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Fortini D, García-Fernández A, Lucarelli C, Dionisi AM, Arena S, Owczarek S, Equestre M, Carattoli A, Sacco F, Rossi S, Ortenzi R, Primavilla S, Villa L. Isolation and Characterisation of Human-Derived blaKPC-3-Producing Salmonella enterica Serovar Rissen in 2018. Antibiotics (Basel) 2023; 12:1377. [PMID: 37760674 PMCID: PMC10525129 DOI: 10.3390/antibiotics12091377] [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: 07/20/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
In this study, we describe a Salmonella enterica serovar (S.) Rissen strain with a reduced susceptibility to meropenem, isolated from a urinary infection in an 89-year-old woman in 2018 during activity surveillance in Italy (Enter-Net Italia). The genomic characteristics, pathogenicity, and antimicrobial resistance mechanisms were investigated via a genomic approach. Antimicrobial susceptibility testing revealed a "susceptible, increased exposure" phenotype to meropenem in the S. Rissen strain (4_29_19). Whole-genome sequencing (WGS) was performed using both the NovaSeq 6000 S4 PE150 XP platform (Illumina, San Diego, CA, USA) and MinION (Oxford Nanopore). The S. Rissen 4_29_19 strain harboured two plasmids: a pKpQIL-like plasmid carrying the blaKPC-3 resistance gene in a Tn4401a transposon (pKPC_4_29_19), and a ColE-like plasmid (p4_4_29_19) without resistance genes, highly prevalent among Enterobacterales. Comparative analysis revealed that the pKPC_4_29_19 plasmid was highly related to the pKpQIL reference plasmid (GU595196), with 57% coverage and 99.96% identity, but lacking a region of about 30 kb, involving the FIIK2 replicon region and the entire transfer locus, causing the loss of its ability to conjugate. To our knowledge, this is the first time that a pKpQIL-like plasmid, carrying blaKPC-3, highly diffused in Klebsiella pneumoniae strains, has been identified in a Salmonella strain in our country. The acquisition of blaKPC genes by Salmonella spp. is extremely rare, and is reported only sporadically. In zoonotic bacteria isolated from humans, the presence of a carbapenem resistance gene carried by mobile genetic elements, usually described in healthcare-associated infection bacteria, represents an important concern for public health.
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Affiliation(s)
- Daniela Fortini
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (A.G.-F.); (C.L.); (A.M.D.); (S.A.); (S.O.)
| | - Aurora García-Fernández
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (A.G.-F.); (C.L.); (A.M.D.); (S.A.); (S.O.)
| | - Claudia Lucarelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (A.G.-F.); (C.L.); (A.M.D.); (S.A.); (S.O.)
| | - Anna Maria Dionisi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (A.G.-F.); (C.L.); (A.M.D.); (S.A.); (S.O.)
| | - Sergio Arena
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (A.G.-F.); (C.L.); (A.M.D.); (S.A.); (S.O.)
| | - Slawomir Owczarek
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (A.G.-F.); (C.L.); (A.M.D.); (S.A.); (S.O.)
| | - Michele Equestre
- Department of Neurosciences, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Alessandra Carattoli
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (A.C.); (F.S.)
| | - Federica Sacco
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (A.C.); (F.S.)
| | - Stefano Rossi
- Hospital Castiglione del Lago, USL Umbria n.1, 06061 Perugia, Italy;
| | - Roberta Ortenzi
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “T. Rosati”, 06126 Perugia, Italy; (R.O.); (S.P.)
| | - Sara Primavilla
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “T. Rosati”, 06126 Perugia, Italy; (R.O.); (S.P.)
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (A.G.-F.); (C.L.); (A.M.D.); (S.A.); (S.O.)
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El-Khoury C, Mansour E, Yuliandra Y, Lai F, Hawkins BA, Du JJ, Sundberg EJ, Sluis-Cremer N, Hibbs DE, Groundwater PW. The role of adjuvants in overcoming antibacterial resistance due to enzymatic drug modification. RSC Med Chem 2022; 13:1276-1299. [PMID: 36439977 PMCID: PMC9667779 DOI: 10.1039/d2md00263a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/16/2022] [Indexed: 02/03/2023] Open
Abstract
Antibacterial resistance is a prominent issue with monotherapy often leading to treatment failure in serious infections. Many mechanisms can lead to antibacterial resistance including deactivation of antibacterial agents by bacterial enzymes. Enzymatic drug modification confers resistance to β-lactams, aminoglycosides, chloramphenicol, macrolides, isoniazid, rifamycins, fosfomycin and lincosamides. Novel enzyme inhibitor adjuvants have been developed in an attempt to overcome resistance to these agents, only a few of which have so far reached the market. This review discusses the different enzymatic processes that lead to deactivation of antibacterial agents and provides an update on the current and potential enzyme inhibitors that may restore bacterial susceptibility.
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Affiliation(s)
- Christy El-Khoury
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Elissar Mansour
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Yori Yuliandra
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Bryson A Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine Atlanta GA 30322 USA
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine Atlanta GA 30322 USA
| | - Nicolas Sluis-Cremer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine Pittsburgh PA 15213 USA
| | - David E Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Paul W Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
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Yang SM, Kim E, Lee W, Kim HY. Genomic characteristics and comparative genomics of Salmonella enterica subsp. enterica serovar Schwarzengrund strain S16 isolated from chicken feces. Gut Pathog 2022; 14:1. [PMID: 34983642 PMCID: PMC8728987 DOI: 10.1186/s13099-021-00476-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/13/2021] [Indexed: 01/18/2023] Open
Abstract
Background Salmonella enterica subsp. enterica serovar Schwarzengrund (S. Schwarzengrund) is most frequently isolated from commensals humans or poultry. Here we report S. Schwarzengrund strain S16, the first sequenced genome in the Republic of Korea. Additionally, genome sequencing for strain S16 was performed and compared with other S. Schwarzengrund genomes obtained from public database. Results Strain S16 was isolated from chicken feces. The complete genome consists of one chromosome and one plasmid. The genome size is 4,822,755 bp with 4852 coding sequences. Strain S16 was determined as serovar Schwarzengrund by in silico serotyping and typed as sequence type (ST) 96. Forty-six S. Schwarzengrund genomes yielded a pangenome of 7112 genes, core-genome of 3374 genes, accessory-genome of 2906 genes, and unique-genome of 835 genes. Eighty-one genes were unique to strain S16, including hypothetical proteins and transcriptional regulators. Genotypic analysis of antibiotic resistance of strain S16 confirmed resistance to amikacin, ciprofloxacin, sulfamethoxazole, streptomycin, and tetracycline. Unlike other S. Schwarzengrund genomes, strain S16 had a mutation of gyrB. Moreover, similar to other S. Schwarzengrund genomes reported in other countries, strain S16 was harbored for 153 virulence genes including Saf operon and cdtB gene. All the antibiotic resistance genes and virulence genes were present in the core- or accessory-genomes. Conclusions Complete genome of strain S16 was sequenced. Comparative genomic analysis revealed several genes responsible for antibiotic resistance and specific genomic features of strain S16 and identified virulence factors that might contribute to the human and animal pathogenicity of other S. Schwarzengrund genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-021-00476-8.
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Affiliation(s)
- Seung-Min Yang
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Woojung Lee
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea.
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Small IncQ1 Plasmid Encoding KPC-2 Expands to Invasive Nontyphoidal Salmonella. Antimicrob Agents Chemother 2021; 65:e0155221. [PMID: 34460308 DOI: 10.1128/aac.01552-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Whole-Genome Sequencing Reveals the Presence of the blaCTX-M-65 Gene in Extended-Spectrum β-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands. Antibiotics (Basel) 2021; 10:antibiotics10030267. [PMID: 33807748 PMCID: PMC8000398 DOI: 10.3390/antibiotics10030267] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 12/24/2022] Open
Abstract
Salmonella Infantis, a common contaminant of poultry products, is known to harbor mobile genetic elements that confer multi-drug resistance (MDR) and have been detected in many continents. Here, we report four MDR S. Infantis strains recovered from poultry house environments in Santa Cruz Island of the Galapagos showing extended-spectrum β-lactamase (ESBL) resistance and reduced fluoroquinolone susceptibility. Whole-genome sequencing (WGS) revealed the presence of the ESBL-conferring blaCTX-M-65 gene in an IncFIB-like plasmid in three S. Infantis isolates. Multi-locus sequence typing (MLST) and single nucleotide variant/polymorphism (SNP) SNVPhyl analysis showed that the S. Infantis isolates belong to sequence type ST32, likely share a common ancestor, and are closely related (1–3 SNP difference) to blaCTX-M-65-containing clinical and veterinary S. Infantis isolates from the United States and Latin America. Furthermore, phylogenetic analysis of SNPs following core-genome alignment (i.e., ParSNP) inferred close relatedness between the S. Infantis isolates from Galapagos and the United States. Prophage typing confirmed the close relationship among the Galapagos S. Infantis and was useful in distinguishing them from the United States isolates. This is the first report of MDR blaCTX-M-65-containing S. Infantis in the Galapagos Islands and highlights the need for increased monitoring and surveillance programs to determine prevalence, sources, and reservoirs of MDR pathogens.
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Novel patterns in the molecular epidemiology of KPC-producing Klebsiella pneumoniae in Tucumán, Argentina. J Glob Antimicrob Resist 2019; 19:183-187. [DOI: 10.1016/j.jgar.2019.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/05/2019] [Accepted: 02/17/2019] [Indexed: 11/30/2022] Open
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Monte DF, Lincopan N, Berman H, Cerdeira L, Keelara S, Thakur S, Fedorka-Cray PJ, Landgraf M. Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000-2016. Sci Rep 2019; 9:11058. [PMID: 31363103 PMCID: PMC6667439 DOI: 10.1038/s41598-019-45838-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/11/2019] [Indexed: 11/09/2022] Open
Abstract
Multidrug-resistant (MDR) Salmonella enterica has been deemed a high-priority pathogen by the World Health Organization. Two hundred and sixty-four Salmonella enterica isolates recovered over a 16-year period (2000 to 2016) from the poultry and swine production chains, in Brazil, were investigated by whole-genome sequencing (WGS). Most international lineages belonging to 28 serovars, including, S. enterica serovars S. Schwarzengrund ST96, S. Typhimurium ST19, S. Minnesota ST548, S. Infantis ST32, S. Heidelberg ST15, S. Newport ST45, S. Brandenburg ST65 and S. Kentucky ST198 displayed MDR and virulent genetic backgrounds. In this regard, resistome analysis revealed presence of qnrE1 (identified for the first time in S. Typhimurium from food chain), qnrB19, qnrS1, blaCTX-M-8, blaCTX-M-2 and blaCMY-2 genes, as well as gyrA mutations; whereas ColpVC, IncHI2A, IncHI2, IncFIA, Incl1, IncA/C2, IncR, IncX1 and po111 plasmids were detected. In addition, phylogenetic analysis revealed multiple independent lineages such as S. enterica serovars S. Infantis, S. Schwarzengrund, S. Minnesota, S. Kentucky and S. Brandenburg. In brief, ocurrence and persistence of international lineages of S. enterica serovars in food production chain is supported by conserved genomes and wide virulome and resistome.
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Affiliation(s)
- Daniel F Monte
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil. .,Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA.
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Hanna Berman
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Shivaramu Keelara
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Mariza Landgraf
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil.
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Draft Genome Sequences of 27 Salmonella enterica Serovar Schwarzengrund Isolates from Clinical Sources. Microbiol Resour Announc 2019; 8:8/12/e01687-18. [PMID: 30938709 PMCID: PMC6430326 DOI: 10.1128/mra.01687-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twenty-seven Salmonella enterica serovar Schwarzengrund isolates from clinical sources were sequenced as part of a larger study to examine phenotypic and genotypic characteristics. The majority of the sequenced strains were isolated from human stool (n = 20) followed by urine (n = 3) and blood (n = 2). Twenty-seven Salmonella enterica serovar Schwarzengrund isolates from clinical sources were sequenced as part of a larger study to examine phenotypic and genotypic characteristics. The majority of the sequenced strains were isolated from human stool (n = 20) followed by urine (n = 3) and blood (n = 2). Four isolate sequences contained plasmids of known incompatibility groups.
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Du X, Jiang X, Ye Y, Guo B, Wang W, Ding J, Xie G. Next generation sequencing for the investigation of an outbreak of Salmonella Schwarzengrund in Nanjing, China. Int J Biol Macromol 2017; 107:393-396. [PMID: 28888545 DOI: 10.1016/j.ijbiomac.2017.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/28/2017] [Accepted: 09/01/2017] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Salmonella Schwarzengrund is most frequently isolated from poultry meat and can cause human infections. S. Schwarzengrund was isolated from diarrheal patients in a food poisoning event in Nanjing, China. METHODS Three strains isolated from patients were microbiologically confirmed as S. Schwarzengrund. Salmonella strains from spiced donkey meat were also confirmed as S. Schwarzengrund. Epidemiology investigation showed evidence of a correlation between the consumption of spiced donkey meat and those cases. Pulsed field gel electrophoresis, antibiotic susceptibility test and next generation sequencing (NGS) were employed to investigate this food poisoning event. RESULTS The 3 strains isolated from patients and the strain isolated from the spiced donkey meat showed same results in PFGE, antibiotic susceptibility test and no SNPs were observed between these 4 strains in NGS analysis. DISCUSSION NGS data could be used in the confirmation of an outbreak and in the tracing of contamination. However, this standard of defining an outbreak with NGS remained a challenge in practice. And the NGS data should be used in combination with other data in epidemiological investigation.
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Affiliation(s)
- Xuefei Du
- Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, China
| | - Xiao Jiang
- Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, China
| | - Yanhua Ye
- Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, China
| | - Baofu Guo
- Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, China
| | - Wei Wang
- Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, China
| | - Jie Ding
- Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, China
| | - Guoxiang Xie
- Nanjing Municipal Center for Disease Control and Prevention, Jiangsu, China.
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Extended-spectrum β-lactamase/AmpC- and carbapenemase-producing Enterobacteriaceae in animals: a threat for humans? Clin Microbiol Infect 2017; 23:826-833. [PMID: 28143782 DOI: 10.1016/j.cmi.2017.01.013] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/18/2016] [Accepted: 01/19/2017] [Indexed: 11/24/2022]
Abstract
There has been a great and long-term concern that extended-spectrum β-lactamase (ESBL)/AmpC- and carbapenemase-producing Enterobacteriaceae occurring in animals may constitute a public-health issue. A large number of factors with complex interrelations contribute to the spread of those bacteria among animals and humans. ESBL/AmpC- or carbapenemase-encoding genes are most often located on mobile genetic elements favouring their dissemination. Some shared reservoirs of ESBL/AmpC or carbapenemase genes, plasmids or clones have been identified and suggest cross-transmissions. Even though exposure to animals is regarded as a risk factor, evidence for a direct transfer of ESBL/AmpC-producing bacteria from animals to humans through close contacts is limited. Nonetheless, the size of the commensal ESBL/AmpC reservoir in non-human sources is dramatically rising. This may constitute an indirect risk to public health by increasing the gene pool from which pathogenic bacteria can pick up ESBL/AmpC/carbapenemase genes. The extent to which food contributes to potential transmission of ESBL/AmpC producers to humans is also not well established. Overall, events leading to the occurrence of ESBL/AmpC- and carbapenemase-encoding genes in animals seem very much multifactorial. The impact of animal reservoirs on human health still remains debatable and unclear; nonetheless, there are some examples of direct links that have been identified.
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Escandón-Vargas K, Reyes S, Gutiérrez S, Villegas MV. The epidemiology of carbapenemases in Latin America and the Caribbean. Expert Rev Anti Infect Ther 2016; 15:277-297. [PMID: 27915487 DOI: 10.1080/14787210.2017.1268918] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Enterobacteriaceae, Pseudomonas spp., and Acinetobacter spp. infections are major causes of morbidity and mortality, especially due to the emergence and spread of β-lactamases. Carbapenemases, which are β-lactamases with the capacity to hydrolyze or inactivate carbapenems, have become a serious concern as they have the largest hydrolytic spectrum and therefore limit the utility of most β-lactam antibiotics. Areas covered: Here, we present an update of the current status of carbapenemases in Latin America and the Caribbean. Expert commentary: The increased frequency of reports on carbapenemases in Latin America and the Caribbean shows that they have successfully spread and have even become endemic in some countries. Countries such as Brazil, Colombia, Argentina, and Mexico account for the majority of these reports. Early suspicion and detection along with implementation of antimicrobial stewardship programs in all healthcare settings are crucial for the control and prevention of carbapenemase-producing bacteria.
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Affiliation(s)
- Kevin Escandón-Vargas
- a Bacterial Resistance and Hospital Epidemiology Unit , International Center for Medical Research and Training (CIDEIM) , Cali , Colombia
| | - Sergio Reyes
- a Bacterial Resistance and Hospital Epidemiology Unit , International Center for Medical Research and Training (CIDEIM) , Cali , Colombia
| | - Sergio Gutiérrez
- a Bacterial Resistance and Hospital Epidemiology Unit , International Center for Medical Research and Training (CIDEIM) , Cali , Colombia
| | - María Virginia Villegas
- a Bacterial Resistance and Hospital Epidemiology Unit , International Center for Medical Research and Training (CIDEIM) , Cali , Colombia.,b Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics , Universidad El Bosque , Bogotá , Colombia
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Intestinal Carriage of Carbapenemase-Producing Organisms: Current Status of Surveillance Methods. Clin Microbiol Rev 2016; 29:1-27. [PMID: 26511484 DOI: 10.1128/cmr.00108-14] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Carbapenemases have become a significant mechanism for broad-spectrum β-lactam resistance in Enterobacteriaceae and other Gram-negative bacteria such as Pseudomonas and Acinetobacter spp. Intestinal carriage of carbapenemase-producing organisms (CPOs) is an important source of transmission. Isolation of carriers is one strategy that can be used to limit the spread of these bacteria. In this review, we critically examine the clinical performance, advantages, and disadvantages of methods available for the detection of intestinal carriage of CPOs. Culture-based methods (Centers for Disease Control and Prevention [CDC] protocols, chromogenic media, specialized agars, and double-disk synergy tests) for detecting carriage of CPOs are convenient due to their ready availability and low cost, but their limited sensitivity and long turnaround time may not always be optimal for infection control practices. Contemporary nucleic acid amplification techniques (NAATs) such as real-time PCR, hybridization assays, loop-mediated isothermal amplification (LAMP), or a combined culture and NAAT approach may provide fast results and/or added sensitivity and specificity compared with culture-based methods. Infection control practitioners and clinical microbiologists should be aware of the strengths and limitations of available methods to determine the most suitable approach for their medical facility to fit their infection control needs.
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Crump JA, Sjölund-Karlsson M, Gordon MA, Parry CM. Epidemiology, Clinical Presentation, Laboratory Diagnosis, Antimicrobial Resistance, and Antimicrobial Management of Invasive Salmonella Infections. Clin Microbiol Rev 2015; 28:901-37. [PMID: 26180063 PMCID: PMC4503790 DOI: 10.1128/cmr.00002-15] [Citation(s) in RCA: 640] [Impact Index Per Article: 71.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Salmonella enterica infections are common causes of bloodstream infection in low-resource areas, where they may be difficult to distinguish from other febrile illnesses and may be associated with a high case fatality ratio. Microbiologic culture of blood or bone marrow remains the mainstay of laboratory diagnosis. Antimicrobial resistance has emerged in Salmonella enterica, initially to the traditional first-line drugs chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole. Decreased fluoroquinolone susceptibility and then fluoroquinolone resistance have developed in association with chromosomal mutations in the quinolone resistance-determining region of genes encoding DNA gyrase and topoisomerase IV and also by plasmid-mediated resistance mechanisms. Resistance to extended-spectrum cephalosporins has occurred more often in nontyphoidal than in typhoidal Salmonella strains. Azithromycin is effective for the management of uncomplicated typhoid fever and may serve as an alternative oral drug in areas where fluoroquinolone resistance is common. In 2013, CLSI lowered the ciprofloxacin susceptibility breakpoints to account for accumulating clinical, microbiologic, and pharmacokinetic-pharmacodynamic data suggesting that revision was needed for contemporary invasive Salmonella infections. Newly established CLSI guidelines for azithromycin and Salmonella enterica serovar Typhi were published in CLSI document M100 in 2015.
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Affiliation(s)
- John A Crump
- Centre for International Health, University of Otago, Dunedin, Otago, New Zealand Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria Sjölund-Karlsson
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melita A Gordon
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Christopher M Parry
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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