New York, USA
| | - Michael Crupain
- Food Safety and Sustainability Center, Consumer Reports, Yonkers, New York, USA
| | - Urvashi Rangan
- Food Safety and Sustainability Center, Consumer Reports, Yonkers, New York, USA
| | - Michael S Gilmore
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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50
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Silver RJ, Paczosa MK, McCabe AL, Balada-Llasat JM, Baleja JD, Mecsas J. Amino Acid Biosynthetic Pathways Are Required for Klebsiella pneumoniae Growth in Immunocompromised Lungs and Are Druggable Targets during Infection. Antimicrob Agents Chemother 2019; 63:e02674-18. [PMID: 31109974 PMCID: PMC6658747 DOI: 10.1128/aac.02674-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/11/2019] [Indexed: 12/16/2022] Open
Abstract
The emergence of multidrug-resistant Klebsiella pneumoniae has rendered a large array of infections difficult to treat. In a high-throughput genetic screen of factors required for K. pneumoniae survival in the lung, amino acid biosynthesis genes were critical for infection in both immunosuppressed and wild-type (WT) mice. The limited pool of amino acids in the lung did not change during infection and was insufficient for K. pneumoniae to overcome attenuating mutations in aroA, hisA, leuA, leuB, serA, serB, trpE, and tyrA in WT and immunosuppressed mice. Deletion of aroA, which encodes 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase class I, resulted in the most severe attenuation. Treatment with the EPSP synthase-specific competitive inhibitor glyphosate decreased K. pneumoniae growth in the lungs. K. pneumoniae expressing two previously identified glyphosate-resistant mutations in EPSP synthase had significant colonization defects in lung infection. Selection and characterization of six spontaneously glyphosate-resistant mutants in K. pneumoniae yielded no mutations in aroA Strikingly, glyphosate treatment of mice lowered the bacterial burden of two of three spontaneous glyphosate-resistant mutants and further lowered the burden of the less-attenuated EPSP synthase catalytic mutant. Of 39 clinical isolate strains, 9 were resistant to glyphosate at levels comparable to those of selected resistant strains, and none appeared to be more highly resistant. These findings demonstrate amino acid biosynthetic pathways essential for K. pneumoniae infection are promising novel therapeutic targets.
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Affiliation(s)
- Rebecca J Silver
- Graduate Program in Immunology, MERGE-ID Track, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Michelle K Paczosa
- Graduate Program in Immunology, MERGE-ID Track, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Anne L McCabe
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | | | - James D Baleja
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Joan Mecsas
- Graduate Program in Immunology, MERGE-ID Track, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
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