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Wang L, Wang L, Liu Y, Wang Z, Chen Q, Liu Z, Hu J. Characterization of type I-F CRISPR-Cas system in Laribacter hongkongensis isolates from animals, the environment and diarrhea patients. Int J Food Microbiol 2021; 346:109153. [PMID: 33744818 DOI: 10.1016/j.ijfoodmicro.2021.109153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022]
Abstract
Laribacter hongkongensis is a foodborne organism that is associated with gastroenteritis and diarrhea in humans. Here we describe the structural characteristics and potential function of CRISPR systems to obtain insight into the genotypic diversity of L. hongkongensis. Specifically, we analyzed the genomic content of six L. hongkongensis genomes and identified two CRISPR loci (CRISPR1 and CRISPR2) belonging to the I-F subtype of CRISPR systems. CRISPR1 was flanked on one side by cas genes and a 170 bp-long putative leader sequence, while CRISPR2 arrays located further and processed by the same cas genes. Then a combination of PCR and sequencing was used to determine the prevalence and distribution of the two CRISPR arrays in 112 L. hongkongensis strains isolated from patients, animals, and water reservoirs. In total, the CRISPR1-Cas system of complete subtype I-F was detected in 91.5% (108/118) of the isolates, whereas CRISPR2 locus existed in 72.0% (85/118). Ten strains only possessed part of the cas genes of subtype I-F and four of them with CRISPR2 array. The two loci contained highly conserved and identical direct repeat sequences which were stable in their RNA secondary structure. Additionally, 2564 total spacers including 980 unique spacers arranged in 59 alleles were identified. Homology analysis showed only 1.8% (18/980) of the spacers matched with plasmid or phage. CRISPR polymorphism present in human isolates and frog isolates was more closely related and more extensive than that of fish isolates based on spacer polymorphism. The elucidation of the structural characteristics of the CRISPR-Cas system may be helpful for further studying the specific mechanism of adaptive immunity and other biological functions mediated by CRISPR in L. hongkongensis. The conservation of CRISPR loci and hypervariable repeat-spacer arrays imply the potential for molecular typing of L. hongkongensis.
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Affiliation(s)
- Ling Wang
- Department of Nosocomial Infection Administration, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Li Wang
- Office, Luohu district Center for Disease Control and Prevention, Shenzhen 518000, China
| | - Youzhao Liu
- Department of AIDS Prevention and Control, Guangdong Center for Disease Control and Prevention, Guangzhou 510300, China
| | - Zhiyun Wang
- Department of Immunization Programmes, Baiyun district Center for Disease Control and Prevention, Guangzhou 510540, China
| | - Qing Chen
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Zhihua Liu
- Department of Infectious Disease, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
| | - Jing Hu
- Department of Nosocomial Infection Administration, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
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Severe underlying liver diseases and high mortality associated with Laribacter hongkongensis bacteremia. Diagn Microbiol Infect Dis 2019; 96:114948. [PMID: 31787408 DOI: 10.1016/j.diagmicrobio.2019.114948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 11/20/2022]
Abstract
We characterized a strain of Laribacter hongkongensis isolated from the blood of a patient with fatal sepsis, who had alcoholic cirrhosis with ascites and portal hypertension. L. hongkongensis bacteremia is associated with underlying liver diseases (P < 0.001) and mortality (P < 0.05), whereas L. hongkongensis gastroenteritis is associated with recent travel history (P < 0.05).
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Furstenau TN, Cocking JH, Sahl JW, Fofanov VY. Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites. BMC Bioinformatics 2018; 19:222. [PMID: 29890941 PMCID: PMC5996513 DOI: 10.1186/s12859-018-2225-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 05/30/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Targeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and strains. Typically, this is accomplished by targeting housekeeping genes that provide resolution down to the family, genera, and sometimes species level. Unfortunately, this level of resolution is not sufficient in many applications where strain-level identification of bacteria is required (biodefense, forensics, clinical diagnostics, and outbreak investigations). Adding more genomic targets will increase the resolution, but the challenge is identifying the appropriate targets. VaST was developed to address this challenge by finding the minimum number of targets that, in combination, achieve maximum strain-level resolution for any strain complex. The final combination of target regions identified by the algorithm produce a unique haplotype for each strain which can be used as a fingerprint for identifying unknown samples in a TAS assay. VaST ensures that the targets have conserved primer regions so that the targets can be amplified in all of the known strains and it also favors the inclusion of targets with basal variants which makes the set more robust when identifying previously unseen strains. RESULTS We analyzed VaST's performance using a number of different pathogenic species that are relevant to human disease outbreaks and biodefense. The number of targets required to achieve full resolution ranged from 20 to 88% fewer sites than what would be required in the worst case and most of the resolution is achieved within the first 20 targets. We computationally and experimentally validated one of the VaST panels and found that the targets led to accurate phylogenetic placement of strains, even when the strains were not a part of the original panel design. CONCLUSIONS VaST is an open source software that, when provided a set of variant sites, can find the minimum number of sites that will provide maximum resolution of a strain complex, and it has many different run-time options that can accommodate a wide range of applications. VaST can be an effective tool in the design of strain identification panels that, when combined with TAS technologies, offer an efficient and inexpensive strain typing protocol.
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Affiliation(s)
- Tara N Furstenau
- The School of Informatics, Computing, and Cyber Systems, Northern Arizona University, 1295 S Knoles Dr., Flagstaff, Arizona, 86001, USA
| | - Jill H Cocking
- The School of Informatics, Computing, and Cyber Systems, Northern Arizona University, 1295 S Knoles Dr., Flagstaff, Arizona, 86001, USA
- Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Flagstaff, Arizona, 86001, USA
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Flagstaff, Arizona, 86001, USA
| | - Viacheslav Y Fofanov
- The School of Informatics, Computing, and Cyber Systems, Northern Arizona University, 1295 S Knoles Dr., Flagstaff, Arizona, 86001, USA.
- Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Flagstaff, Arizona, 86001, USA.
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Wu HK, Chen JH, Yang L, Li AR, Su DH, Lin YP, Chen DQ. Emergence and genomic analysis of MDR Laribacter hongkongensis strain HLGZ1 from Guangzhou, China. J Antimicrob Chemother 2017; 73:643-647. [PMID: 29244123 DOI: 10.1093/jac/dkx470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/13/2017] [Indexed: 12/28/2022] Open
Affiliation(s)
- Hong-Kai Wu
- Department of Laboratory Medicine, State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ling Yang
- Department of Laboratory Medicine, State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - A-Rong Li
- Department of Laboratory Medicine, State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Dan-Hong Su
- Department of Laboratory Medicine, State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Yong-Ping Lin
- Department of Laboratory Medicine, State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
- Research Centre for Translational Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Ding-Qiang Chen
- Department of Laboratory Medicine, State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
- Research Centre for Translational Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
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Tsang AKL, Lee HH, Yiu SM, Lau SKP, Woo PCY. Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny. Sci Rep 2017; 7:4536. [PMID: 28674428 PMCID: PMC5495804 DOI: 10.1038/s41598-017-04707-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/18/2017] [Indexed: 11/09/2022] Open
Abstract
Although multilocus sequence typing (MLST) is highly discriminatory and useful for outbreak investigations and epidemiological surveillance, it has always been controversial whether clustering and phylogeny inferred from the MLST gene loci can represent the real phylogeny of bacterial strains. In this study, we compare the phylogenetic trees constructed using three approaches, (1) concatenated blocks of homologous sequence shared between the bacterial genomes, (2) genome single-nucleotide polymorphisms (SNP) profile and (3) concatenated nucleotide sequences of gene loci in the corresponding MLST schemes, for 10 bacterial species with >30 complete genome sequences available. Major differences in strain clustering at more than one position were observed between the phylogeny inferred using genome/SNP data and MLST for all 10 bacterial species. Shimodaira-Hasegawa test revealed significant difference between the topologies of the genome and MLST trees for nine of the 10 bacterial species, and significant difference between the topologies of the SNP and MLST trees were present for all 10 bacterial species. Matching Clusters and R-F Clusters metrics showed that the distances between the genome/SNP and MLST trees were larger than those between the SNP and genome trees. Phylogeny inferred from MLST failed to represent genome phylogeny with the same bacterial species.
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Affiliation(s)
- Alan K L Tsang
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Hwei Huih Lee
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Siu-Ming Yiu
- Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong. .,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pok Fu Lam, Hong Kong. .,Research Centre of Infection and Immunology, The University of Hong Kong, Pok Fu Lam, Hong Kong. .,Carol Yu Centre for Infection, The University of Hong Kong, Pok Fu Lam, Hong Kong. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pok Fu Lam, Hong Kong.
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong. .,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pok Fu Lam, Hong Kong. .,Research Centre of Infection and Immunology, The University of Hong Kong, Pok Fu Lam, Hong Kong. .,Carol Yu Centre for Infection, The University of Hong Kong, Pok Fu Lam, Hong Kong. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pok Fu Lam, Hong Kong.
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Multi-locus sequence typing of Laribacter hongkongensis isolates from freshwater animals, environment and diarrhea patients in southern China. Int J Food Microbiol 2017; 245:98-104. [DOI: 10.1016/j.ijfoodmicro.2017.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 12/29/2022]
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Woo PCY, Poon RWS, Foo CH, To KKW, Lau SKP. First Report of Laribacter hongkongensis Peritonitis in Continuous Ambulatory Peritoneal Dialysis. Perit Dial Int 2016; 36:105-7. [PMID: 26838992 DOI: 10.3747/pdi.2014.00270] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The most common pathogens associated with peritonitis in patients on continuous ambulatory peritoneal dialysis (CAPD) are gram-positive bacteria, which constitute 60 - 80% of all isolates. With the advancement of molecular technologies for bacterial identification, cases of CAPD-related peritonitis caused by bacteria previously not known to be associated with this clinical condition have been reported. Here we report the first case of CAPD-related peritonitis due to Laribacter hongkongensis.
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Affiliation(s)
- Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Rosana W S Poon
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Chuen-Hing Foo
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Kelvin K W To
- Department of Microbiology, The University of Hong Kong, Hong Kong Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong
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Multilocus sequence typing of Ochrobactrum spp. isolated from gastric niche. J Infect Public Health 2016; 10:201-210. [PMID: 27287730 DOI: 10.1016/j.jiph.2016.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 03/17/2016] [Accepted: 04/03/2016] [Indexed: 12/31/2022] Open
Abstract
The human stomach is colonized by diverse bacterial species. The presence of non-Helicobacter pylori bacteria in urease-positive biopsies of individuals has been reported. Bacteria belonging to the Ochrobactrum genus have been documented in the human gastric niche. The co-occurrence of Ochrobactrum spp. with H. pylori was previously reported in an antral biopsy of a non-ulcer dyspeptic (NUD) subject from Northern India. There is no information on the genetic diversity of Ochrobactrum spp. isolated from the gastric niche in the stomach. We aimed to study the species distribution and diversity of Ochrobactrum spp. with and without H. pylori in urease-positive biopsies across three different geographical regions in India. Sixty-two Ochrobactrum isolates recovered from patients with an upper gastric disorder (n=218) were subjected to molecular identification and multilocus sequence typing. H. pylori DNA was found in the majority of biopsies, which had a variable degree of Ochrobactrum spp present. Interestingly, some of the urease-positive biopsies only had Ochrobactrum without any H. pylori DNA. Based on phylogenetic analysis, the Ochrobactrum isolates were distributed into the O. intermedium, O. anthropi and O. oryzae groups. This indicates there are multiple species in the gastric niche irrespective of the presence or absence of H. pylori. Antibiotyping based on colistin and polymyxin B could differentiate between O. intermedium and O. anthropi without revealing the resistance-driven diversity. Considering the prevalence of multiple Ochrobactrum spp. in the human gastric niche, it is important to evaluate the commensal and/or pathogenic nature of non-H. pylori bacteria with respect to their geographical distribution, lifestyle and nutrition needs.
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Xie J, He JB, Shi JW, Xiao Q, Li L, Woo PC. An adult zebrafish model for Laribacter hongkongensis infection: Koch's postulates fulfilled. Emerg Microbes Infect 2014; 3:e73. [PMID: 26038498 PMCID: PMC4217094 DOI: 10.1038/emi.2014.73] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 12/15/2022]
Abstract
Laribacter hongkongensis is a gram-negative emerging bacterium associated with invasive bacteremic infections in patients with liver disease and fish-borne community-acquired gastroenteritis and traveler's diarrhea. Although the complete genome of L. hongkongensis has been sequenced, no animal model is available for further study of its pathogenicity mechanisms. In this study, we showed that adult zebrafish infected with L. hongkongensis by immersion following dermal abrasion or intraperitoneal injection suffered mortality in a dose-dependent manner, with lethal dose 50 (LD50) of 2.1×10(4) and 1.9×10(4) colony-forming units (CFU)/mL, respectively. All mortalities occurred in the first four days post-infection. Zebrafish that died showed characteristic clinicopathological features: swimming near water surface, marked lethargy and sidestroke; abdominal hemorrhage, ulcers and marked swelling with ascites; and hydropic degeneration and necrosis of hepatocytes around central vein and inflammatory cells infiltration. L. hongkongensis was recovered from the ascitic fluid and tissues of zebrafish that died. Of the 30 zebrafish infected with 2.1×10(4) CFU/mL (LD50) L. hongkongensis isolated from dead zebrafish using the immersion following dermal abrasion method, 18 (60%) died. All zebrafish that died also showed the characteristic clinical and pathological features. Histopathological studies also showed dilation of hepatic central vein and hydropic degeneration. L. hongkongensis was isolated from the zebrafish that died. The Koch's postulates for L. hongkongensis as an infectious agent have been fulfilled. This highly reproducible and effective zebrafish model is of crucial importance for future studies on virulence factors for L. hongkongensis infection.
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Affiliation(s)
- Jun Xie
- The Second Clinical Medical College, Southern Medical University , Guangzhou 510515, Guangdong Province, China
| | - Jia-Bei He
- The Second Clinical Medical College, Southern Medical University , Guangzhou 510515, Guangdong Province, China
| | - Jia-Wei Shi
- The First Clinical Medical College, Southern Medical University , Guangzhou 510515, Guangdong Province, China
| | - Qiang Xiao
- Biosafety Level-3 Laboratory, School of Public Health and Tropical Medicine, Southern Medical University , Guangzhou 510515, Guangdong Province, China
| | - Ling Li
- Biosafety Level-3 Laboratory, School of Public Health and Tropical Medicine, Southern Medical University , Guangzhou 510515, Guangdong Province, China
| | - Patrick Cy Woo
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong , Hong Kong, China
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Tse CW, Curreem SO, Cheung I, Tang BS, Leung KW, Lau SK, Woo PC. A novel MLST sequence type discovered in the first fatal case of Laribacter hongkongensis bacteremia clusters with the sequence types of other human isolates. Emerg Microbes Infect 2014; 3:e41. [PMID: 26038743 PMCID: PMC4078790 DOI: 10.1038/emi.2014.39] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/13/2014] [Accepted: 04/15/2014] [Indexed: 11/09/2022]
Abstract
Laribacter hongkongensis is a gram-negative, facultative anaerobic, motile, S-shaped, asaccharolytic, urease-positive bacillus in the Neisseriaceae family of β-proteobacteria. To date, all patients with L. hongkongensis infection have survived, including the two patients with L. hongkongensis bacteremia and patients with L. hongkongensis gastroenteritis. In this study, we describe the clinical, microbiological and molecular characterization of the first fatal case associated with L. hongkongensis bacteremia in a patient with colonic carcinoma that metastasized to the liver. The identity of the isolate was confirmed via phenotypic tests and 16S rRNA gene sequencing. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), using the Bruker database extended with L. hongkongensis reference strains, also identified the isolate as L. hongkongensis, with a top match score of 2.473. Multilocus sequence typing revealed a new sequence type (ST), and phylogenetic analysis and eBURST demonstrated unambiguously that the ST of the isolate was clustered with two other STs found exclusively in human patients, consistent with the theory that some clones of L. hongkongensis could be more virulent than others. Underlying liver diseases and ascites potentially represent distinct risk factors for invasive L. hongkongensis infection. More widespread use of MALDI-TOF MS for identification and improvements of selective media should facilitate the identification of more cases of L. hongkongensis infection.
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Affiliation(s)
- Cindy Ws Tse
- Department of Microbiology, Kwong Wah Hospital , Hong Kong, China
| | - Shirly Ot Curreem
- Department of Microbiology, The University of Hong Kong , Hong Kong, China
| | - Ingrid Cheung
- Department of Microbiology, Kwong Wah Hospital , Hong Kong, China
| | - Bone Sf Tang
- Department of Pathology, Hong Kong Sanatorium and Hospital , Hong Kong, China
| | - Kit-Wah Leung
- Department of Microbiology, The University of Hong Kong , Hong Kong, China
| | - Susanna Kp Lau
- Department of Microbiology, The University of Hong Kong , Hong Kong, China ; Research Centre of Infection and Immunology, The University of Hong Kong , Hong Kong, China ; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong , Hong Kong, China ; Carol Yu Centre for Infection, The University of Hong Kong , Hong Kong, China
| | - Patrick Cy Woo
- Department of Microbiology, The University of Hong Kong , Hong Kong, China ; Research Centre of Infection and Immunology, The University of Hong Kong , Hong Kong, China ; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong , Hong Kong, China ; Carol Yu Centre for Infection, The University of Hong Kong , Hong Kong, China
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12
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Xiong L, Teng JLL, Watt RM, Kan B, Lau SKP, Woo PCY. Arginine deiminase pathway is far more important than urease for acid resistance and intracellular survival in Laribacter hongkongensis: a possible result of arc gene cassette duplication. BMC Microbiol 2014; 14:42. [PMID: 24533585 PMCID: PMC3936950 DOI: 10.1186/1471-2180-14-42] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 02/10/2014] [Indexed: 12/27/2022] Open
Abstract
Background Laribacter hongkongensis is a Gram-negative, urease-positive bacillus associated with invasive bacteremic infections in liver cirrhosis patients and fish-borne community-acquired gastroenteritis and traveler’s diarrhea. Its mechanisms of adaptation to various environmental niches and host defense evasion are largely unknown. During the process of analyzing the L. hongkongensis genome, a complete urease cassette and two adjacent arc gene cassettes were found. We hypothesize that the urease cassette and/or the arc gene cassettes are important for L. hongkongensis to survive in acidic environment and macrophages. In this study, we tested this hypothesis by constructing single, double and triple non-polar deletion mutants of the urease and two arc gene cassettes of L. hongkongensis using the conjugation-mediated gene deletion system and examining their effects in acidic environment in vitro, in macrophages and in a mouse model. Results HLHK9∆ureA, HLHK9∆ureC, HLHK9∆ureD and HLHK9∆ureE all exhibited no urease activity. HLHK9∆arcA1 and HLHK9∆arcA2 both exhibited arginine deiminase (ADI) activities, but HLHK9∆arcA1/arcA2 double deletion mutant exhibited no ADI activity. At pH 2 and 3, survival of HLHK9∆arcA1/arcA2 and HLHK9∆ureA/arcA1/arcA2 were markedly decreased (p < 0.001) but that of HLHK9∆ureA was slightly decreased (p < 0.05), compared to wild type L. hongkongensis HLHK9. Survival of HLHK9∆ureA/arcA1/arcA2 and HLHK9∆arcA1/arcA2 in macrophages were also markedly decreased (p < 0.001 and p < 0.01 respectively) but that of HLHK9∆ureA was slightly decreased (p < 0.05), compared to HLHK9, although expression of arcA1, arcA2 and ureA genes were all upregulated. Using a mouse model, HLHK9∆ureA exhibited similar survival compared to HLHK9 after passing through the murine stomach, but survival of HLHK9∆arcA1/arcA2 and HLHK9∆ureA/arcA1/arcA2 were markedly reduced (p < 0.01). Conclusions In contrast to other important gastrointestinal tract pathogens, ADI pathway is far more important than urease for acid resistance and intracellular survival in L. hongkongensis. The gene duplication of the arc gene cassettes could be a result of their functional importance in L. hongkongensis.
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Affiliation(s)
| | | | | | | | - Susanna K P Lau
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, University Pathology Building, Hong Kong, China.
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Tang BSF, Lau SKP, Teng JLL, Chan TM, Chan WS, Wong TY, Tong YT, Fan RYY, Yuen KY, Woo PCY. Matrix-assisted laser desorption ionisation-time of flight mass spectrometry for rapid identification of Laribacter hongkongensis. J Clin Pathol 2013; 66:1081-3. [PMID: 23814260 DOI: 10.1136/jclinpath-2013-201651] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Laribacter hongkongensis is a Gram-negative, facultative anaerobic, motile, S-shaped, urease-positive bacillus associated with invasive infections in liver cirrhosis patients and community-acquired gastroenteritis. Most cases of L hongkongensis infections occur in eastern countries. Information is lacking on the usefulness of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of bacteria important in eastern countries. Using the Bruker database extended with 21 L hongkongensis reference strains, all 240 L hongkongensis isolates recovered from patients, fish, frogs and water were correctly identified, with 224 (93.3%) strains having top match scores ≥2.0. Notably, the strain of Chromobacterium violaceum was not reliably identified although it is included in the database. MALDI-TOF MS is useful for the accurate routine identification of L hongkongensis after adding reference L hongkongensis main spectra to the database. The number of strains for each species in MALDI-TOF MS databases should be expanded to cover intraspecies variability.
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Affiliation(s)
- Bone S F Tang
- Department of Pathology, Hong Kong Sanatorium and Hospital, , Hong Kong, China
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Feng JL, Lin JY, Jiang XB, Zhang O, Zhu JF, Hu J, Shi L, Chen Q. Development of an ERIC sequence typing scheme for Laribacter hongkongensis, an emerging pathogen associated with community-acquired gastroenteritis and travellers’ diarrhoea. J Med Microbiol 2013; 62:701-707. [DOI: 10.1099/jmm.0.049858-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Laribacter hongkongensis is a potential emerging pathogen, associated with community-acquired diarrhoea. For epidemiological purposes, different molecular typing methods, such as pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing, have been developed for this pathogen. However, these methods require specialized equipment and costly reagents. More importantly, they are labour-intensive and time-consuming, which is not really suitable for foodborne disease outbreak investigations. In this study, we developed a rapid and reliable method using 22-mer primers specific for the enterobacterial repetitive intergenic consensus sequence (ERIC). PFGE was used for comparison, to evaluate this method. A total of 81 isolates of L. hongkongensis were examined: 79 isolates recovered from food of diverse origins and two strains derived from patients with L. hongkongensis-associated infection. Typing patterns and clustering analysis indicated that the 81 L. hongkongensis isolates were grouped into 21 and 13 genotypes by ERIC-PCR and PFGE, respectively. ERIC-PCR was found as reproducible as PFGE. A high percentage (70.4 %) of isolates yielded distinguishable ERIC-PCR patterns, which were concordant with the results from PFGE. These results suggest that ERIC-PCR is valuable for use in the epidemiological investigation of L. hongkongensis.
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Affiliation(s)
- Jia-Li Feng
- Key Laboratory of Prevention and Control of Emerging Infectious Diseases of Guangdong Higher Education Institutes, Southern Medical University, Guangzhou, Guangdong Province 510515, China
- Department of Epidemiology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jin-Yan Lin
- Department of Epidemiology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xiao-Bing Jiang
- College of Light Industry and Food Science, South China University of Technology Guangzhou, 510000, China
| | - Ou Zhang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jiang-Feng Zhu
- Department of Epidemiology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jing Hu
- Key Laboratory of Prevention and Control of Emerging Infectious Diseases of Guangdong Higher Education Institutes, Southern Medical University, Guangzhou, Guangdong Province 510515, China
- Department of Epidemiology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Lei Shi
- College of Light Industry and Food Science, South China University of Technology Guangzhou, 510000, China
| | - Qing Chen
- Key Laboratory of Prevention and Control of Emerging Infectious Diseases of Guangdong Higher Education Institutes, Southern Medical University, Guangzhou, Guangdong Province 510515, China
- Department of Epidemiology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China
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15
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Woo PCY, Tsang AKL, Wong AYP, Chen H, Chu J, Lau SKP, Yuen KY. Analysis of multilocus sequence typing schemes for 35 different bacteria revealed that gene loci of 10 bacteria could be replaced to improve cost-effectiveness. Diagn Microbiol Infect Dis 2011; 70:316-23. [PMID: 21558049 DOI: 10.1016/j.diagmicrobio.2011.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/09/2011] [Accepted: 03/09/2011] [Indexed: 11/17/2022]
Abstract
Although multilocus sequence typing (MLST) has been widely used for bacterial typing, the contribution of the gene loci to the discriminatory power of each MLST scheme is unknown. We analyzed the discriminatory powers of 36 MLST schemes using all combinations of the 7 loci and contributions of each locus to the schemes. In 10 schemes, sequencing 6 loci can achieve the discriminatory powers of 7 loci. For the other 26 schemes, the median marginal increase in discriminatory power when 7 instead of 6 loci were used is 0.0004. Sequencing the 7 loci of 50 strains each of Pseudomonas aeruginosa and Acinetobacter baumannii revealed that the discriminatory power for P. aeruginosa was 0.9861 when either 6 (without trp) or 7 loci were used and that for A. baumannii was 0.9363 when 5, 6, or 7 loci were used. Genes that have no additional or minimal contribution to the overall discriminatory powers should be replaced.
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Affiliation(s)
- Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.
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16
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Lau SK, Wong GK, Tsang AK, Teng JL, Fan RY, Tse H, Yuen KY, Woo PC. Virulence determinants, drug resistance and mobile genetic elements of Laribacter hongkongensis: a genome-wide analysis. Cell Biosci 2011; 1:17. [PMID: 21711902 PMCID: PMC3125207 DOI: 10.1186/2045-3701-1-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 04/19/2011] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea. In this study, we performed an in-depth annotation of the genes in its genome related to the various steps in the infective process, drug resistance and mobile genetic elements. RESULTS For acid and bile resistance, L. hongkongensis possessed a urease gene cassette, two arc gene clusters and bile salt efflux systems. For intestinal colonization, it possessed a putative adhesin of the autotransporter family homologous to those of diffusely adherent Escherichia coli (E. coli) and enterotoxigenic E. coli. To evade from host defense, it possessed superoxide dismutase and catalases. For lipopolysaccharide biosynthesis, it possessed the same set of genes that encode enzymes for synthesizing lipid A, two Kdo units and heptose units as E. coli, but different genes for its symmetrical acylation pattern, and nine genes for polysaccharide side chains biosynthesis. It contained a number of CDSs that encode putative cell surface acting (RTX toxin and hemolysins) and intracellular cytotoxins (patatin-like proteins) and enzymes for invasion (outer membrane phospholipase A). It contained a broad variety of antibiotic resistance-related genes, including genes related to β-lactam (n = 10) and multidrug efflux (n = 54). It also contained eight prophages, 17 other phage-related CDSs and 26 CDSs for transposases. CONCLUSIONS The L. hongkongensis genome possessed genes for acid and bile resistance, intestinal mucosa colonization, evasion of host defense and cytotoxicity and invasion. A broad variety of antibiotic resistance or multidrug resistance genes, a high number of prophages, other phage-related CDSs and CDSs for transposases, were also identified.
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Affiliation(s)
- Susanna Kp Lau
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Gilman Km Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Alan Kl Tsang
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Jade Ll Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Rachel Yy Fan
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Herman Tse
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Patrick Cy Woo
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
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17
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Woo PCY, Wong SSY, Teng JLL, Leung KW, Ngan AHY, Zhao DQ, Tse H, Lau SKP, Yuen KY. Leptotrichia hongkongensis sp. nov., a novel Leptotrichia species with the oral cavity as its natural reservoir. J Zhejiang Univ Sci B 2010; 11:391-401. [PMID: 20506569 DOI: 10.1631/jzus.b1000056] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A straight, non-sporulating, Gram-variable bacillus (HKU24(T)) was recovered from the blood culture of a patient with metastatic breast carcinoma. After repeated subculturing in BACTEC Plus Anaerobic/F blood culture broth, HKU24(T) grew on brucella agar as non-hemolytic, pinpoint colonies after 96 h of incubation at 37 degrees C in an anaerobic environment and aerobic environment with 5% CO2. Growth was enhanced with a streak of Staphylococcus aureus. HKU24(T) was non-motile and catalase-negative, but positive for alkaline phosphatase, beta-glucosidase, and alpha-glucosidase. It hydrolyzed phenylphosphonate and reduced resazurin. 16S rRNA, groEL, gyrB, recA, and rpoB sequencing showed that HKU24(T) occupies a distinct phylogenetic position among the Leptotrichia species, being most closely related to Leptotrichia trevisanii. Using HKU24(T) groEL, gyrB, recA, and rpoB gene-specific primers, fragments of these genes were amplified from one of 20 oral specimens. Based on phenotypic and genotypic characteristics, we propose a new species, Leptotrichia hongkongensis sp. nov., to describe this bacterium.
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Affiliation(s)
- Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.
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18
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The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS Genet 2009; 5:e1000416. [PMID: 19283063 PMCID: PMC2652115 DOI: 10.1371/journal.pgen.1000416] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 02/10/2009] [Indexed: 11/19/2022] Open
Abstract
Laribacter hongkongensis is a newly discovered Gram-negative bacillus of the Neisseriaceae family associated with freshwater fish-borne gastroenteritis and traveler's diarrhea. The complete genome sequence of L. hongkongensis HLHK9, recovered from an immunocompetent patient with severe gastroenteritis, consists of a 3,169-kb chromosome with G+C content of 62.35%. Genome analysis reveals different mechanisms potentially important for its adaptation to diverse habitats of human and freshwater fish intestines and freshwater environments. The gene contents support its phenotypic properties and suggest that amino acids and fatty acids can be used as carbon sources. The extensive variety of transporters, including multidrug efflux and heavy metal transporters as well as genes involved in chemotaxis, may enable L. hongkongensis to survive in different environmental niches. Genes encoding urease, bile salts efflux pump, adhesin, catalase, superoxide dismutase, and other putative virulence factors-such as hemolysins, RTX toxins, patatin-like proteins, phospholipase A1, and collagenases-are present. Proteomes of L. hongkongensis HLHK9 cultured at 37 degrees C (human body temperature) and 20 degrees C (freshwater habitat temperature) showed differential gene expression, including two homologous copies of argB, argB-20, and argB-37, which encode two isoenzymes of N-acetyl-L-glutamate kinase (NAGK)-NAGK-20 and NAGK-37-in the arginine biosynthesis pathway. NAGK-20 showed higher expression at 20 degrees C, whereas NAGK-37 showed higher expression at 37 degrees C. NAGK-20 also had a lower optimal temperature for enzymatic activities and was inhibited by arginine probably as negative-feedback control. Similar duplicated copies of argB are also observed in bacteria from hot springs such as Thermus thermophilus, Deinococcus geothermalis, Deinococcus radiodurans, and Roseiflexus castenholzii, suggesting that similar mechanisms for temperature adaptation may be employed by other bacteria. Genome and proteome analysis of L. hongkongensis revealed novel mechanisms for adaptations to survival at different temperatures and habitats.
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