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Chen T, Wang Y, Chi X, Xiong L, Lu P, Wang X, Chen Y, Luo Q, Shen P, Xiao Y. Genetic, virulence, and antimicrobial resistance characteristics associated with distinct morphotypes in ST11 carbapenem-resistant Klebsiella pneumoniae. Virulence 2024; 15:2349768. [PMID: 38736039 PMCID: PMC11093053 DOI: 10.1080/21505594.2024.2349768] [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: 11/27/2023] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
ST11 is the most common lineage among carbapenem-resistant Klebsiella pneumoniae (CRKP) infections in Asia. Diverse morphotypes resulting from genetic mutations are associated with significant differences in microbial characteristics among K. pneumoniae isolates. Here, we investigated the genetic determinants and critical characteristics associated with distinct morphotypes of ST11 CRKP. An ST11-KL47 CRKP isolate carrying a pLVPK-like virulence plasmid was isolated from a patient with a bloodstream infection; the isolate had the "mcsw" morphotype. Two distinct morphotypes ("ntrd" and "msdw") were derived from this strain during in vitro passage. Whole genome sequencing was used to identify mutations that cause the distinct morphotypes of ST11 CRKP. Transmission electron microscopy, antimicrobial susceptibility tests, growth assays, biofilm formation, virulence assays, membrane permeability assays, and RNA-seq analysis were used to investigate the specific characteristics associated with different morphotypes of ST11 CRKP. Compared with the parental mcsw morphotype, the ntrd morphotype resulted from mutation of genes involved in capsular polysaccharide biosynthesis (wza, wzc, and wbaP), a result validated by gene knockout experiments. This morphotype showed capsule deficiency and lower virulence potential, but higher biofilm production. By contrast, the msdw morphotype displayed competition deficiency and increased susceptibility to chlorhexidine and polymyxin B. Further analyses indicated that these characteristics were caused by interruption of the sigma factor gene rpoN by insertion mutations and deletion of the rpoN gene, which attenuated membrane integrity presumably by downregulating the phage shock protein operon. These data expand current understanding of genetic, virulence, and antimicrobial resistance characteristics associated with distinct morphotypes in ST11 CRKP.
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Affiliation(s)
- Tao Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaohui Chi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Luying Xiong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ping Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xueting Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
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Staudacher M, Hotz JF, Kriz R, Schefberger K, Schneider L, Spettel K, Starzengruber P, Hagemann JB, Leutzendorff A, Burgmann H, Lagler H. Differences in oxazolidinone resistance mechanisms and small colony variants emergence of Staphylococcus aureus induced in an in vitro resistance development model. Emerg Microbes Infect 2024; 13:2292077. [PMID: 38055244 PMCID: PMC10849000 DOI: 10.1080/22221751.2023.2292077] [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: 10/25/2022] [Accepted: 12/03/2023] [Indexed: 12/07/2023]
Abstract
Invasive Staphylococcus aureus infections are associated with a high burden of disease, case fatality rate and healthcare costs. Oxazolidinones such as linezolid and tedizolid are considered potential treatment choices for conditions involving methicillin resistance or penicillin allergies. Additionally, they are being investigated as potential inhibitors of toxins in toxin-mediated diseases. In this study, linezolid and tedizolid were evaluated in an in vitro resistance development model for induction of resistance in S. aureus. Whole genome sequencing was conducted to elucidate resistance mechanisms through the identification of causal mutations. After inducing resistance to both linezolid and tedizolid, several partially novel single nucleotide variants (SNVs) were detected in the rplC gene, which encodes the 50S ribosome protein L3 in S. aureus. These SNVs were found to decrease the binding affinity, potentially serving as the underlying cause for oxazolidinone resistance. Furthermore, in opposite to linezolid we were able to induce phenotypically small colony variants of S. aureus after induction of resistance with tedizolid for the first time in literature. In summary, even if different antibiotic concentrations were required and SNVs were detected, the principal capacity of S. aureus to develop resistance to oxazolidinones seems to differ between linezolid and tedizolid in-vivo but not in vitro. Stepwise induction of resistance seems to be a time and cost-effective tool for assessing resistance evolution. Inducted-resistant strains should be examined and documented for epidemiological reasons, if MICs start to rise or oxazolidinone-resistant S. aureus outbreaks become more frequent.
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Affiliation(s)
- Moritz Staudacher
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- Department of Angiology, Medical University of Vienna, Vienna, Austria
| | - Julian Frederic Hotz
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- Department of Neurology, Evangelic Hospital Vienna, Vienna, Austria
| | - Richard Kriz
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Katharina Schefberger
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Lisa Schneider
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Kathrin Spettel
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Peter Starzengruber
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | | | - Amelie Leutzendorff
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Heinz Burgmann
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Heimo Lagler
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
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3
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Shi Q, Hu H, Yu Q, Huang W, Wang Y, Quan J, Zhou J, Weng R, Zhang P, Meng Y, Liu H, Jiang Y, Yu Y, Du X. Chromosomal integration and plasmid fusion occurring in ST20 carbapenem-resistant Klebsiella pneumoniae isolates coharboring blaNDM-1 and blaIMP-4 induce resistance transmission and fitness variation. Emerg Microbes Infect 2024; 13:2339942. [PMID: 38584569 PMCID: PMC11022923 DOI: 10.1080/22221751.2024.2339942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 04/03/2024] [Indexed: 04/09/2024]
Abstract
To investigate the epidemiology of ST20 carbapenem-resistant Klebsiella pneumoniae (CRKP) in China, and further explore the genomic characteristics of blaIMP-4 and blaNDM-1 coharboring isolates and plasmid contributions to resistance and fitness. Seven ST20 CRKP isolates were collected nationwide, and antimicrobial susceptibility testing was performed. Antimicrobial resistance genes, virulence genes, and plasmid replicons were identified via whole-genome sequencing, and clonality assessed via core-genome multilocus sequence typing. Furthermore, we found four dual-metallo-β-lactamases (MBL)-harbouring isolates, the gene location was detected by Southern blotting, and plasmid location analysis showed that blaIMP-4 was located on a separate plasmid, a self-conjugative fusion plasmid, or the bacterial chromosome. These isolates were subjected to long-read sequencing, the presence of blaIMP-4 in different locations was identified by genomic comparison, and transposon units were detected via inverse PCR. We subsequently found that blaIMP-4 on the fusion plasmid and bacterial chromosome was formed via intact plasmid recombination by the IS26 and ltrA, respectively, and the circular transposon unit was related to cointegration, however, blaIMP-4 in different locations did not affect the gene stability. The blaNDM-1-harbouring plasmid contributed to the increased resistance to β-lactams and shortened survival lag time which was revealed in plasmid cured isolates. In summary, the K. pneumoniae ST20 clone is a high-risk resistant clone. With the use of ceftazidime/avibactam, MBL-positive isolates, especially dual-MBL-harbouring isolates, should be given additional attention.
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Affiliation(s)
- Qiucheng Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Huangdu Hu
- Center for General Practice Medicine, Department of Infectious Diseases, Zhejiang Provincial People’s Hospital, Hangzhou Medical College Affiliated People’s Hospital, Hangzhou, People’s Republic of China
| | - Qian Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Weiyi Huang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yinping Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Jingjing Quan
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Junxin Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Rui Weng
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Ping Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yan Meng
- Department of Clinical Laboratory, Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Haiyang Liu
- Center of Laboratory Medicine, Zhejiang Provincial People’s Hospital, Hangzhou Medical College Affiliated People’s Hospital, Hangzhou, People’s Republic of China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Xiaoxing Du
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
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Sattler J, Noster J, Stelzer Y, Spille M, Schäfer S, Xanthopoulou K, Sommer J, Jantsch J, Peter S, Göttig S, Gatermann SG, Hamprecht A. OXA-48-like carbapenemases in Proteus mirabilis - novel genetic environments and a challenge for detection. Emerg Microbes Infect 2024; 13:2353310. [PMID: 38712879 PMCID: PMC11123474 DOI: 10.1080/22221751.2024.2353310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 05/05/2024] [Indexed: 05/08/2024]
Abstract
OXA-48-like enzymes represent the most frequently detected carbapenemases in Enterobacterales in Western Europe, North Africa and the Middle East. In contrast to other species, the presence of OXA-48-like in Proteus mirabilis leads to an unusually susceptible phenotype with low MICs for carbapenems and piperacillin-tazobactam, which is easily missed in the diagnostic laboratory. So far, there is little data available on the genetic environments of the corresponding genes, blaOXA-48-like, in P. mirabilis. In this study susceptibility phenotypes and genomic data of 13 OXA-48-like-producing P. mirabilis were investigated (OXA-48, n = 9; OXA-181, n = 3; OXA-162, n = 1). Ten isolates were susceptible to meropenem and ertapenem and three isolates were susceptible to piperacillin-tazobactam. The gene blaOXA-48 was chromosomally located in 7/9 isolates. Thereof, in three isolates blaOXA-48 was inserted into a P. mirabilis genomic island. Of the three isolates harbouring blaOXA-181 one was located on an IncX3 plasmid and two were located on a novel MOBF plasmid, pOXA-P12, within the new transposon Tn7713. In 5/6 isolates with plasmidic location of blaOXA-48-like, the plasmids could conjugate to E. coli recipients in vitro. Vice versa, blaOXA-48-carrying plasmids could conjugate from other Enterobacterales into a P. mirabilis recipient. These data show a high diversity of blaOXA-48-like genetic environments compared to other Enterobacterales, where genetic environments are quite homogenous. Given the difficult-to-detect phenotype of OXA-48-like-producing P. mirabilis and the location of blaOXA-48-like on mobile genetic elements, it is likely that OXA-48-like-producing P. mirabilis can disseminate, escape most surveillance systems, and contribute to a hidden spread of OXA-48-like.
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Affiliation(s)
- Janko Sattler
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
- German Centre for Infection Research (DZIF)
| | - Janina Noster
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
| | - Yvonne Stelzer
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
| | - Martina Spille
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
| | - Sina Schäfer
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF)
| | - Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF)
| | - Julian Sommer
- Goethe University Frankfurt, University Hospital, Institute of Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Jonathan Jantsch
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF)
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University Hospital Tuebingen, Tuebingen, Germany
- German Centre for Infection Research (DZIF)
| | - Stephan Göttig
- Goethe University Frankfurt, University Hospital, Institute of Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Sören G. Gatermann
- National Reference Laboratory for Multidrug-Resistant Gram-negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
- German Centre for Infection Research (DZIF)
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García-Martín AB, Aguilar-Bultet L, Gómez-Sanz E, Hug MA, Furger R, Eichenberger L, Schindler R, Steffen I, Egli A, Stadler T, Bagutti C, Tschudin-Sutter S. Prospective One-Health investigation into low-abundant extended-spectrum β-lactamase producing Enterobacterales enables detection of potential dissemination events and persistence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175078. [PMID: 39069185 DOI: 10.1016/j.scitotenv.2024.175078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Following a one-health approach, we sought to determine reservoirs of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-PE), other than Escherichia coli or Klebsiella pneumoniae complex species (i.e., low-abundant species), and their associated ESBL genes and plasmid-replicon profiles. METHODS From 06/2017-05/2019, ESBL-PE isolates were recovered from clinical samples routinely collected at the University Hospital Basel (Basel, Switzerland), as well as from wastewater and foodstuffs collected monthly at predefined locations throughout the city of Basel. Whole-genome sequencing was performed for characterization of ESBL-PE isolates. RESULTS Among 1634 isolates recovered, 114 (7%) belonged to 17 low-abundant ESBL-PE species. Seven species originated from more than one compartment, mainly from clinical and wastewater samples (6/17). Sixteen different ESBL genes were identified, with blaCTX-M-15 (27%), blaFONA-6 (23%) and blaSHV-12 (16%) being most frequent. The blaCTX-M-1 gene was the only ESBL gene recovered from all three compartments. Putative plasmids constituted 60% of ESBL gene-containing contigs, while chromosomes comprised 40%. Foodstuff isolates showed the highest proportion (91%, 41/45) of ESBL genes located on chromosomes, whereas wastewater isolates had the highest proportion (95%, 37/39) of putative plasmids. Multi-replicon combinations were identified in 81% of the isolates. Epidemiological links were found among some clinical and wastewater isolates. CONCLUSIONS The dominance of blaCTX-M-15 among low-abundant ESBL-PE species supports its species-independent transmission potential beyond the E. coli and K. pneumoniae complex, and blaCTX-M-1 may be transmitted between strains recovered from different compartments. The substantial overlap between low-abundant ESBL-PE present in wastewater and clinical samples supports the utility of wastewater surveillance for antibiotic resistance monitoring.
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Affiliation(s)
- Ana B García-Martín
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland; Department of Clinical Research, University Hospital Basel, Basel, Switzerland.
| | - Lisandra Aguilar-Bultet
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland; Department of Clinical Research, University Hospital Basel, Basel, Switzerland.
| | - Elena Gómez-Sanz
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland; Department of Clinical Research, University Hospital Basel, Basel, Switzerland.
| | | | - Reto Furger
- State Laboratory Basel-City, Basel, Switzerland.
| | | | - Ruth Schindler
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland; Department of Clinical Research, University Hospital Basel, Basel, Switzerland.
| | | | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | | | - Sarah Tschudin-Sutter
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland; Department of Clinical Research, University Hospital Basel, Basel, Switzerland.
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Yao S, Yu J, Zhang T, Xie J, Yan C, Ni X, Guo B, Cui C. Comprehensive analysis of distribution characteristics and horizontal gene transfer elements of bla NDM-1-carrying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:173907. [PMID: 38906294 DOI: 10.1016/j.scitotenv.2024.173907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/08/2024] [Accepted: 06/08/2024] [Indexed: 06/23/2024]
Abstract
The worldwide dissemination of New Delhi metallo-β-lactamase-1 (NDM-1), which mediates resistance to almost all clinical β-lactam antibiotics, is a major public health problem. The global distribution, species, sources, and potential transfer risk of blaNDM-1-carrying bacteria are unclear. Results of a comprehensive analysis of literature in 2010-2022 showed that a total of 6002 blaNDM-1 carrying bacteria were widely distributed around 62 countries with a high trend in the coastal areas. Opportunistic pathogens or pathogens like Klebsiella sp., Escherichia sp., Acinetobacter sp. and Pseudomonas sp. were the four main species indicating the potential microbial risk. Source analysis showed that 86.45 % of target bacteria were isolated from the source of hospital (e.g., Hospital patients and wastewater) and little from surface water (5.07 %) and farms (3.98 %). A plasmid-encoded blaNDM-1Acinetobacter sp. with the resistance mechanisms of antibiotic efflux pump, antibiotic target change and antibiotic degradation was isolated from the wastewater of a typical tertiary hospital. Insertion sequences (IS3 and IS30) located in the adjacent 5 kbp of blaNDM-1-bleMBL gene cluster indicating the transposon-mediated horizontal gene transfer risk. These results showed that the worldwide spread of blaNDM-1-carrying bacteria and its potential horizontal gene transfer risk deserve good control.
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Affiliation(s)
- Shijie Yao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaqin Yu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Tianyang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Jianhao Xie
- Children's Hospital of Fudan University, Shanghai 200233, China
| | - Chicheng Yan
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xuan Ni
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bingbing Guo
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Shanghai environmental protection key laboratory on environmental standard and risk management of chemical pollutants, East China University of Science & Technology, Shanghai 200237, China.
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7
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Habib I, Mohamed MYI, Lakshmi GB, Ghazawi A, Khan M, Abdalla A, Anes F. High prevalence and genomic features of multidrug-resistant Salmonella enterica isolated from chilled broiler chicken on retail sale in the United Arab Emirates. Int J Food Microbiol 2024; 423:110828. [PMID: 39032201 DOI: 10.1016/j.ijfoodmicro.2024.110828] [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: 04/30/2024] [Revised: 06/22/2024] [Accepted: 07/15/2024] [Indexed: 07/22/2024]
Abstract
Non-typhoidal Salmonella represents a significant global concern for food safety and One Health. Despite the United Arab Emirates (UAE) being a leading consumer of chicken meat globally, there is a lack of comprehensive understanding regarding the prevalence and genomic characteristics of Salmonella within the country. This study aims to address this gap by conducting a thorough analysis of Salmonella prevalence, antimicrobial resistance, and genomic profiles of isolates obtained from whole broiler carcasses retailed under chilled conditions in the UAE. Our findings reveal that Salmonella was detected in 41.2 % (130/315) of the sampled chilled broiler carcasses, with notable variability observed among samples sourced from six different companies. Phenotypic antimicrobial resistance (AMR) testing, among 105 isolates, highlighted high resistance rates to tetracycline (97.1 %), nalidixic acid (93.3 %), ampicillin (92.4 %), azithromycin (75.2 %), ciprofloxacin (63.8 %), and ceftriaxone (54.3 %). Furthermore, a concerning 99 % (104/105) of the isolates exhibited multidrug resistance. Whole-genome sequencing (WGS) of 60 isolates identified five serovars, with S. infantis/Sequence Type (ST) 32 (55 %) and S. Minnesota/ST-458 (28.3 %) being the most prevalent. WGS analysis unveiled 34 genes associated with antimicrobial resistance, including mcr-1.1 (only in two isolates), conferring resistance to colistin. The two major serovars, Infantis and Minnesota, exhibited significant variation (P-values <0.001) in the distribution of major AMR genes (aadA1, blaCMY-2, blaSHV-12, qnrB19, qnrS1, sul1, and sul2). Notably, the gene qacEdelta, conferring resistance to quaternary ammonium compounds commonly found in disinfectants, was universally present in all S. Infantis isolates (n = 33), compared to only one S. Minnesota isolate. Additionally, all S. Infantis isolates harbored the IncFIB (pN55391) plasmid replicon type. Major serovars exhibited distinct distributions of antimicrobial resistance genes, underscoring the importance of serovar-specific surveillance. These findings emphasize the critical need for continuous surveillance and intervention measures to address Salmonella contamination risks in poultry products, providing valuable insights for public health and regulatory strategies not only in the UAE but also globally.
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Affiliation(s)
- Ihab Habib
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates.
| | - Mohamed-Yousif Ibrahim Mohamed
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates
| | - Glindya Bhagya Lakshmi
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates
| | - Mushtaq Khan
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates
| | - Afra Abdalla
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates
| | - Febin Anes
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates
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Aldeia C, Campos-Madueno EI, Endimiani A. Genomic insights into Leminorella grimontii and its chromosomal class A GRI β-lactamase. Eur J Clin Microbiol Infect Dis 2024; 43:1855-1860. [PMID: 38958811 DOI: 10.1007/s10096-024-04888-7] [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: 05/23/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024]
Abstract
Leminorella grimontii strain LG-KP-E1-2-T0 was isolated from Zophobas morio larvae. It showed a susceptibility phenotype compatible with the expression of an inducible extended-spectrum β-lactamase. The presence of a chromosomal bla gene encoding for the class A GRI-1 β-lactamase was revealed by whole-genome sequencing. GRI-1 shared the highest amino acid identity with RIC-1 and OXY-type β-lactamases (76-80%). Analysis of six further publicly-available L. grimontii draft genomes deposited in NCBI revealed that blaGRI-1 was always present. Core-genome analysis indicated that LG-KP-E1-2-T0 was unique from other strains. We provided the first complete genome of L. grimontii and new insights on its chromosomal β-lactamases.
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Affiliation(s)
- Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 25, Bern, CH-3001, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 25, Bern, CH-3001, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 25, Bern, CH-3001, Switzerland.
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Kotzamanidis C, Malousi A, Paraskeva A, Vafeas G, Giantzi V, Hatzigiannakis E, Dalampakis P, Kinigopoulou V, Vrouhakis I, Zouboulis A, Yiangou M, Zdragas A. River waters in Greece: A reservoir for clinically relevant extended-spectrum-β-lactamases-producing Escherichia coli. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 941:173554. [PMID: 38823724 DOI: 10.1016/j.scitotenv.2024.173554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/10/2024] [Accepted: 05/24/2024] [Indexed: 06/03/2024]
Abstract
In the current study, the genotypic characteristics such as antimicrobial resistance and virulence genes, and plasmid replicons and phenotypic characteristics such as biofilm formation and antimicrobial resistance of 87 extended-spectrum beta-lactamase (ESBL)-producing E. coli (ESBL-Ec) isolated from 7 water bodies in northern Greece were investigated. Our data show a high prevalence (60.0 %) of ESBL-Ec in surface waters that exhibit high genetic diversity, suggesting multiple sources of their transmission into the aquatic environment. When evaluating the antimicrobial resistance of isolates, wide variation in their resistance profiles has been detected, with all isolates being multi-drug resistant (MDR). Regarding biofilm formation capacity and phylogenetic groups, the majority (54.0 %, 47/87) of ESBL-Ec were classified as no biofilm producers mainly assigned to phylogroup A (35.6 %; 31/87), followed by B2 (26.5 %; 23/87). PCR screening showed that a high proportion of the isolates tested positive for the blaCTX-M-1 group genes (69 %, 60/87), followed by blaTEM (55.2 %, 48/87), blaOXA (25.3 %, 22/87) and blaCTX-M-9 (17.2 %, 15/87). A subset of 28 ESBL-Ec strains was further investigated by applying whole genome sequencing (WGS), and among them, certain clinically significant sequence types were identified, such as ST131 and ST10. The corresponding in silico analysis predicted all these isolates as human pathogens, while a significant proportion of WGS-ESBL-Ec were assigned to extraintestinal pathogenic E. coli (ExPEC; 32.1 %), and urinary pathogenic E. coli (UPEC; 28.6 %) pathotypes. Comparative phylogenetic analysis, showed that the genomes of the ST131-O25:H4-H30 isolates are genetically linked to the human clinical strains. Here, we report for the first time the detection of a plasmid-mediated mobile colistin resistance gene in ESBL-Ec in Greece isolated from an environmental source. Overall, this study underlines the role of surface waters as a reservoir for antibiotic resistance genes and for presumptive pathogenic ESBL-Ec.
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Affiliation(s)
- Charalampos Kotzamanidis
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Campus of Thermi, Thermi 570 01, Greece.
| | - Andigoni Malousi
- School of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece; Genomics and Epigenomics Translational Research Group, Center for Interdisciplinary Research and Innovation, Thessaloniki 57001, Greece
| | - Anastasia Paraskeva
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - George Vafeas
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Campus of Thermi, Thermi 570 01, Greece
| | - Virginia Giantzi
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Campus of Thermi, Thermi 570 01, Greece
| | - Evaggelos Hatzigiannakis
- Soil & Water Resources Institute, Hellenic Agricultural Organisation-DEMETER, Sindos, Central Macedonia 57400, Greece
| | - Paschalis Dalampakis
- Soil & Water Resources Institute, Hellenic Agricultural Organisation-DEMETER, Sindos, Central Macedonia 57400, Greece
| | - Vasiliki Kinigopoulou
- Soil & Water Resources Institute, Hellenic Agricultural Organisation-DEMETER, Sindos, Central Macedonia 57400, Greece
| | - Ioannis Vrouhakis
- Soil & Water Resources Institute, Hellenic Agricultural Organisation-DEMETER, Sindos, Central Macedonia 57400, Greece
| | - Anastasios Zouboulis
- Department of Chemistry, Division of Chemical & Industrial Technology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Minas Yiangou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonios Zdragas
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Campus of Thermi, Thermi 570 01, Greece
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Peng J, Xiao R, Wu C, Zheng Z, Deng Y, Chen K, Xiang Y, Xu C, Zou L, Liao M, Zhang J. Characterization of the prevalence of Salmonella in different retail chicken supply modes using genome-wide and machine-learning analyses. Food Res Int 2024; 191:114654. [PMID: 39059904 DOI: 10.1016/j.foodres.2024.114654] [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: 04/22/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/28/2024]
Abstract
Salmonella is a foodborne pathogen that causes salmonellosis, of which retail chicken meat is a major source. However, the prevalence of Salmonella in different retail chicken supply modes and the threat posed to consumers remains unclear. The prevalence, serotype distribution, antibiotic resistance, and genomic characteristics of Salmonella in three supply modes of retail chicken (live poultry, frozen, and chilled) were investigated using whole-genome sequencing (WGS) and machine learning (ML). In this study, 480 retail chicken samples from live poultry, frozen, and chilled supply modes in Guangzhou from 2020 to 2021, as well as 253 Salmonella isolates (total isolation rate = 53.1 %), were collected. The prevalence of isolates in the live poultry mode (67.5 %, 81/120) was statistically higher than in the frozen (50.0 %, 120/240) and chilled (43.3 %, 52/120) (P < 0.05) modes. Serotype identification showed significant differences in the serotype distribution of Salmonella in different supply modes. S. Enteritis (46.7 %) and S. Indiana (14.2 %) were predominant in the frozen mode. S. Agona (23.5 %) and S. Saintpaul (13.6 %) were predominant in live poultry, while S. Enteritis (40.4 %) and S. Kentucky (17.3 %) were predominant in chilled mode. Antibiotic testing showed that frozen mode isolates were more resistant; the multidrug-resistant (MDR) rate of isolates in the frozen mode reached 91.8 %, significantly higher than in the chilled (86.5 %) and live (74.1 %) (P < 0.05) modes. WGS was performed on 155 top serotypes (S. Enteritidis, S. Kentucky, S. Indiana, and S. Agona). The antibiotic resistance gene analysis showed that the abundance and carrying rate of antibiotic resistance genes of Salmonella in the frozen mode (54 types, 16.1 %) were significantly higher than in other modes (live poultry: 36 types, 9.4 %, P < 0.05; chilled: 31 types, 11.6 %). The blaNDM-1 and blaNDM-9 genes encoding carbapenem resistance were found in frozen mode isolates on a complex transposon consisting of TnAS3-IS26. Virulence factors and plasmid replicons were abundant in the studied frozen mode isolates. In addition, single nucleotide polymorphism (SNP) phylogenetic tree results showed that in the frozen supply mode, the S. Enteritidis clonal clade continued to contaminate retail chicken meat and was homologous to S. Enteritidis strains found in farm chicken embryos, slaughterhouse chicken carcasses, and patients from hospitals in China (SNP 0 = 10). Notably, the pan-genome-based ML model showed that characteristic genes in frozen and live poultry isolates differed. The narZ gene was a key characteristic gene in frozen isolates, encoding nitrate reductase, relating to anaerobic bacterial growth. The ydgJ gene is a key characteristic gene in the live mode and encodes an oxidoreductase related to oxidative function in bacteria. The high prevalence of live poultry mode Salmonella and the transmission of frozen mode MDR Salmonella in this study pose serious risks to food safety and public health, emphasizing the importance of improving disinfection and cold storage measures to reduce Salmonella contamination and transmission. In conclusion, the continued surveillance of Salmonella across different supply models and the development of an epidemiological surveillance system based on WGS is necessary.
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Affiliation(s)
- Junhao Peng
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Renhang Xiao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Canji Wu
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zexin Zheng
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yuhui Deng
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Kaifeng Chen
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yuwei Xiang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Chenggang Xu
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Likou Zou
- College of Resource, Sichuan Agricultural University, 611130 Yaan, China
| | - Ming Liao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; School of Resources and Environmental, Zhongkai College of Agricultural Engineering, Guangxin Road No. 388, Baiyun District, Guangzhou 510550, Guangdong, China.
| | - Jianmin Zhang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control; Key Laboratory of Zoonoses, Ministry of Agriculture; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
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Romão FT, Santos ACM, Puño-Sarmiento JJ, Sperandio V, Hernandes RT, Gomes TAT. Expression of the locus of enterocyte effacement genes during the invasion process of the atypical enteropathogenic Escherichia coli 1711-4 strain of serotype O51:H40. Microbiol Spectr 2024:e0030424. [PMID: 39189752 DOI: 10.1128/spectrum.00304-24] [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: 02/02/2024] [Accepted: 07/01/2024] [Indexed: 08/28/2024] Open
Abstract
Atypical enteropathogenic Escherichia coli (aEPEC) is a significant cause of diarrhea in low- and middle-income countries. Certain aEPEC strains, including the Brazilian representative strain of serotype O51:H40 called aEPEC 1711-4, can use flagella to attach to, invade, and persist in T84 and Caco-2 intestinal cells. It can also translocate from the gut to extraintestinal sites in a rat model. Although various aspects of the virulence of this strain were studied and the requirement of a type III secretion system for the efficiency of the invasion process was demonstrated, the expression of the locus of enterocyte effacement (LEE) genes during the invasion and intracellular persistence remains unclear. To address this question, the expression of flagella and the different LEE operons was evaluated during kinetic experiments of the interaction of aEPEC 1711-4 with enterocytes in vitro. The genome of the strain was also sequenced. The results showed that flagella expression remained unchanged, but the expression of eae and escJ increased during the early interaction and invasion of aEPEC 1711-4 into Caco-2 cells, and there was no change 24 h post-infection during the persistence period. The number of actin accumulation foci formed on HeLa cells also increased during the 6-h analysis. No known gene related to the invasion process was identified in the genome of aEPEC 1711-4, which was shown to belong to the global EPEC lineage 10. These findings suggest that the LEE components and the intimate adherence promoted by intimin are necessary for the invasion and persistence of aEPEC 1711-4, but the detailed mechanism needs further study.IMPORTANCEAtypical enteropathogenic Escherichia coli (aEPEC) is a major cause of diarrhea, especially in low- and middle-income countries, like Brazil. However, due to the genome heterogeneity of each clonal group, it is difficult to comprehend the pathogenicity of this strain fully. Among aEPEC strains, 1711-4 can invade eukaryotic cells in vitro, cross the gut barrier, and reach extraintestinal sites in animal models. By studying how different known aEPEC virulence factors are expressed during the invasion process, we can gain insight into the commonalities of this phenotype among other aEPEC strains. This will help in developing preventive measures to control infections caused by invasive strains. No known virulence-encoding genes linked to the invasion process were found. Nevertheless, additional studies are still necessary to evaluate the role of other factors in this phenotype.
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Affiliation(s)
- Fabiano T Romão
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Ana C M Santos
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Juan J Puño-Sarmiento
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vanessa Sperandio
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Rodrigo T Hernandes
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Tânia A T Gomes
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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12
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Khdhiri M, Thomas E, de Smet C, Chandar P, Chandrakumar I, Davidson JM, Anderson P, Chorlton SD. refMLST: reference-based multilocus sequence typing enables universal bacterial typing. BMC Bioinformatics 2024; 25:280. [PMID: 39192191 DOI: 10.1186/s12859-024-05913-4] [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: 09/18/2023] [Accepted: 08/22/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND Commonly used approaches for genomic investigation of bacterial outbreaks, including SNP and gene-by-gene approaches, are limited by the requirement for background genomes and curated allele schemes, respectively. As a result, they only work on a select subset of known organisms, and fail on novel or less studied pathogens. We introduce refMLST, a gene-by-gene approach using the reference genome of a bacterium to form a scalable, reproducible and robust method to perform outbreak investigation. RESULTS When applied to multiple outbreak causing bacteria including 1263 Salmonella enterica, 331 Yersinia enterocolitica and 6526 Campylobacter jejuni genomes, refMLST enabled consistent clustering, improved resolution, and faster processing in comparison to commonly used tools like chewieSnake. CONCLUSIONS refMLST is a novel multilocus sequence typing approach that is applicable to any bacterial species with a public reference genome, does not require a curated scheme, and automatically accounts for genetic recombination. AVAILABILITY AND IMPLEMENTATION refMLST is freely available for academic use at https://bugseq.com/academic .
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Affiliation(s)
| | - Ella Thomas
- California Polytechnic State University, San Luis Obispo, CA, USA
| | - Chanel de Smet
- California Polytechnic State University, San Luis Obispo, CA, USA
| | - Priyanka Chandar
- California Polytechnic State University, San Luis Obispo, CA, USA
| | | | - Jean M Davidson
- California Polytechnic State University, San Luis Obispo, CA, USA
| | - Paul Anderson
- California Polytechnic State University, San Luis Obispo, CA, USA
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Arjun OK, Sethi M, Parida D, Dash J, Kumar Das S, Prakash T, Senapati S. Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India. Gene 2024:148882. [PMID: 39182659 DOI: 10.1016/j.gene.2024.148882] [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: 03/18/2024] [Revised: 08/11/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain's genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism's ability to efficiently utilize diverse resources and contribute to the host's nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.
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Affiliation(s)
- O K Arjun
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India
| | - Manisha Sethi
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Deepti Parida
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Jayalaxmi Dash
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Suraja Kumar Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Tulika Prakash
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India.
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Capitani V, Arcari G, Ambrosi C, Scribano D, Ceparano M, Polani R, De Francesco A, Raponi G, Ceccarelli G, Villari P, Palamara AT, Marzuillo C, Carattoli A. In vivo evolution to hypermucoviscosity and ceftazidime/avibactam resistance in a liver abscess caused by Klebsiella pneumoniae sequence type 512. mSphere 2024:e0042324. [PMID: 39171923 DOI: 10.1128/msphere.00423-24] [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: 05/20/2024] [Accepted: 07/15/2024] [Indexed: 08/23/2024] Open
Abstract
Carbapenemase-producing Klebsiella pneumoniae represents a major public health issue globally. Isolates with resistance to the newest drugs, like ceftazidime/avibactam (CZA), are increasingly reported. In this study, we analyzed the evolution of KPC-3-producing sequence type (ST) 512 K. pneumoniae strains isolated at three different times (hospitalization days 45, 56, and 78) from the same patient, two of which were observed in a pericholecystic liver abscess. The three K. pneumoniae isolates (295Kp, 304Kp, and hmv-318Kp) from the same patient were subjected to antimicrobial susceptibility testing, whole-genome sequencing, sedimentation assay, biofilm measurement, serum resistance assay, macrophage phagocytosis, and adhesion assays. KPC-producing isolate hmv-318Kp exhibited carbapenem susceptibility, hypermucoviscous (hmv) colony phenotype and CZA resistance. Virulence markers of hypervirulent Klebsiella were absent. Two non-synonymous mutations were identified in the hmv-318Kp genome comparing with isogenic strains: a single-nucleotide polymorphism (SNP) occurred in the pKpQIL plasmid, changing blaKPC-3 in the blaKPC-31 gene variant, conferring CZA resistance; and a second SNP occurred in the wzc gene of the capsular biosynthesis cluster, encoding a tyrosine kinase, resulting in the F557S Wzc protein mutation. The Klebsiella pneumoniae strain exhibiting an hmv phenotype (hmv-Kp) phenotype has been previously associated with amino acid substitutions occurring in the Wzc tyrosin kinase protein. We observed in vivo evolution of the ST512 strain to CZA resistance and acquisition of hypermucoviscosity. The pathogenetic role of the detected Wzc substitution is not fully elucidated, but other Wzc mutations were previously reported in hmv K. pneumoniae. Wzc mutants may be more frequent than expected and an underreported cause of hypermucoviscosity in K. pneumoniae clinical isolates. IMPORTANCE Here we describe the evolution of KPC-3-producing ST512 K. pneumoniae isolated at three different times from the same patient of which the last one, from a biliary abscess, showed CZA resistance by KPC-31 production and manifested hmv colony phenotype. Hypervirulent Klebsiella pneumoniae (hv-Kp) isolates are increasingly reported worldwide. Their hypervirulent traits are associated with the presence of rmpA/A2 genes and an hmv. In this study, we identified an hmv-Kp that lacked the rmpA-D cluster but showed an amino acid substitution in the Wzc tyrosin kinase protein, involved in the capsular biosynthesis. This hmv-Kp strain emerged in vivo and evolved resistance to ceftazidime/avibactam resistance in a liver abscess of a patient. Our findings suggest that wzc mutations may be underreported, making it challenging to distinguish hv-Kp from "classic" K. pneumoniae with an hmv phenotype.
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Affiliation(s)
- Valerio Capitani
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Cecilia Ambrosi
- Department of Promotion of Human Sciences and Quality of Life, San Raffaele University, Rome, Italy
- Laboratory of Microbiology of Chronic-Neurodegenerative Diseases, IRCCS San Raffaele Roma, Rome, Italy
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Mariateresa Ceparano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Riccardo Polani
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Alice De Francesco
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Giammarco Raponi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Clinical Microbiology Unit, University Hospital, Policlinico Umberto I, Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
- Clinical Microbiology Unit, University Hospital, Policlinico Umberto I, Rome, Italy
| | - Paolo Villari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Laboratory affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Rome, Italy
| | - Carolina Marzuillo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
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15
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Ogundare ST, Fasina FO, Makumbi JP, van der Zel GA, Geertsma PF, Kock MM, Smith AM, Ehlers MM. Epidemiology and antimicrobial resistance profiles of pathogenic Escherichia coli from commercial swine and poultry abattoirs and farms in South Africa: A One Health approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175705. [PMID: 39181266 DOI: 10.1016/j.scitotenv.2024.175705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
Pathogenic Escherichia coli (PEC) are important foodborne bacteria that can cause severe illness in humans. The PECs thrive within the intestines of humans as well as animals and may contaminate multiple ecosystems, including food and water, via faecal transmission. Abattoir and farm employees are at high risk of PEC exposure, which could translate to community risk through person-to-person contact. To determine the epidemiology and resistome of PECs in Gauteng and Limpopo provinces of South Africa, 198 swine faecal samples, 220 poultry cloacal swabs, 108 human hand swabs, 11 run-off water samples from abattoirs and farms were collected from four swine and five poultry commercial abattoirs and two swine farms. One effluent sample each was collected from four wastewater treatment plants (WWTP) and a tertiary hospital setting. Phenotypic and genotypic techniques were used including polymerase chain reaction, pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). Results showed EHEC and EPEC prevalence was 4.1 % (22/542) and 20.8 % (113/542), respectively, with the O26 serogroup detected the most in PEC isolates. According to the PFGE dendrogram, isolates from poultry, human hand swabs and run-off water clustered together. Diverse virulence factors such as the novel stx2k subtype and eae genes were detected among the 36 representative PEC isolates according to WGS. The results showed that 66.7 % (24/36) of sequenced PECs presented with multi-drug resistance (MDR) to β-lactamase 13.9 % (5/36), aminoglycoside 61.1 % (22/36), tetracycline 41.7 % (15/36) and quinolones 38.9 % (14/36). No colistin nor carbapenem resistance was detected. Sequence types (STs) associated with MDR in this study were: ST752, ST189, ST206, ST10, ST48 and ST38. The findings highlight the threat of zoonotic pathogens to close human contacts and the need for enhanced surveillance to mitigate the spread of MDR foodborne PECs.
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Affiliation(s)
- Samuel T Ogundare
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
| | - Folorunso O Fasina
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa; Food and Agriculture Organisation of the United Nations, FAO Headquarters, Rome, Italy
| | - John-Paul Makumbi
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Gerbrand A van der Zel
- Gauteng Department of Agriculture, Rural Development and Environment, Pretoria, South Africa
| | - Peter F Geertsma
- Gauteng Department of Agriculture, Rural Development and Environment, Pretoria, South Africa
| | - Marleen M Kock
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; Department of Medical Microbiology, National Health Laboratory Service, Tshwane Academic Division, Pretoria, South Africa
| | - Anthony M Smith
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Marthie M Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; Department of Medical Microbiology, National Health Laboratory Service, Tshwane Academic Division, Pretoria, South Africa
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16
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Fu Y, Nawrocki EM, M’ikanatha NM, Dudley EG. Host species shapes genotype, antimicrobial resistance, and virulence profiles of enterotoxigenic Escherichia coli (ETEC) from livestock in the United States. Appl Environ Microbiol 2024; 90:e0074924. [PMID: 39082811 PMCID: PMC11337801 DOI: 10.1128/aem.00749-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/01/2024] [Indexed: 08/22/2024] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) are significant pathogen in both cattle and pigs, causing diarrhea in these animals and leading to economic losses in the livestock industry. Understanding the dissimilarity in genotype, antimicrobial resistance (AMR), and virulence between bovine and swine ETEC is crucial for development of targeted preventive and therapeutic approaches for livestock. However, a comprehensive study on this area remains lacking. Here, we performed whole-genome sequencing-based analyses of bovine (n = 554) and swine (n = 623) ETEC collected in the United States over a 53-year period. We identified distinct ETEC genotypes (fimH type, O antigen, H antigen, sequence type) in cattle and pigs. Furthermore, specific AMR and virulence profiles were associated with bovine and swine ETEC. Compared to swine ETEC, bovine ETEC were less diverse in genotypes and had a significantly (P < 0.001) lower number of AMR genes per isolate but higher co-occurrence of Shiga toxin and enterotoxin genes. Our results provide an overview of the key genomic differences between bovine and swine ETEC in the United States, which might be attributed to host adaptation and antibiotic usage practice. Ongoing surveillance and research are essential to monitor the genetic diversity and AMR patterns of ETEC in different host species. IMPORTANCE Enterotoxigenic Escherichia coli (ETEC)-associated diarrhea represent one of the most economically important diseases in the livestock industry. By analyzing over a thousand livestock-derived ETEC samples in the United States, our study unveiled a clear distinction in ETEC's genetic traits (i.e., genotypes, antimicrobial resistance [AMR], and virulence profiles) that might be tied to the different use of antibiotics in cattle and pigs, and the bacteria's adaptation to their specific animal hosts. This understanding is crucial for tailoring preventive and therapeutic strategies. It also highlights the significance of ongoing surveillance and research into the evolution of bacterial pathogens like ETEC in livestock by using advanced techniques such as whole-genome sequencing.
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Affiliation(s)
- Yezhi Fu
- School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Erin M. Nawrocki
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Edward G. Dudley
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- E. coli Reference Center, The Pennsylvania State University, University Park, Pennsylvania, USA
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17
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Duller S, Kumpitsch C, Moissl-Eichinger C, Wink L, Koskinen Mora K, Mahnert A. In-hospital areas with distinct maintenance and staff/patient traffic have specific microbiome profiles, functions, and resistomes. mSystems 2024; 9:e0072624. [PMID: 38980054 PMCID: PMC11334533 DOI: 10.1128/msystems.00726-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 06/11/2024] [Indexed: 07/10/2024] Open
Abstract
Hospitals are subject to strict microbial control. Stringent cleaning and confinement measures in hospitals lead to a decrease in microbial diversity, but an increase in resistance genes. Given the rise of antimicrobial resistances and healthcare-associated infections, understanding the hospital microbiome and its resistome is crucial. This study compared the microbiome and resistome at different levels of confinement (CL) within a single hospital. Using amplicon sequencing, shotgun metagenomics, and genome/plasmid reconstruction, we demonstrate that microbial composition differs in a stable way between the CLs and that the most restrictive confinement level CL1 had the lowest microbial but the highest functional diversity. This CL also exhibited a greater abundance of functions related to virulence, disease, defense, and stress response. Comparison of antibiotic resistance also showed differences among CLs in terms of the selection process and specific mechanisms for antimicrobial/antibiotic resistance. The resistances found in the samples of CL1 were mostly mediated via antibiotic efflux pumps and were mainly located on chromosomes, whereas in the other, less restrictive CL antibiotic resistances were more present on plasmids. This could be of particular importance for patient-related areas (CL2), as the potential spread of antibiotic resistances could be a major concern in this area. Our results show that there are differences in the microbiome and resistome even within a single hospital, reflecting room utilization and confinement. Since restrictive confinement selects for resistant microorganisms, strategies are required to deepen our understanding of dynamic processes of microbiome and resistome within hospital environments. IMPORTANCE Effective measures to combat antibiotic resistances and healthcare-associated infections are urgently needed, including optimization of microbial control. However, previous studies have indicated that stringent control can lead to an increase in the resistance capacities of microbiomes on surfaces. This study adds to previous knowledge by focusing on the conditions in a single hospital, resolving the microbiomes and their resistomes in three different confinement levels (CL): operating room, patient-related areas, and non-patient-related areas. We were able to identify stable key taxa; profiled the capacities of taxa, functions, and antimicrobial resistances (AMR); and reconstruct genomes and plasmids in each CL. Our results show that the most restrictive CL indeed had the highest functional diversity, but that resistances were mostly encoded on chromosomes, indicating a lower possibility of resistance spread. However, clever strategies are still required to strike a balance between microbial control and selective pressures in environments where patients need protection.
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Affiliation(s)
- Stefanie Duller
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christina Kumpitsch
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Lisa Wink
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Kaisa Koskinen Mora
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Alexander Mahnert
- D&R Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
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18
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Akinduti PA, Motayo BO, Maged EA, Isibor PO. Pathogenomic profile and clonal diversity of potential zoonotic MRSA-CC7-ST789-t091-SCCmecV from human skin and soft tissue infections. Sci Rep 2024; 14:19326. [PMID: 39164371 PMCID: PMC11335753 DOI: 10.1038/s41598-024-67388-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 07/10/2024] [Indexed: 08/22/2024] Open
Abstract
The whole genome sequence (WGS) of prevalent MRSA strains harboring mecA gene obtained from skin and soft tissue infections (SSTIs) in Nigerian hospitals were profiled for pathogenomic structure and evaluated for clonal diversity. The two MRSA strains identified among 66 isolated multi-drug resistant S. aureus from a collection of 256 clinical samples were phenotyped for antibiotic resistance and genotyped for mecA, SCCmec, and spa types. The mecA positive MRSA was analysed using whole-genome sequencing for resistomes, virulomes, phylogenomic profiles and clonal diversity. The identified MRSA-CC7-ST789-t091-SCCmecV strains from a female child (aged 1 year) with severe otorrhea and an adult male (aged 23) with purulent wound abscess showed high-level resistance to streptomycin, vancomycin, kanamycin, sulfamethoxazole and ciprofloxacin. Both strains harbored abundant resistomes, inherent plasmids, chromosomal replicons and typical seven housekeeping genes (arc3, aroE4, glpF1, gmk4, pta4, tpi6, yqiL3). The most abundant putative virulomes were pathogenesis-associated proteins (included hemolysin gamma, leucocidins, proteases, staphylococcal superantigen/enterotoxin-like genes (Set/Ssl), capsule- and biofilm-associated genes, and hyaluronate lyase). Comparative phylogenomic analysis revealed the relatedness of the two clonal strains with prevalent MRSA-CC7 pathotypes observed in Italy (2013 and 2014), Denmark (2014), Thailand (2015 and 2016), USA (2018), and Nigeria (2016 and 2020); and share high genetic similarities with livestock strains from cow milk and cattle. Identified MRSA-CC7-ST789-t091-SCCmecV pathotypes implicated in SSTIs from Nigeria harboring repertoires of antibiotic resistance and virulence genes, and genetic relatedness with livestock strains; show the possibility of gene transfer between animal and human. Adequate hospital MRSA infection control and geno-epidemiological surveillance for animal and human transfer is required.
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Affiliation(s)
- Paul Akinniyi Akinduti
- Microbiology Unit, Department of Biological Sciences, Covenant University, Ota, Nigeria.
| | | | - El-Ashker Maged
- Department of Internal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
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19
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Bolkenov B, Lee KY, Atwill ER, Pitesky M, Rickard M, Hung-Fan M, Shafii M, Lavelle K, Huang A, Sebti J, Tanaka MM, Yang X, Li X. Phenotypic and genotypic characterization of antimicrobial resistance of non-typhoidal Salmonella from retail meat in California. Int J Food Microbiol 2024; 421:110785. [PMID: 38878703 DOI: 10.1016/j.ijfoodmicro.2024.110785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 07/06/2024]
Abstract
Antimicrobial resistance (AMR) is a global emerging problem for food safety and public health. Retail meat is one of the vehicles that may transmit antimicrobial resistant bacteria to humans. Here we assessed the phenotypic and genotypic resistance of non-typhoidal Salmonella from retail meat collected in California in 2019 by the National Antimicrobial Resistance Monitoring System (NARMS) Retail Food Surveillance program. A total of 849 fresh meat samples were collected from randomly selected grocery stores in Northern and Southern California from January to December 2019. The overall prevalence of Salmonella was 15.31 %, with a significantly higher occurrence in Southern (28.38%) than in Northern (5.22 %) California. The prevalence of Salmonella in chicken (24.01 %) was higher (p < 0.001) compared to ground turkey (5.42 %) and pork (3.08 %) samples. No Salmonella were recovered from ground beef samples. The prevalence of Salmonella in meat with reduced antibiotic claim (20.35 %) was higher (p < 0.001) than that with conventional production (11.96 %). Salmonella isolates were classified into 25 serotypes with S. Kentucky (47.73 %), S. typhimurium (11.36 %), and S. Alachua (7.58 %) as predominant serotypes. Thirty-two out of 132 (24.24 %) Salmonella isolates were susceptible to all tested antimicrobial drugs, while 75.76 % were resistant to one or more drugs, 62.88 % to two or more drugs, and 9.85 % to three or more drugs. Antimicrobials that Salmonella exhibited high resistance to were tetracycline (82/132, 62.12 %) and streptomycin (79/132, 59.85 %). No significant difference was observed between reduced antibiotic claim and conventional production in the occurrence of single and multidrug resistance. A total of 23 resistant genes, a D87Y mutation of gyrA, and 23 plasmid replicons were identified from resistant Salmonella isolates. Genotypic and phenotypic results were well correlated with an overall sensitivity of 96.85 %. S. infantis was the most resistant serotype which also harbored the IncFIB (pN55391) plasmid replicon and gyrA (87) mutation. Data from Northern and Southern California in this study helps us to understand the AMR trends in Salmonella from retail meat sold in the highly populous and demographically diverse state of California.
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Affiliation(s)
- Bakytzhan Bolkenov
- Department of Animal Sciences, University of California, Davis, CA 95616, United States
| | - Katie Y Lee
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
| | - Edward R Atwill
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
| | - Maurice Pitesky
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
| | - Maribel Rickard
- Contra Costa Public Health Laboratory, Martinez, CA 94553, United States
| | - Melody Hung-Fan
- Contra Costa Public Health Laboratory, Martinez, CA 94553, United States
| | - Marzieh Shafii
- Contra Costa Public Health Laboratory, Martinez, CA 94553, United States
| | - Kurtis Lavelle
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
| | - Anny Huang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
| | - Jade Sebti
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
| | - Macie M Tanaka
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
| | - Xiang Yang
- Department of Animal Sciences, University of California, Davis, CA 95616, United States.
| | - Xunde Li
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, United States.
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20
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Ikhimiukor OO, Zac Soligno NI, Akintayo IJ, Marcovici MM, Souza SSR, Workman A, Martin IW, Andam CP. Clonal background and routes of plasmid transmission underlie antimicrobial resistance features of bloodstream Klebsiella pneumoniae. Nat Commun 2024; 15:6969. [PMID: 39138200 PMCID: PMC11322185 DOI: 10.1038/s41467-024-51374-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Bloodstream infections caused by the opportunistic pathogen Klebsiella pneumoniae are associated with adverse health complications and high mortality rates. Antimicrobial resistance (AMR) limits available treatment options, thus exacerbating its public health and clinical burden. Here, we aim to elucidate the population structure of K. pneumoniae in bloodstream infections from a single medical center and the drivers that facilitate the dissemination of AMR. Analysis of 136 short-read genome sequences complemented with 12 long-read sequences shows the population consisting of 94 sequence types (STs) and 99 clonal groups, including globally distributed multidrug resistant and hypervirulent clones. In vitro antimicrobial susceptibility testing and in silico identification of AMR determinants reveal high concordance (90.44-100%) for aminoglycosides, beta-lactams, carbapenems, cephalosporins, quinolones, and sulfonamides. IncF plasmids mediate the clonal (within the same lineage) and horizontal (between lineages) transmission of the extended-spectrum beta-lactamase gene blaCTX-M-15. Nearly identical plasmids are recovered from isolates over a span of two years indicating long-term persistence. The genetic determinants for hypervirulence are carried on plasmids exhibiting genomic rearrangement, loss, and/or truncation. Our findings highlight the importance of considering both the genetic background of host strains and the routes of plasmid transmission in understanding the spread of AMR in bloodstream infections.
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Affiliation(s)
- Odion O Ikhimiukor
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA.
| | - Nicole I Zac Soligno
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Ifeoluwa J Akintayo
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Michael M Marcovici
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Stephanie S R Souza
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Adrienne Workman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Isabella W Martin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Cheryl P Andam
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA.
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21
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Siderius NL, Sapula SA, Hart BJ, Hutchings JL, Venter H. Enterobacter adelaidei sp. nov. Isolation of an extensively drug resistant strain from hospital wastewater in Australia and the global distribution of the species. Microbiol Res 2024; 288:127867. [PMID: 39163716 DOI: 10.1016/j.micres.2024.127867] [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: 05/16/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 08/22/2024]
Abstract
BACKGROUND Enterobacter species are included among the normal human gut microflora and persist in a diverse range of other environmental niches. They have become important opportunistic nosocomial pathogens known to harbour plasmid-mediated multi-class antimicrobial resistance (AMR) determinants. Global AMR surveillance of Enterobacterales isolates shows the genus is second to Klebsiella in terms of frequency of carbapenem resistance. Enterobacter taxonomy is confusing and standard species identification methods are largely inaccurate or insufficient. There are currently 27 named species and a total of 46 taxa in the genus distinguishable via average nucleotide identity (ANI) calculation between pairs of genomic sequences. Here we describe an Enterobacter strain, ECC3473, isolated from the wastewater of an Australian hospital whose species could not be determined by standard methods nor by ribosomal RNA gene multi-locus typing. AIM To characterise ECC3473 in terms of phenotypic and genotypic antimicrobial resistance, biochemical characteristics and taxonomy as well as to determine the global distribution of the novel species to which it belongs. METHODS Standard broth dilution and disk diffusion were used to determine phenotypic AMR. The strain's complete genome, including plasmids, was obtained following long- and short read sequencing and a novel long/short read hybrid assembly and polishing, and the genomic basis of AMR was determined. Phylogenomic analysis and quantitative measures of relatedness (ANI, digital DNA-DNA hybridisation, and difference in G+C content) were used to study the taxonomic relationship between ECC3473 and Enterobacter type-strains. NCBI and PubMLST databases and the literature were searched for additional members of the novel species to determine its global distribution. RESULTS ECC3473 is one of 21 strains isolated globally belonging to a novel Enterobacter species for which the name, Enterobacter adelaidei sp. nov. is proposed. The novel species was found to be resilient in its capacity to persist in contaminated water and adaptable in its ability to accumulate multiple transmissible AMR determinants. CONCLUSION E. adelaidei sp. nov. may become increasingly important to the dissemination of AMR.
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Affiliation(s)
- Naomi L Siderius
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Sylvia A Sapula
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Bradley J Hart
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Joshua L Hutchings
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
| | - Henrietta Venter
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia.
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22
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Jia X, Zhu Y, Jia P, Li C, Chu X, Sun T, Liu X, Yu W, Chen F, Xu Y, Yang Q. The key role of iroBCDN-lacking pLVPK-like plasmid in the evolution of the most prevalent hypervirulent carbapenem-resistant ST11-KL64 Klebsiella pneumoniae in China. Drug Resist Updat 2024; 77:101137. [PMID: 39178714 DOI: 10.1016/j.drup.2024.101137] [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: 03/20/2024] [Revised: 07/31/2024] [Accepted: 08/11/2024] [Indexed: 08/26/2024]
Abstract
AIMS Hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP), coharboring hypervirulence and carbapenem-resistance genes mediated by plasmids, causes infections with extremely high mortality and seriously impacts public health. Exploring the transfer mechanisms of virulence/carbapenem-resistance plasmids, as well as the formation and evolution pathway of hv-CRKP is of great significance to the control of hv-CRKP infections. METHODS In this study, we identified the predominant clone of hv-CRKP in China and elucidated its genomic characteristics and formation route based on 239 multicenter clinical K. pneumoniae isolates and 1014 GenBank genomes by using comparative genomic analysis. Further, we revealed the factors affecting the transfer of virulence plasmids, and explained the genetic foundation for the prevalence of Chinese predominant hv-CRKP clone. RESULTS ST11-KL64 is the predominant clone of hv-CRKP in China and primarily evolved from ST11-KL64 CRKP by acquiring the pLVPK-like virulence plasmid from hvKP. Significantly, the virulence gene cluster iroBCDN was lost in the virulence plasmid of ST11-KL64 hv-CRKP but existed in that of hvKP. Moreover, the absence of iroBCDN didn't decrease the virulence of hv-CRKP, which was proved by bacterial test, cell-interaction test and mice infection model. On the contrary, loss of iroBCDN was observed to regulate virulence/carbapenem-resistance plasmid transfer and oxidative stress-related genes in strains and thus promoted the mobilization of nonconjugative virulence plasmid from hvKP into ST11-KL64 CRKP, forming hv-CRKP which finally had elevated antioxidant capacity and enhanced survival capacity in macrophages. The loss of iroBCDN increased the survival ability of hv-CRKP without decreasing its virulence, endowing it with an evolutionary advantage. CONCLUSIONS Our work provides new insights into the key role of iroBCDN loss in convergence of CRKP and hvKP, and the genetic and biological foundation for the widespread prevalence of ST11-KL64 hv-CRKP in China.
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Affiliation(s)
- Xinmiao Jia
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Center for bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Zhu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Peiyao Jia
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cuidan Li
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiaobing Chu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Tianshu Sun
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Clinical Biobank, Center for Biomedical Technology, National Science and Technology Key Infrastructure on Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyu Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Yu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Chen
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China.
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Geofrey MA, Sauli E, Kanje LE, Beti M, Shayo MJ, Kuchaka D, van Zwetselaar M, Wadugu B, Mmbaga B, Mkumbaye SI, Kumburu H, Sonda T. Genomic characterization of methicillin-resistant Staphylococcus aureus isolated from patients attending regional referral hospitals in Tanzania. BMC Med Genomics 2024; 17:211. [PMID: 39143496 PMCID: PMC11323609 DOI: 10.1186/s12920-024-01979-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 08/01/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) colonization increases the risk of subsequent infection by MRSA strain complex interlinking between hospital and community-acquired MRSA which increases the chance of drug resistance and severity of the disease. OBJECTIVE Genomic characterization of Staphylococcus aures strains isolated from patients attending regional referral hospitals in Tanzania. METHODOLOGY A laboratory-based cross-sectional study using short read-based sequencing technology, (Nextseq550,Illumina, Inc. San diego, California, USA). The samples used were collected from patients attending selected regional referral hospitals in Tanzania under the SeqAfrica project. Sequences were analyzed using tools available in the center for genomic and epidemiology server, and visualization of the phylogenetic tree was performed in ITOL 6.0. SPSS 28.0 was used for statistical analysis. RESULTS Among 103 sequences of S. aureus, 48.5% (50/103) carry the mecA gene for MRSA. High proportions of MRSA were observed among participants aged between 18 and 34 years (52.4%), in females (54.3%), and among outpatients (60.5%). The majority of observed MRSA carried plasmids rep5a (92.0%), rep16 (90.0%), rep7c (90.0%), rep15 (82.0%), rep19 (80.0%) and rep10 (72.0%). Among all plasmids observed rep5a, rep16, rep20, and repUS70 carried the blaZ gene, rep10 carried the erm(C) gene and rep7a carried the tet(K) gene. MLST and phylogeny analysis reveal high diversity among MRSA. Six different clones were observed circulating at selected regional hospitals and MRSA with ST8 was dominant. CONCLUSION The study reveals a significant presence of MRSA in Staphylococcus aureus strains from Tanzanian regional hospitals, with nearly half carrying the mecA gene. MRSA is notably prevalent among young adults, females, and outpatients, showing high genetic diversity and dominance of ST8. Various plasmids carrying resistance genes indicate a complex resistance profile, highlighting the need for targeted interventions to manage MRSA infections in Tanzania.
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Affiliation(s)
- Mujungu A Geofrey
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania.
- Catholic University of Health and Allied Sciences, Mwanza, Tanzania.
| | - Elingarami Sauli
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Livin E Kanje
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Melkiory Beti
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Mariana J Shayo
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Department of Biological and Pre-Clinical Studies, Muhimbili University, Dar es salaam, Tanzania
| | - Davis Kuchaka
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | | | - Boaz Wadugu
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Blandina Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Department of Clinical Laboratory, Kilimanjaro Christian Medical Centre, Kilimanjaro, Tanzania
| | - Sixbert Isdory Mkumbaye
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Department of Clinical Laboratory, Kilimanjaro Christian Medical Centre, Kilimanjaro, Tanzania
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Department of Clinical Laboratory, Kilimanjaro Christian Medical Centre, Kilimanjaro, Tanzania
| | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Department of Clinical Laboratory, Kilimanjaro Christian Medical Centre, Kilimanjaro, Tanzania
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Solis Cayo L, Hammerbauerová I, Sommer J, Nemati Z, Ballhorn W, Tsukayama P, Dichter A, Votýpka J, Kempf VAJ. Genome sequences of three Bartonella schoenbuchensis strains from Czechia. Microbiol Resour Announc 2024; 13:e0039724. [PMID: 38953338 PMCID: PMC11320913 DOI: 10.1128/mra.00397-24] [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: 04/17/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
Bartonella schoenbuchensis causes bacteremia in ruminants and is transmitted by deer keds. Here, we report the complete genome sequences of three B. schoenbuchensis strains (L2, L19, and L24) recently isolated from deer keds (Lipoptena fortisetosa) in Czechia.
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Affiliation(s)
- Luis Solis Cayo
- Laboratorio de Microbiología Molecular y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Laboratorio de Genómica Microbiana, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical “Alexander von Humboldt,” Universidad Peruana Cayetano Heredia, Lima, Peru
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Iva Hammerbauerová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czechia
| | - Julian Sommer
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Zahra Nemati
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Wibke Ballhorn
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Pablo Tsukayama
- Laboratorio de Genómica Microbiana, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alexander Dichter
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Jan Votýpka
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czechia
| | - Volkhard A. J. Kempf
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
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Akinyemi MO, Oyedele OA, Kleyn MS, Onarinde BA, Adeleke RA, Ezekiel CN. Draft genome sequences of Weissella cibaria GM93m3, a promising probiotic strain from raw goat milk. Microbiol Resour Announc 2024; 13:e0027024. [PMID: 38958438 PMCID: PMC11320988 DOI: 10.1128/mra.00270-24] [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: 03/18/2024] [Accepted: 04/28/2024] [Indexed: 07/04/2024] Open
Abstract
The draft genome of a previously documented potential probiotic Weissella cibaria strain GM93m3 from raw goat milk in Nigeria is reported. The total genome size was 2,447,229 with 46 contigs and G+C content of 44.86%.
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Affiliation(s)
- Muiz O. Akinyemi
- National Centre for Food Manufacturing, University of Lincoln, Lincoln, United Kingdom
- Unit for Environmental Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | | | - Mariska S. Kleyn
- Unit for Environmental Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Bukola A. Onarinde
- National Centre for Food Manufacturing, University of Lincoln, Lincoln, United Kingdom
| | - Rasheed A. Adeleke
- Unit for Environmental Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Chibundu N. Ezekiel
- Department of Microbiology, Babcock University, Ilishan Remo, Ogun State, Nigeria
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, BOKU University, Vienna, Austria
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Zhang XW, Song JJ, Zeng SH, Huang YL, Luo JJ, Guo WL, Li XY. Plasmid-mediated azithromycin resistance in non-typhoidal Salmonella recovered from human infections. J Antimicrob Chemother 2024:dkae281. [PMID: 39119898 DOI: 10.1093/jac/dkae281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
OBJECTIVES Mechanisms of non-typhoidal Salmonella (NTS) resistance to azithromycin have rarely been reported. Here we investigate the epidemiology and genetic features of 10 azithromycin-resistant NTS isolates. METHODS A total of 457 NTS isolates were collected from a tertiary hospital in Guangzhou. We performed antimicrobial susceptibility tests, conjugation experiments, efflux pump expression tests, whole-genome sequencing and bioinformatics analysis to conduct the study. RESULTS The results showed that 10 NTS isolates (2.8%) were resistant to azithromycin with minimum inhibitory concentration values ranging from 128 to 512 mg/L and exhibited multidrug resistance. The phylogenetic tree revealed that 5 S. London isolates (AR1-AR5) recognized at different times and departments were closely related [3-74 single-nucleotide polymorphisms (SNPs)] and 2 S. Typhimurium isolates (AR7 and AR8) were clones (<3 SNPs) at 3-month intervals. The azithromycin resistance was conferred by mph(A) gene found on different plasmids, including IncFIB, IncHI2, InFII, IncC and IncI plasmids. Among them, IncFIB, InFII and IncHI2 plasmids carried different IS26-class 1 integron (intI1) arrangement patterns that mediated multidrug resistance transmission. Conjugative IncC plasmid encoded resistance to ciprofloxacin, ceftriaxone and azithromycin. Furthermore, phylogenetic analysis demonstrated that mph(A)-positive plasmids closely related to 10 plasmids in this study were mainly discovered from NTS, Escherichia coli, Klebsiella pneumonia and Enterobacter hormaechei. The genetic environment of mph(A) in 10 NTS isolates was IS26-mph(A)-mrx(A)-mphR(A)-IS6100/IS26 that co-arranged with intI1 harbour multidrug-resistant (MDR) gene cassettes on diverse plasmids. CONCLUSIONS These findings highlighted that the dissemination of these plasmids carrying mph(A) and various intI1 MDR gene cassettes would seriously restrict the availability of essential antimicrobial agents for treating NTS infections.
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Affiliation(s)
- Xi-Wei Zhang
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Jing-Jie Song
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Shi-Han Zeng
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Yu-Lan Huang
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Jia-Jun Luo
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Wei-Long Guo
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Xiao-Yan Li
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), No. 1 Jiazi Road, Lunjiao, Shunde District, Foshan City, Guangdong Province, China
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Haeberle AL, Greenwood-Quaintance KE, Zar S, Johnson S, Patel R, Willett JLE. Genotypic and phenotypic characterization of Enterococcus faecalis isolates from periprosthetic joint infections. Microbiol Spectr 2024; 12:e0056524. [PMID: 38912797 PMCID: PMC11302728 DOI: 10.1128/spectrum.00565-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/25/2024] Open
Abstract
Over 2.5 million prosthetic joint implantation surgeries occur annually in the United States. Periprosthetic joint infections (PJIs), though occurring in only 1-2% of patients receiving replacement joints, are challenging to diagnose and treat and are associated with significant morbidity. The Gram-positive bacterium Enterococcus faecalis, which can be highly antibiotic-resistant and is a robust biofilm producer on indwelling medical devices, accounts for 2-11% of PJIs. E. faecalis PJIs are understudied compared to those caused by other pathogens, such as Staphylococcus aureus. This motivates the need to generate a comprehensive understanding of E. faecalis PJIs to guide future treatments for these infections. To address this, we describe a panel of E. faecalis strains isolated from the surface of prosthetic joints in a cohort of individuals treated at the Mayo Clinic in Rochester, MN. Here, we present the first complete genome assemblage of E. faecalis PJI isolates. Comparative genomics shows differences in genome size, virulence factors, antimicrobial resistance genes, plasmids, and prophages, underscoring the genetic diversity of these strains. These isolates have strain-specific differences in in vitro biofilm biomass, biofilm burden, and biofilm morphology. We measured robust changes in biofilm architecture and aggregation for all isolates when grown in simulated synovial fluid (SSF). Finally, we evaluated the antibiotic efficacy of these isolates and found strain-specific changes across all strains when grown in SSF. Results of this study highlight the existence of genetic and phenotypic heterogeneity among E. faecalis PJI isolates which will provide valuable insight and resources for future E. faecalis PJI research. IMPORTANCE Periprosthetic joint infections (PJIs) affect ~1-2% of those who undergo joint replacement surgery. Enterococcus faecalis is a Gram-positive opportunistic pathogen that causes ~10% of PJIs in the United States each year, but our understanding of how and why E. faecalis causes PJIs is limited. E. faecalis infections are typically biofilm-associated and can be difficult to clear with antibiotic therapy. Here, we provide complete genomes for four E. faecalis PJI isolates from the Mayo Clinic. These isolates have strain-specific differences in biofilm formation, aggregation, and antibiotic susceptibility in simulated synovial fluid. These results provide important insight into the genomic and phenotypic features of E. faecalis isolates from PJI.
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Affiliation(s)
- Amanda L. Haeberle
- Department of Microbiology & Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Kerryl E. Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah Zar
- Department of Microbiology & Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Stephen Johnson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Julia L. E. Willett
- Department of Microbiology & Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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Khan MAS, Chaity SC, Hosen MA, Rahman SR. Genomic epidemiology of multidrug-resistant clinical Acinetobacter baumannii in Bangladesh. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105656. [PMID: 39116952 DOI: 10.1016/j.meegid.2024.105656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/04/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
The rising frequency of multidrug-resistant (MDR) Acinetobacter baumannii infections represents a significant public health challenge in Bangladesh. Genomic analysis of bacterial pathogens enhances surveillance and control efforts by providing insights into genetic diversity, antimicrobial resistance (AMR) profiles, and transmission dynamics. In this study, we conducted a comprehensive bioinformatic analysis of 82 whole-genome sequences (WGS) of A. baumannii from Bangladesh to understand their genomic epidemiological characteristics. WGS of the MDR and biofilm-forming A. baumannii strain S1C revealed the presence of 28 AMR genes, predicting its pathogenicity and classification within sequence type ST2. Multi-locus sequence typing (MLST) genotyping suggested heterogeneity in the distribution of clinical A. baumannii strains in Bangladesh, with a predominance of ST575. The resistome diversity was evident from the detection of 82 different AMR genes, with antibiotic inactivation being the most prevalent resistance mechanism. All strains were predicted to be multidrug-resistant. The observed virulence genes were associated with immune evasion, biofilm formation, adherence, nutrient acquisition, effector delivery, and other mechanisms. Mobile genetic elements carrying AMR genes were predicted in 68.29% (N = 56) of the genomes. The "open" state of the pan-genome and a high proportion of accessory genes highlighted the genome plasticity and diversity of A. baumannii in Bangladesh. Additionally, phylogenomic analysis indicated clustering of A. baumannii strains into three separate clades according to sequence type. In summary, our findings offer detailed insights into the genomic landscape of A. baumannii in Bangladesh, contributing to our understanding of its epidemiology and pathogenicity and informing strategies to combat this pathogen.
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Affiliation(s)
| | | | - Md Arman Hosen
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
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Gbégbé DA, Kacou OBC, N'zi NP, Angaman DM. Priestia flexa as a Novel Urinary Tract Pathogen in Daloa, Côte d'Ivoire: Insights From Genomic Sequencing. Int J Genomics 2024; 2024:6239250. [PMID: 39131828 PMCID: PMC11316909 DOI: 10.1155/2024/6239250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/13/2024] [Indexed: 08/13/2024] Open
Abstract
Bacterial strains coded 21LM367, 21LM07, and 21LM1136 were isolated from the urine of patients with urinary tract infections (UTIs) at the Centre Hospitalier Régional de Daloa in Côte d'Ivoire. Based on average nucleotide identity (ANI) analysis, DNA-DNA digital hybridisation (dDDH), and other comparative genomic methods, strains 21LM07, 21LM367, and 21LM1136 were determined to be Priestia flexa. The size of the assembled complete genomes ranged from 8,624,538 to 4,007,501 bp. The average GC content was 37.76%, 46.33%, and 43.03% for strains 21LM07, 21LM367, and 21LM1136, respectively. The total number of coding regions (CDS) in each genome was 4172, 8497, and 6795, respectively, for strains 21LM07, 21LM367, and 21LM1136. Genomic prediction analysis revealed that a total of 4241, 8583, and 6881 genes were annotated in the 21LM07, 21LM367, and 21LM1136 genomes, respectively. No virulence or resistance genes were predicted in the genomes of strains 21LM07 and 21LM1136. On the other hand, two genes conferring resistance to beta-lactam and tetracyclines as well as nine virulence genes were predicted in the genome of 21LM367. In addition, 438, 350, and 153 mobile genetic elements (MGEs) were predicted in the genomes of strains 21LM367, 21LM1136, and 21LM07, respectively. Strain 21LM07 was characterised by the absence of plasmids in its genome. Two plasmids were predicted in the genomes of isolates 21LM367 and 21LM1136; however, rep7a and IncI2 were predicted to contain the tet(K) resistance gene. No typical multilocus sequences could be characterised in the genomes of the different strains.
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Affiliation(s)
- Dého Aristide Gbégbé
- Department of Biochemistry-MicrobiologyJean Lorougnon Guédé University, Daloa, Côte d'Ivoire
| | | | - N'goran Parfait N'zi
- Department of Biochemistry-MicrobiologyJean Lorougnon Guédé University, Daloa, Côte d'Ivoire
- Department of Bacteriology-VirologyNational Reference Center for AntibioticsInstitut Pasteur, Abidjan, Côte d'Ivoire
| | - Djédoux Maxime Angaman
- Department of Biochemistry-MicrobiologyJean Lorougnon Guédé University, Daloa, Côte d'Ivoire
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Mills EG, Smith AB, Griffith MP, Hewlett K, Pless L, Sundermann AJ, Harrison LH, Zackular JP, Van Tyne D. Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.01.24311290. [PMID: 39132485 PMCID: PMC11312660 DOI: 10.1101/2024.08.01.24311290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is a prevalent healthcare-acquired pathogen. Gastrointestinal colonization can lead to difficult-to-treat bloodstream infections with high mortality rates. Prior studies have investigated VREfm population structure within healthcare centers. However, little is known about how and why hospital-adapted VREfm populations change over time. We sequenced 710 healthcare-associated VREfm clinical isolates from 2017-2022 from a large tertiary care center as part of the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT) program. Although the VREfm population in our center was polyclonal, 46% of isolates formed genetically related clusters, suggesting a high transmission rate. We compared our collection to 15,631 publicly available VREfm genomes spanning 20 years. Our findings describe a drastic shift in lineage replacement within nosocomial VREfm populations at both the local and global level. Functional and genomic analysis revealed, antimicrobial peptide, bacteriocin T8 may be a driving feature of strain emergence and persistence in the hospital setting.
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Affiliation(s)
- Emma G. Mills
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alexander B. Smith
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marissa P. Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Katharine Hewlett
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lora Pless
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alexander J. Sundermann
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lee H. Harrison
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph P. Zackular
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Microbial Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Mason LCE, Charles H, Thorley K, Chong CE, De Silva PM, Jenkins C, Baker KS. The re-emergence of sexually transmissible multidrug resistant Shigella flexneri 3a, England, United Kingdom. NPJ ANTIMICROBIALS AND RESISTANCE 2024; 2:20. [PMID: 39100870 PMCID: PMC11296952 DOI: 10.1038/s44259-024-00038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/30/2024] [Indexed: 08/06/2024]
Abstract
Shigellosis is an enteric infection that transmits through the faecal-oral route, which can occur during sex between men who have sex with men (MSM). Between 2009 and 2014, an epidemic of sexually transmissible Shigella flexneri 3a occurred in England that subsequently declined. However, from 2019 to 2021, despite SARS-CoV-2 restrictions, S. flexneri 3a continued to re-emerge. We explored possible drivers of re-emergence by comparing host demography and pathogen genomics. Cases were primarily among 35-64 year old men in London. Genomic analyses of 502 bacterial isolates showed that the majority (58%) of re-emerging MSM strains were a clonal replacement of the original, with reduced antimicrobial resistance, conservation of plasmid col156_1, and two SNPs with 19 predicted effects. The absence of major changes in the pathogen or host demographics suggest that other factors may have driven the re-emergence of S. flexneri 3a and highlight the need for further work in the area.
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Affiliation(s)
- Lewis C. E. Mason
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | | | | | - Charlotte E. Chong
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - P. Malaka De Silva
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Claire Jenkins
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
- UK Health Security Agency (UKHSA), London, UK
| | - Kate S. Baker
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
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Wang S, Ma S, Sun S, Wang Q, Ding Q, Jin L, Chen F, Yin G, Wu X, Wang R, Wang H. Global evolutionary dynamics of virulence genes in ST11-KL47 carbapenem-resistant Klebsiella pneumoniae. Int J Antimicrob Agents 2024; 64:107245. [PMID: 38906484 DOI: 10.1016/j.ijantimicag.2024.107245] [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: 11/23/2023] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024]
Abstract
ST11-KL47 is a hypervirulent carbapenem-resistant Klebsiella pneumoniae (CRKP) that is highly prevalent in China and poses a major public health risk. To investigate the evolutionary dynamics of virulence genes in this subclone, we analysed 78 sequenced isolates obtained from a long-term study across 29 centres from 17 cities in China. Virulence genes were located in large hybrid pNDM-Mar-like plasmids (length: ∼266 kilobases) rather than in classical pK2044-like plasmids. These hybrid plasmids, derived from the fusion of pK2044 and pNDM-Mar plasmids mediated by insertion sequence (IS) elements (such as ISKpn28 and IS26), integrated virulence gene fragments into the chromosome. Analysis of 217 sequences containing the special IncFIB (pNDM-Mar) replicon using public databases indicated that these plasmids typically contained T4SS-related and multiple antimicrobial resistance genes, were present in 24 countries, and were found in humans, animals, and the environment. Notably, the chromosomal integration of virulence genes was observed in strains across five countries across two continents. In vivo and in vitro models showed that the large hybrid plasmid increased the host fitness cost while increasing virulence. Conversely, virulence genes transferred to chromosomes resulted in increased fitness and lower virulence. In conclusion, virulence genes in the plasmids of ST11-KL47 CRKP are evolving, driven by adaptive negative selection, to enable vertical chromosomal inheritance along with conferring a survival advantage and low pathogenicity.
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Affiliation(s)
- Shuyi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Shuai Ma
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Shijun Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Qi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Qi Ding
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Longyang Jin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Fengning Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Guankun Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Xingyu Wu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China.
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Parzygnat JL, Dunn RR, Koci MD, Crespo R, Harden L, Thakur S. Fluoroquinolone-resistant Campylobacter in backyard and commercial broiler production systems in the United States. JAC Antimicrob Resist 2024; 6:dlae102. [PMID: 38974944 PMCID: PMC11227224 DOI: 10.1093/jacamr/dlae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/13/2024] [Indexed: 07/09/2024] Open
Abstract
Objectives Campylobacter spp. are one of the leading foodborne pathogens in the world, and chickens are a known reservoir. This is significant considering broiler chicken is the top consumed meat worldwide. In the USA, backyard poultry production is increasing, but little research has been done to investigate prevalence and antimicrobial resistance associated with Campylobacter in these environments. Methods Our study encompasses a farm-to-genome approach to identify Campylobacter and investigate its antimicrobial resistance phenotypically and genotypically. We travelled to 10 backyard and 10 integrated commercial broiler farms to follow a flock throughout production. We sampled at days 10, 31 and 52 for backyard and 10, 24 and 38 for commercial farms. Bird faecal (n = 10) and various environmental samples (soil n = 5, litter/compost n = 5, and feeder and waterer swabs n = 6) were collected at each visit and processed for Campylobacter. Results Our results show a higher prevalence of Campylobacter in samples from backyard farms (21.9%) compared to commercial (12.2%). Most of our isolates were identified as C. jejuni (70.8%) and the remainder as C. coli (29.2%). Antimicrobial susceptibility testing reveals phenotypic resistance to ciprofloxacin (40.2%), an important treatment drug for Campylobacter infection, and tetracycline (46.6%). A higher proportion of resistance was found in C. jejuni isolates and commercial farms. Whole-genome sequencing revealed resistance genes, such as tet(O) and gyrA_T86I point mutation, that may confer resistance. Conclusion Overall, our research emphasizes the need for interventions to curb prevalence of resistant Campylobacter spp. on broiler production systems.
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Affiliation(s)
- Jessica L Parzygnat
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Matthew D Koci
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Rocio Crespo
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Lyndy Harden
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
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Megur A, Lastauskienė E, Burokas A. Draft genome sequence data of Lactiplantibacillus plantarum 33C isolated from Lithuanian fermented food. Data Brief 2024; 55:110750. [PMID: 39100785 PMCID: PMC11295458 DOI: 10.1016/j.dib.2024.110750] [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: 04/26/2024] [Revised: 06/13/2024] [Accepted: 07/09/2024] [Indexed: 08/06/2024] Open
Abstract
This strain was isolated from traditionally (homemade) fermented Lithuanian cherry tomatoes. The genome consists of 55 contigs with a total size of 3,326,119 bp, an N50 of 170738, and a GC% of 44.3 %. According to the COG annotation, most of these proteins were divided into three categories related to transcription (K category: 307), amino acid transport and metabolism (E category: 222), and carbohydrate transport and metabolism (G category: 268). No genes associated with antimicrobial resistance or virulence factors were identified. The data presented here can be used in comparative genomics to identify antimicrobial resistance genes and virulence factors that may be present in relevant Lactobacillus species. PlasmidFinder server revealed the presence of plasmid pR18 (assessment number JN601038) in the genome that has lincomycin resistance, can be transferred from one bacterium to another, and is one of the most common plasmids in the genera Bacillus and Lactobacillus. The draft genome sequence data have been deposited with NCBI under Bioproject under accession number PRJNA947394.
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Affiliation(s)
- Ashwinipriyadarshini Megur
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, LT, Vilnius 10257, Lithuania
| | - Eglė Lastauskienė
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, LT, Vilnius 10257, Lithuania
| | - Aurelijus Burokas
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, LT, Vilnius 10257, Lithuania
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Ma L, Xie M, Yang Y, Ding X, Li Y, Yan Z, Chan EWC, Chen S, Chen G, Zhang R. Prevalence and genomic characterization of clinical Escherichia coli strains that harbor the plasmid-borne tet(X4) gene in China. Microbiol Res 2024; 285:127730. [PMID: 38805981 DOI: 10.1016/j.micres.2024.127730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/30/2024]
Abstract
The tigecycline resistance gene tet(X4) has been widely reported in animals and animal products in some Asian countries including China in recent years but only sporadically detected in human. In this study, we investigated the prevalence and genetic features of tet(X4)-positive clinical E. coli strains. A total of 462 fecal samples were collected from patients in four hospitals located in four provinces in China in 2023. Nine tet(X4)-positive E. coli strains were isolated and subjected to characterization of their genetic and phenotypic features by performing antimicrobial susceptibility test, whole-genome sequencing, bioinformatic and phylogenetic analysis. The majority of the test strains were found to exhibit resistance to multiple antimicrobial agents including tigecycline but remained susceptible to colistin and meropenem. A total of seven different sequence types (STs) and an unknown ST type were identified among the nine tet(X4)-positive strains. Notably, the tet(X4) gene in six out of these nine tet(X4)-positive E. coli strains was located in a IncFIA-HI1A-HI1B hybrid plasmid, which was an tet(X4)-bearing epidemic plasmid responsible for dissemination of the tet(X4) gene in China. Furthermore, the tet(X4) gene in four out of nine tet(X4)-positive E. coli isolates could be successfully transferred to E. coli EC600 through conjugation. In conclusion, this study characterized the epidemic tet(X4)-bearing plasmids and tet(X4)-associated genetic environment in clinical E. coli strains, suggested the importance of continuous surveillance of such tet(X4)-bearing plasmids to control the increasingly widespread dissemination of tigecycline-resistant pathogens in clinical settings in China.
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Affiliation(s)
- Lan Ma
- Department of Clinical Laboratory, Second Hospital of Lanzhou University, Lanzhou, People's Republic of China
| | - Miaomiao Xie
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Yongxin Yang
- Department of Clinical Laboratory, Second Hospital of Lanzhou University, Lanzhou, People's Republic of China
| | - Xinying Ding
- Department of Clinical Laboratory, Zibo First Hospital, Zibo, People's Republic of China
| | - Yuanyuan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People's Republic of China
| | - Zelin Yan
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, Hangzhou, People's Republic of China
| | - Edward Wai-Chi Chan
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Sheng Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region.
| | - Gongxiang Chen
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, Hangzhou, People's Republic of China
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, Hangzhou, People's Republic of China.
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Tang C, Shen S, Yang W, Shi Q, Ding L, Han R, Hu F. Dynamic evolution of ceftazidime-avibactam resistance from a single patient through the IncX3_NDM-5 plasmid transfer and bla KPC mutation. Int J Antimicrob Agents 2024; 64:107228. [PMID: 38823494 DOI: 10.1016/j.ijantimicag.2024.107228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/22/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024]
Abstract
The rapid dissemination of carbapenem-resistant Enterobacterales (CRE) especially carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a great threat to global public health. Ceftazidime-avibactam, a novel β-lactam/β-lactamase inhibitor combination, has been widely used due to its excellent antibacterial activity against KPC-producing K. pneumoniae. However, several resistance mechanisms have been reported since its use. Here, we conducted a series of in vitro experiments to reveal and demonstrate the dynamic evolution of ceftazidime-avibactam resistance including interspecies IncX3_NDM-5 plasmid transfer between Enterobacter cloacae and K. pneumoniae and blaKPC mutation from blaKPC-2 to blaKPC-33. Through the analysis of conjugation frequency and fitness cost, the IncX3_NDM-5 plasmid in this study showed strong transmissibility and stability in E. coli EC600 and clinical strain K. pneumoniae 5298 as recipient strain. With increasing ceftazidime-avibactam concentration, the conjugation frequency remained at 10-3-10-5, while the mutation frequency of K. pneumoniae 5298 was 10-6-10-8 at the same concentration. Further plasmid analysis (the IncX3_NDM plasmid from this study and other 658 plasmids from the NCBI database) revealed the diverse origin and genetic structure of blaNDM-5 carrying plasmids. E. coli (42.9%), China (43.9%), IncX3 (66.6%) are the most common strains, regions, and Inc types respectively. By analysing of genetic environment detected in IncX3 plasmids, the dominant structures (168/258, 65.1%) were identified: ISKox3-IS26-blaNDM-5-IS5-ISAba125-Tn3000-Tn3. In additon, several structural variations were found in the core gene structure. In conclusion, the high fitness and transmissibility of the IncX3_NDM-5 plasmids were noteworthy. More importantly, the diverse ceftazidime-avibactam resistance mechanisms including blaNDM-5 tranfer and blaKPC-2 mutation highlighted the importance of the continuous monitoring of antimicrobial susceptibility and carbapenemases subtype during ceftazidime-avibactam treatment.
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Affiliation(s)
- Chengkang Tang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Siquan Shen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Weiwei Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Qingyu Shi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Li Ding
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Renru Han
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China.
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Zhuang M, Yan W, Xiong Y, Wu Z, Cao Y, Sanganyado E, Siame BA, Chen L, Kashi Y, Leung KY. Horizontal plasmid transfer promotes antibiotic resistance in selected bacteria in Chinese frog farms. ENVIRONMENT INTERNATIONAL 2024; 190:108905. [PMID: 39089095 DOI: 10.1016/j.envint.2024.108905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/02/2024] [Accepted: 07/21/2024] [Indexed: 08/03/2024]
Abstract
The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem.
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Affiliation(s)
- Mei Zhuang
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel; Department of Biotechnology and Food Engineering Program, Guangdong Technion-Israel Institute of Technology, Shantou 515063, China
| | - Waner Yan
- Department of Microbiology and Molecular Genetics, The Hebrew University of Jerusalem, POB 12272, Jerusalem 91120, Israel
| | - Yifei Xiong
- Department of Microbiology and Molecular Genetics, The Hebrew University of Jerusalem, POB 12272, Jerusalem 91120, Israel
| | - Zhilin Wu
- Department of Microbiology and Molecular Genetics, The Hebrew University of Jerusalem, POB 12272, Jerusalem 91120, Israel
| | - Yuping Cao
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel; Department of Biotechnology and Food Engineering Program, Guangdong Technion-Israel Institute of Technology, Shantou 515063, China
| | - Edmond Sanganyado
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, UK
| | - Bupe A Siame
- Department of Biology, Trinity Western University, Langley, British Columbia V2Y 1Y1, Canada
| | - Liang Chen
- Department of Computer Science, College of Mathematics and Computer, Shantou University, Shantou 515063, China.
| | - Yechezkel Kashi
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ka Yin Leung
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel; Department of Biotechnology and Food Engineering Program, Guangdong Technion-Israel Institute of Technology, Shantou 515063, China.
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Li R, Zhang N, Deng X, Tao C, Pei X, Yue Y, Xu X, Wang J, Shen Z, Shen Q, Li R. Tomato bacterial wilt disease outbreaks are accompanied by an increase in soil antibiotic resistance. ENVIRONMENT INTERNATIONAL 2024; 190:108896. [PMID: 39068748 DOI: 10.1016/j.envint.2024.108896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/18/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]
Abstract
The presence of soil-borne disease obstacles and antibiotic resistance genes (ARGs) in soil leads to serious economic losses and health risks to humans. One area in need of attention is the evolution of ARGs as pathogenic soil gradually develops, which introduces uncertainty to the dynamic ability of conventional farming models to predict ARGs. Here, we investigated variations in tomato bacterial wilt disease accompanied by the resistome by metagenomic analysis in soils over 13 seasons of monoculture. The results showed that the abundance and diversity of ARGs and mobile genetic elements (MGEs) exhibited a significant and positive correlation with R. solanacearum. Furthermore, the binning approach indicated that fluoroquinolone (qepA), tetracycline (tetA), multidrug resistance genes (MDR, mdtA, acrB, mexB, mexE), and β-lactamases (ampC, blaGOB) carried by the pathogen itself were responsible for the increase in overall soil ARGs. The relationships between pathogens and related ARGs that might underlie the breakdown of soil ARGs were further studied in R. solanacearum invasion pot experiments. This study revealed the dynamics of soil ARGs as soil-borne diseases develop, indicating that these ecological trends can be anticipated. Overall, this study enhances our understanding of the factors driving ARGs in disease-causing soils.
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Affiliation(s)
- Ruochen Li
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Na Zhang
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Xuhui Deng
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Chengyuan Tao
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Xin Pei
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Yang Yue
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Xu Xu
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Jiabao Wang
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Zongzhuan Shen
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China.
| | - Qirong Shen
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Rong Li
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China.
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Abdelhamed H, Mannan SB, Riman MM, Tekedar HC, Lawrence ML. Comparative analysis of three plasmids from Plesiomonas shigelloides strain MS-17-188 and their role in antimicrobial resistance. JAC Antimicrob Resist 2024; 6:dlae109. [PMID: 39035015 PMCID: PMC11258559 DOI: 10.1093/jacamr/dlae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024] Open
Abstract
Background Plesiomonas shigelloides strain MS-17-188 was isolated from a deceased catfish from East Mississippi and showed resistance to florfenicol, tetracyclines and a sulphonamide. WGS of strain MS-17-188 revealed three plasmids (pPSMS-171881, pPSMS-171882 and pPSMS-171883). Objectives To accurately determine the impact of three plasmids found in P. shigelloides strain MS-17-188 on the dissemination of antibiotic resistance genes and to provide insights into the molecular structure of these plasmids. Methods The genetic features of these plasmids in terms of genes associated with antimicrobial resistance (AMR), virulence, transfer, maintenance and replication were identified using bioinformatic tools. Additionally, we investigated the in vitro mobilization and stability of plasmid-mediated resistance. The Comprehensive Antibiotic Resistance Database and Virulence Factors Database were used to detect the AMR genes and virulence genes of P. shigelloides plasmids. Moreover, plasmid mobility was evaluated by a filter-mating assay using strain MS-17-188 as a donor and azide-resistant Escherichia coli J53 as a recipient strain. A stability experiment was conducted to explore the persistence of plasmid-mediated antibiotic resistance in strain MS-17-188 in the absence and presence of selection. Results pPSMS-171881 harboured multidrug efflux complex (adeF) and two genes responsible for arsenic resistance (arsB and arsC). pPSMS-171882 had a region of 7085 bp encoding type IV secretion system proteins. pPSMS-171883 carried the tetracycline resistance genes tet(A) and tet(R), and a phenicol resistance gene (floR), which were flanked by two transposable elements and mobilization proteins, suggesting that there is a conjugative mechanism by which this plasmid can be mobilized. Results from the stability experiment indicated that pPSMS-171883 is lost over time in the absence of selective pressure. Moreover, pPSMS-171883 is more stable in P. shigelloides at growth temperatures of 30°C and 37°C compared with 40°C and 43°C. After intraperitoneal injection in catfish, P. shigelloides strain MS-17-188 resulted in no mortalities. Conclusions This is the first study to report plasmid-mediated AMR in Plesiomonas isolated from cultured fish, which needs continued monitoring. This study will provide an understanding of the genetic mechanisms of AMR and virulence of P. shigelloides.
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Affiliation(s)
- Hossam Abdelhamed
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Shahnewaj Bin Mannan
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Munshi Mustafiz Riman
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Hasan C Tekedar
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Mark L Lawrence
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
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Prakash Tamang J, Kharnaior P, Pariyar P. Whole genome sequencing of the poly-γ-glutamic acid-producing novel Bacillus subtilis Tamang strain, isolated from spontaneously fermented kinema. Food Res Int 2024; 190:114655. [PMID: 38945588 DOI: 10.1016/j.foodres.2024.114655] [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: 05/26/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/02/2024]
Abstract
Kinema, a traditional fermented soybean food from the Himalayas, is well-liked for its sticky texture and flavourful umami taste. Among 175 bacterial strains from spontaneously fermented kinema samples, Bacillus subtilis Tamang strain stood out for its high stickiness and viscosity. The strain's Poly-γ-glutamic acid (γ-PGA) contains various groups of glutamic acid and has a molecular weight of 660 kDa. It demonstrates the ability to solubilize iron, preserve ferritin in Caco-2 cells, and exhibit antibacterial properties. The genome of B. subtilis Tamang is devoid of plasmid elements but does feature nine insert elements. Noteworthy is the presence of unique secondary metabolites with potential antimicrobial effects, such as amyloliquecidin GF610, bogorol A, and thermoactinoamide A. A total of 132 carbohydrate-active enzymes (CAZy) were identified, hinting at possible prebiotic characteristics. The genome analysis revealed genes responsible for γ-PGA production via the capBCA complex. Furthermore, genes associated with fibrinolytic activity, taste enhancement, biopeptides, immunomodulators, and vitamins like B12 and K2 were found, along with probiotics and various health benefits. The genetic material for L-asparaginase production, known for its anti-cancer properties, was also detected, as well as CRISPR-Cas systems. The absence of virulence factors and antimicrobial resistance genes confirms the safety of consuming B. subtilis Tamang as a food-grade bacterium.
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Affiliation(s)
- Jyoti Prakash Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, Science Building, Gangtok 737102, Sikkim, India.
| | - Pynhunlang Kharnaior
- Department of Microbiology, School of Life Sciences, Sikkim University, Science Building, Gangtok 737102, Sikkim, India
| | - Priyambada Pariyar
- Department of Microbiology, School of Life Sciences, Sikkim University, Science Building, Gangtok 737102, Sikkim, India
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Findlay J, Poirel L, Cherkaoui A, Schrenzel J, Nordmann P. Characterisation of a novel AmpC beta-lactamase, DHA-33, resistant to inhibition by cloxacillin. Diagn Microbiol Infect Dis 2024; 109:116356. [PMID: 38763036 DOI: 10.1016/j.diagmicrobio.2024.116356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/21/2024]
Abstract
Plasmid-encoded DHA-type AmpCs have been extensively reported in Enterobacterales. The expression of the genes encoding these plasmid-mediated enzymes are inducible and these enzymes are capable of conferring resistance to a wide spectrum of beta-lactams including penicillins and broad-spectrum cephalosporins. The identification of infections caused by AmpC-producing bacteria is a necessity, both for infection control/epidemiology purposes and to inform treatment choices. A common testing method for AmpC production in the clinical laboratory setting is to supplement Mueller-Hinton agar plates used for antibiotic disk diffusion with cloxacillin, a potent inhibitor of AmpC enzymes. Here we describe a novel DHA variant, produced by a clinical Escherichia coli isolate, which is resistant to cloxacillin inhibition.
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Affiliation(s)
- Jacqueline Findlay
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.
| | - Laurent Poirel
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
| | - Abdessalam Cherkaoui
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland; Genomic Research Laboratory, University of Geneva, Geneva, Switzerland
| | - Patrice Nordmann
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
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Naidoo Y, Pierneef RE, Cowan DA, Valverde A. Characterization of the soil resistome and mobilome in Namib Desert soils. Int Microbiol 2024; 27:967-975. [PMID: 37968548 PMCID: PMC11300574 DOI: 10.1007/s10123-023-00454-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.
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Affiliation(s)
- Yashini Naidoo
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria, 0110, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Angel Valverde
- IRNASA-CSIC, Cordel de Merinas, 37008, Salamanca, Spain.
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Nisa TT, Sugawara Y, Hamaguchi S, Takeuchi D, Abe R, Kuroda E, Morita M, Zuo H, Ueda A, Nishi I, Hossain N, Hasan MM, Siddiqee MH, Nakatani D, Nakata K, Akeda Y. Genomic characterization of carbapenemase-producing Enterobacterales from Dhaka food markets unveils the spread of high-risk antimicrobial-resistant clones and plasmids co-carrying bla NDM and mcr-1.1. JAC Antimicrob Resist 2024; 6:dlae124. [PMID: 39119043 PMCID: PMC11306930 DOI: 10.1093/jacamr/dlae124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 07/05/2024] [Indexed: 08/10/2024] Open
Abstract
Background The transmission of carbapenemase-producing Enterobacterales (CPE) in the external environment, especially through food, presents a significant public health risk. Objectives To investigate the prevalence and genetic characteristics of CPE in food markets of Dhaka, Bangladesh, using WGS. Methods CPE isolates were obtained from different food and water samples collected from food markets in the southern part of Dhaka, Bangladesh. The isolates subsequently underwent molecular typing, WGS employing both short- and long-read sequencers, and plasmid analysis. Results This study unveiled an extensive spread of CPE, with no significant difference in contamination rates observed in samples (N = 136), including meat (n = 8), fish (n = 5), vegetables (n = 36) or various food-washed water (n = 65) from markets near hospitals or residential areas. Thirty-eight Enterobacterales from 33 samples carried carbapenemase genes (bla NDM-1, -4, -7, bla KPC-2, bla OXA-181 or bla IMI-1). Among these, the high-risk Escherichia coli ST410 clone was the most prevalent and distributed across various locations. Furthermore, the identification of IncHI2 plasmids co-harbouring resistance genes like bla NDM-5 and mcr-1.1, without discernible epidemiological connections, is a unique finding, suggesting their widespread dissemination. Conclusions The analysis unveils a dynamic landscape of CPE dissemination in food markets, underscored by the proliferation of novel IncHI2 hybrid plasmids carrying both colistin- and carbapenem-resistance genes. This illuminates the ever-evolving landscape of antimicrobial resistance in Dhaka, urging us to confront its emergent challenges.
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Affiliation(s)
- Tania Tabassum Nisa
- Global and Innovative Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yo Sugawara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shigeto Hamaguchi
- Division of Infection Control and Prevention, Osaka University Hospital, Osaka, Japan
- Department of Transformative Analysis for Human Specimen, Graduate School of Medicine, Osaka University, Osaka, Japan
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka, Japan
| | - Dan Takeuchi
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Ryuichiro Abe
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Eisuke Kuroda
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka, Japan
- Department of Transformative Infection Control Development Studies, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hui Zuo
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akiko Ueda
- Laboratory for Clinical Investigation, Osaka University Hospital, Osaka, Japan
| | - Isao Nishi
- Laboratory for Clinical Investigation, Osaka University Hospital, Osaka, Japan
| | - Nowrin Hossain
- Molecular and Environmental Microbiology (MEM) Laboratory, Department of Mathematics and Natural Sciences (MNS), BRAC University, Dhaka, Bangladesh
| | - Md Mahmudul Hasan
- Molecular and Environmental Microbiology (MEM) Laboratory, Department of Mathematics and Natural Sciences (MNS), BRAC University, Dhaka, Bangladesh
| | - Mahbubul H Siddiqee
- Molecular and Environmental Microbiology (MEM) Laboratory, Department of Mathematics and Natural Sciences (MNS), BRAC University, Dhaka, Bangladesh
| | - Daisaku Nakatani
- Global and Innovative Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Ken Nakata
- Global and Innovative Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yukihiro Akeda
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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Zhou H, Lu Z, Liu X, Bie X, Cui X, Wang Z, Sun X, Yang J. Characterization and transmission of plasmid-mediated multidrug resistance in foodborne Vibrio parahaemolyticus. Front Microbiol 2024; 15:1437660. [PMID: 39144225 PMCID: PMC11322368 DOI: 10.3389/fmicb.2024.1437660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/19/2024] [Indexed: 08/16/2024] Open
Abstract
Objectives The purpose of this study was to determine the structural features and transferability of the multidrug-resistance (MDR) plasmid, and resistance phenotypes for the tested antimicrobials in foodborne Vibrio parahaemolyticus. Methods Plasmids were isolated from a V. parahaemolyticus strain of seafood origin, then sequenced using the Illumina NovaSeq 6000 and PacBio Sequel II sequencing platforms to obtain the complete genome data. Characterization of the MDR plasmid pVP52-1, including determination of antimicrobial resistance genes (ARGs), plasmid incompatibility groups, and transferability, was carried out. Results V. parahaemolyticus strain NJIFDCVp52 contained two circular chromosomes and two circular plasmids (pVP52-1 and pVP52-2). Plasmid typing indicated that pVP52-1 belonged to the incompatibility group IncA/C2 and the sequence type pST3. pVP52-1 carried 12 different ARGs, an IS110-composite transposon consisting of aac(6')-Ib-cr, qnrVC1, aac(6')-Ib, dfrA14, and the IS26-mphA-IS6100 unit flanked by inverted sequences of IS5075 and IS4321. pVP52-2 carried no ARGs. A plasmid elimination assay showed that only pVP52-1 and its ARGs were lost, the loss of resistance to several antimicrobials, causing a change from the ampicillin-ampicillin/sulbactam-cefazolin-cefoxitin-ceftazidime-cefotaxime-imipenem-trimethoprim/sulfamethoxazole resistance pattern to the ampicillin resistance pattern. In accordance, a conjugation transfer assay showed that only pVP52-1 and its ARGs were horizontally transferred, leading to increased antimicrobial resistance in Escherichia coli strain EC600, causing a change from the ampicillin-nalidixic acid resistance pattern to the ampicillin-ampicillin/sulbactam-cefazolin-cefoxitin-ceftazidime-cefotaxime-imipenem-nalidixic acid-chloramphenicol-tetracycline-trimethoprim/sulfamethoxazole-azithromycin resistance pattern. Further transferability experiments revealed that pVP52-1 could be transferred to other enterobacterial strains of E. coli and Salmonella. Discussion This study emphasizes the urgent need for continued surveillance of resistance plasmids and changes in antimicrobial resistance profiles among the V. parahaemolyticus population.
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Affiliation(s)
- Haibo Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Detection and Traceability Technology of Foodborne Pathogenic Bacteria for Jiangsu Province Market Regulation, Nanjing Institute for Food and Drug Control, Nanjing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xinmei Liu
- Key Laboratory of Detection and Traceability Technology of Foodborne Pathogenic Bacteria for Jiangsu Province Market Regulation, Nanjing Institute for Food and Drug Control, Nanjing, China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xinping Cui
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zuwei Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaojie Sun
- Key Laboratory of Detection and Traceability Technology of Foodborne Pathogenic Bacteria for Jiangsu Province Market Regulation, Nanjing Institute for Food and Drug Control, Nanjing, China
| | - Jun Yang
- Key Laboratory of Detection and Traceability Technology of Foodborne Pathogenic Bacteria for Jiangsu Province Market Regulation, Nanjing Institute for Food and Drug Control, Nanjing, China
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Reinhardt F, Kaiser A, Prömel S, Stadler PF. Evolution of neuropeptide Y/RFamide-like receptors in nematodes. Heliyon 2024; 10:e34473. [PMID: 39130429 PMCID: PMC11315170 DOI: 10.1016/j.heliyon.2024.e34473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 08/13/2024] Open
Abstract
The Neuropeptide Y/RFamide-like receptors belong to the Rhodopsin-like G protein-coupled receptors G protein-coupled receptors (GPCRs) and are involved in functions such as locomotion, feeding and reproduction. With 41 described receptors they form the best-studied group of neuropeptide GPCRs in Caenorhabditis elegans. In order to understand the expansion of the Neuropeptide Y/RFamide-like receptor family in nematodes, we started from the sequences of selected receptor paralogs in C. elegans as query and surveyed the corresponding orthologous sequences in another 159 representative nematode target genomes. To this end we employed a automated pipeline based on ExonMatchSolver, a tool that solves the paralog-to-contig assignment problem. Utilizing subclass-specific HMMs we were able to detect a total of 1557 Neuropeptide Y/RFamide-like receptor sequences (1100 NPRs, 375 FRPRs and 82 C09F12.3) in the 159 target nematode genomes investigated here. These sequences demonstrate a good conservation of the Neuropeptide Y/RFamide-like receptors across the Nematoda and highlight the diversification of the family in nematode evolution. No other genus shares all Neuropeptide Y/RFamide-like receptors with the genus Caenorhabditis. At the same time, we observe large numbers of clade specific duplications and losses of family members across the phylum Nematoda.
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Affiliation(s)
- Franziska Reinhardt
- Bioinformatics Group, Institute of Computer Science, Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, Leipzig, D-04107, Germany
| | - Anette Kaiser
- Leipzig University, Faculty of Medicine, Department of Anesthesiology and Intensive Care, Liebigstr. 19, Leipzig, D-04103, Germany
- Leipzig University, Faculty of Life Sciences, Institute of Biochemistry, Brüderstraße 34, Leipzig, D-04103, Germany
| | - Simone Prömel
- Heinrich Heine University Düsseldorf, Universitätsstraße 1/ Gebäude 26.24, Düsseldorf, D-40225, Germany
| | - Peter F. Stadler
- Bioinformatics Group, Institute of Computer Science, Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, Leipzig, D-04107, Germany
- Max-Planck-Institute for Mathematics in the Sciences, Inselstrße 22, D-04103 Leipzig, Germany
- Inst. f. Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
- Facultad de Ciencias, Universidad National de Colombia, Sede Bogota, Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
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Aborode AT, Kumar N, Olowosoke CB, Ibisanmi TA, Ayoade I, Umar HI, Jamiu AT, Bolarinwa B, Olapade Z, Idowu AR, Adelakun IO, Onifade IA, Akangbe B, Abacheng M, Ikhimiukor OO, Awaji AA, Adesola RO. Predictive identification and design of potent inhibitors targeting resistance-inducing candidate genes from E. coli whole-genome sequences. FRONTIERS IN BIOINFORMATICS 2024; 4:1411935. [PMID: 39132675 PMCID: PMC11310021 DOI: 10.3389/fbinf.2024.1411935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/12/2024] [Indexed: 08/13/2024] Open
Abstract
Introduction: This work utilizes predictive modeling in drug discovery to unravel potential candidate genes from Escherichia coli that are implicated in antimicrobial resistance; we subsequently target the gidB, MacB, and KatG genes with some compounds from plants with reported antibacterial potentials. Method: The resistance genes and plasmids were identified from 10 whole-genome sequence datasets of E. coli; forty two plant compounds were selected, and their 3D structures were retrieved and optimized for docking. The 3D crystal structures of KatG, MacB, and gidB were retrieved and prepared for molecular docking, molecular dynamics simulations, and ADMET profiling. Result: Hesperidin showed the least binding energy (kcal/mol) against KatG (-9.3), MacB (-10.7), and gidB (-6.7); additionally, good pharmacokinetic profiles and structure-dynamics integrity with their respective protein complexes were observed. Conclusion: Although these findings suggest hesperidin as a potential inhibitor against MacB, gidB, and KatG in E. coli, further validations through in vitro and in vivo experiments are needed. This research is expected to provide an alternative avenue for addressing existing antimicrobial resistances associated with E. coli's MacB, gidB, and KatG.
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Affiliation(s)
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Udaipur, Rajasthan, India
| | - Christopher Busayo Olowosoke
- Department of Biotechnology, Federal University of Technology, Akure, Nigeria
- Institute of Bioinformatics and Molecular Therapeutics, Osogbo, Nigeria
| | | | - Islamiyyah Ayoade
- Computer-Aided Therapeutic Discovery and Design Platform, Federal University of Technology, Akure, Nigeria
- Department of Biochemistry, Federal University of Technology, Akure, Nigeria
| | - Haruna Isiyaku Umar
- Computer-Aided Therapeutic Discovery and Design Platform, Federal University of Technology, Akure, Nigeria
- Department of Biochemistry, Federal University of Technology, Akure, Nigeria
| | - Abdullahi Temitope Jamiu
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa
| | - Basit Bolarinwa
- College of Medicine, Richmond Gabriel University, Richmond, Saint Vincent and the Grenadines
| | - Zainab Olapade
- Department of Biology, Lamar University, Lamar, TX, United States
| | - Abidemi Ruth Idowu
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, United States
| | - Ibrahim O. Adelakun
- Department of Chemistry, State University of New York Albany, Albany, NY, United States
| | | | - Benjamin Akangbe
- Department of Epidemiology, School of Public Health, Georgia State University, Atlanta, GA, United States
| | - Modesta Abacheng
- School of Public Health, Georgia State University, Atlanta, GA, United States
| | - Odion O. Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
| | - Aeshah A. Awaji
- Department of Biology, Faculty of Science, University College of Taymaa, University of Tabuk, Tabuk, Saudi Arabia
| | - Ridwan Olamilekan Adesola
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
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Bucka-Kolendo J, Kiousi DE, Dekowska A, Mikołajczuk-Szczyrba A, Karadedos DM, Michael P, Galanis A, Sokołowska B. Exploration of Alicyclobacillus spp. Genome in Search of Antibiotic Resistance. Int J Mol Sci 2024; 25:8144. [PMID: 39125715 PMCID: PMC11312215 DOI: 10.3390/ijms25158144] [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: 06/03/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
The study investigates the antibiotic resistance (AR) profiles and genetic determinants in three strains of guaiacol-producing Alicyclobacillus spp. isolated from orchard soil and pears. Their phenotypic characteristics, such as spore formation; resistance to different factors, including drugs or disinfectants; or production of off-flavor compounds, can affect the taste and aroma of spoiled products. Food and beverages are potential vectors for the transfer of antibiotic resistance genes, which is a growing health concern; thus, microorganisms in food and beverages should not be a potential source of drug resistance to consumers. Whole-genome sequencing (WGS) was utilized to identify antibiotic resistance genes, metabolic pathways, and elements associated with guaiacol and halophenol production. Minimum inhibitory concentration (MIC) testing revealed that all strains were susceptible to eight out of nine tested antibiotics (ampicillin, gentamycin, kanamycin, streptomycin, clindamycin, tetracycline, chloramphenicol, and vancomycin) but exhibited high resistance to erythromycin. Analysis indicated that the erythromycin resistance gene, ribosomal RNA small subunit methyltransferase A (RsmA), was intrinsic and likely acquired through horizontal gene transfer (HGT). The comprehensive genomic analysis provides insights into the molecular mechanisms of antibiotic resistance in Alicyclobacillus spp., highlighting the potential risk of these bacteria as vectors for antibiotic resistance genes in the food chain. This study expands the understanding of the genetic makeup of these spoilage bacteria and their role in antimicrobial resistance dissemination.
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Affiliation(s)
- Joanna Bucka-Kolendo
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (A.D.); (A.M.-S.)
| | - Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (P.M.); (A.G.)
| | - Agnieszka Dekowska
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (A.D.); (A.M.-S.)
| | - Anna Mikołajczuk-Szczyrba
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (A.D.); (A.M.-S.)
| | - Dimitrios Marinos Karadedos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (P.M.); (A.G.)
| | - Panagiotis Michael
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (P.M.); (A.G.)
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (P.M.); (A.G.)
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (A.D.); (A.M.-S.)
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Kasiano P, Morita M, Kodama T, Hiyoshi H, Kavai S, Kiiru S, Kariuki S. Salmonella Typhi genotypic diversity, cluster identification and antimicrobial resistance determinants in Mukuru settlement, Nairobi Kenya. BMC Infect Dis 2024; 24:727. [PMID: 39048963 PMCID: PMC11267832 DOI: 10.1186/s12879-024-09635-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Understanding the source of typhoid infections and the genetic relatedness of Salmonella Typhi (S. Typhi) by cluster identification in endemic settings is critical for establishing coordinated public health responses for typhoid fever management. This study investigated the genotypic diversity, antibiotic resistance mechanisms, and clustering of 35 S.Typhi strains isolated from cases and carriers in the Mukuru Informal Settlement. METHODS We studied 35 S.Typhi isolates, including 32 from cases and 3 from carriers, from study participants in the informal settlement of Mukuru, Nairobi, Kenya. Genomic DNA was extracted, and whole-genome sequencing (WGS) was performed to determine the phylogenetic relatedness of strains and detect antimicrobial resistance determinants (AMR). WGS data were analyzed using bioinformatics tools available at the Center for Genomic Epidemiology and Pathogenwatch platforms. RESULTS Genotype 4.3.1.2 EA3 was found to be dominant at 46% (16/35), followed by 4.3.1.2 EA2 at 28% (10/35), and 4.3.1.1 EA1 at 27% (9/35). A comparison of the isolates with global strains from Pathogenwatch identified close clustering with strains from Uganda, Tanzania, Rwanda, and India. Three isolates (9%) distributed in each cluster were isolated from carriers. All genotype 4.3.1.2 EA3 isolates were genotypically multidrug-resistant to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole. Single mutations in the quinolone resistance-determining region were identified in the gyrA (S83Y) and gyrB (S464F) genes. All isolates associated with multidrug resistance showed the presence of the IncQ1 plasmid with the following genes: blaTEM-1B, catA1, sul1, sul2, and dfrA7. CONCLUSION The close phylogenetic relatedness between antimicrobial-resistant case isolates and carriage isolates indicates that typhoid carriage is a possible source of infection in the community. Comparative analysis with global isolates revealed that the Kenyan isolates share common lineages with strains from neighboring East African countries and India, suggesting regional dissemination of specific MDR clones. AMR was a major feature of the isolates. Surveillance and testing for antimicrobial susceptibility should inform options for the management of cases.
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Affiliation(s)
- Purity Kasiano
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya.
- Jomo Kenyatta University of Agriculture and Technology, JKUAT, Nairobi, Kenya.
| | - Masatomo Morita
- Department of Bacteriology I, National Institute for Infectious Diseases, Tokyo, Japan
| | - Toshio Kodama
- Department of Bacteriology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki, Japan
| | - Hirotaka Hiyoshi
- Department of Bacteriology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Susan Kavai
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Susan Kiiru
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture and Technology, JKUAT, Nairobi, Kenya
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
- Drugs for Neglected Diseases initiative, Eastern Africa, Nairobi, Kenya
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Chen J, Wu Y, Zhang G, Kang W, Wang T, Li J, Zhou M, Zhang L, Liu Y, Xu X, Jia X, Xu Y, Liu Y. Tracing the possible evolutionary trends of Morganella morganii: insights from molecular epidemiology and phylogenetic analysis. mSystems 2024; 9:e0030624. [PMID: 38884495 PMCID: PMC11264931 DOI: 10.1128/msystems.00306-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/07/2024] [Indexed: 06/18/2024] Open
Abstract
Morganella morganii, encompassing two subspecies, subsp. morganii and subsp. sibonii, is a common opportunistic pathogen, notable for intrinsic resistance to multiple antimicrobial agents. Despite its clinical significance, research into the potential evolutionary dynamics of M. morganii remains limited. This study involved the analysis of genome sequences from 431 M. morganii isolates, comprising 206 isolates that cause host infections, obtained from this study and 225 from the NCBI genome data sets. A diverse array of antimicrobial resistance genes (ARGs) was identified in M. morganii isolates, including mcr-1, tet(X4), tmexCD-toprJ, and various carbapenemase genes. In addition, a novel blaKPC-2-bearing plasmid with demonstrated conjugative capability was discovered in M. morganii. The majority of virulence-related genes (VRGs), except for the hlyCABD gene cluster, were found in almost all M. morganii. Three novel genospecies of M. morganii were identified, designated as M. chanii, M. variant1, and M. variant2. Compared to M. sibonii, M. chanii genospecies possessed a greater number of flagellar-related genes, typically located within mobile genetic elements (MGEs), suggesting potential for better environmental adaptability. Phylogenetic analysis further disclosed that M. morganii was divided into 12 sequence clusters (SCs). Particularly, SC9 harbored an elevated abundance of ARGs and VRGs, mainly toxin-related genes, and was associated with a higher presence of MGEs compared to non-SC9 strains. The collective findings suggest that M. morganii undergoes evolution driven by the influence of MGEs, thereby significantly enhancing its adaptability to selective pressures of environmental changes and clinical antimicrobial agents.IMPORTANCEThe growing clinical significance of Morganella morganii arises from its abundant virulence factors and antimicrobial resistance genes, resulting in elevated infection rates and increased clinical scrutiny. However, research on the molecular epidemiology and evolutionary trends of M. morganii has been scarce. Our study established a list of virulence-related genes (VRGs) for M. morganii and conducted a large-scale epidemiological investigation into these VRGs. Based on genomic classification, three novel genotypes of M. morganii were identified, representing evolutionary adaptations and responses to environmental challenges. Furthermore, we discovered the emergence of a sequence cluster enriched with antimicrobial resistance genes, VRGs, and mobile genetic elements, attributed to the selective pressure of antimicrobial agents. In addition, we identified a novel conjugative plasmid harboring the blaKPC-2 gene. These findings hold significance in monitoring and comprehending the epidemiology of M. morganii.
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Affiliation(s)
- Jiawei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yun Wu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ge Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Kang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tong Wang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jin Li
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Menglan Zhou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Liu
- Department of Clinical Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xuesong Xu
- Department of Clinical Laboratory, China-Japan Union Hospital, Jilin University, Changchun, China
| | - Xinmiao Jia
- Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yingchun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yali Liu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Le DQ, Nguyen TT, Nguyen CH, Ho TH, Vo NS, Nguyen T, Nguyen HA, Vinh LS, Dang TH, Cao MD, Nguyen SH. AMRomics: a scalable workflow to analyze large microbial genome collections. BMC Genomics 2024; 25:709. [PMID: 39039439 PMCID: PMC11264974 DOI: 10.1186/s12864-024-10620-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024] Open
Abstract
Whole genome analysis for microbial genomics is critical to studying and monitoring antimicrobial resistance strains. The exponential growth of microbial sequencing data necessitates a fast and scalable computational pipeline to generate the desired outputs in a timely and cost-effective manner. Recent methods have been implemented to integrate individual genomes into large collections of specific bacterial populations and are widely employed for systematic genomic surveillance. However, they do not scale well when the population expands and turnaround time remains the main issue for this type of analysis. Here, we introduce AMRomics, an optimized microbial genomics pipeline that can work efficiently with big datasets. We use different bacterial data collections to compare AMRomics against competitive tools and show that our pipeline can generate similar results of interest but with better performance. The software is open source and is publicly available at https://github.com/amromics/amromics under an MIT license.
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Affiliation(s)
- Duc Quang Le
- AMROMICS JSC, Nghe An, Vietnam.
- Faculty of Information Technology, VNU University of Engineering and Technology, Hanoi, Vietnam.
- Faculty of IT, Hanoi University of Civil Engineering, Hanoi, Vietnam.
| | - Tam Thi Nguyen
- Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - Canh Hao Nguyen
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Tho Huu Ho
- Department of Medical Microbiology, The 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
- Department of Genomics & Cytogenetics, Institute of Biomedicine & Pharmacy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Nam S Vo
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
| | | | | | - Le Sy Vinh
- Faculty of Information Technology, VNU University of Engineering and Technology, Hanoi, Vietnam
| | - Thanh Hai Dang
- Faculty of Information Technology, VNU University of Engineering and Technology, Hanoi, Vietnam
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