Fengqin Li

Emergence and Diversity of Salmonella enterica Serovar Indiana Isolates with Concurrent Resistance to Ciprofloxacin and Cefotaxime from Patients and Food-Producing Animals in China.

ABSTRACT Salmonellosis is a major global foodborne infection, and strains that are resistant to a great variety of antibiotics have become a major public health concern. The aim of this study was to identify genes conferring resistance to fluoroquinolones and extended-spectrum β-lactams in nontyphoidal Salmonella (NTS) from patients and food-producing animals in China. In total, 133 and 21 NTS isolates from animals and humans, respectively, exhibiting concurrent resistance to ciprofloxacin and cefotaxime were cultured independently from 2009 to ∼2013. All of the isolates were identified, serotyped, and subjected to antimicrobial susceptibility testing. Importantly, the isolates with concurrent resistance to ciprofloxacin and cefotaxime all were confirmed as S. enterica serovar Indiana. The presence of fluoroquinolone resistance genes and extended-spectrum β-lactamases (ESBLs) was established by PCR and DNA sequencing. The occurrence and diversity of different genes conferring fluoroquinolone resistance [qepA, oqxAB, and aac(6′)-Ib-cr] with mutations in topoisomerase-encoding genes (gyrA and parC) and several ESBLs (including CTX-M-65, CTX-M-27, CTX-M-15, CTX-M-14, and CTX-M-14/CTX-M-15) were noteworthy. Genes located on mobile genetic elements were identified by conjugation and transformation. Pulsed-field gel electrophoresis, used to determine the genetic relationships between these isolates, generated 91 pulsotypes from 133 chicken isolates and 17 pulsotypes from the 21 clinical isolates that showed considerable diversity. Analysis of the pulsotypes obtained with the isolates showed some clones appeared to have existed for several years and had been disseminating between humans and food-producing animals. This study highlights the emergence of ciprofloxacin- and cefotaxime-resistant S. enterica serovar Indiana, posing a threat to public health.

Enterotoxigenicity and Antimicrobial Resistance of Staphylococcus aureus Isolated from Retail Food in China

Staphylococcus aureus is one of the most common causes of zoonotic agent in the world, which are attributable to the contamination of food with enterotoxins. In this study, a total of 1,150 S. aureus isolates were cultured from 27,000 retail foods items from 203 cities of 24 provinces in China in 2015 and were test for antimicrobial susceptibility. Additionally, the role of the genes responsible for the staphylococcal enterotoxins (SEA to SEE), methicillin resistance (mecA) and the toxigenic capabilities were also assessed. The results showed that 4.3% retail foods were contaminated with S. aureus, and 7.9% retail foods isolates were mecA positive. Some 97.6% of S. aureus isolates were resistant to at least one antimicrobial compound, and 57.5% of these were multi drug resistant (MDR). Resistance to penicillin (83.7%, 963/1,150), was common, followed by linezolid (67.7%, 778/1,150) and erythromycin (52.1%, 599/1,150). The isolates cultured from raw meats showed high levels of resistant to tetracycline (42.8%), ciprofloxacin (17.4%), and chloramphenicol (12.0%) and expressed a MDR phenotype (62.4%). A total of 29.7% S. aureus isolates harbored the classical SEs genes (sea, seb, sec, and sed). The sea and seb genes were the most frequent SEs genes detected. Of note, 22% of the SEs genes positive S. aureus harbored two or three SEs genes, and 16 isolates were confirmed with the capacity to simultaneously produce two or three enterotoxin types. Moreover, nearly 50% of the MRSA isolates were positive for at least one SE gene in this study. Therefore, it is important to monitor the antimicrobial susceptibility and enterotoxigenicity of MDR S. aureus and MRSA in the food chain and to use these data to develop food safety measures, designed to reduce the contamination and transmission of this bacterium.

A novel disrupted mcr-1 gene and a lysogenized phage P1-like sequence detected from a large conjugative plasmid, cultured from a human atypical enteropathogenic Escherichia coli (aEPEC) recovered in China

Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, The People’s Republic of China; UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, The People’s Republic of China; Institute for Nutrition and Food Hygiene, Beijing Center for Disease Prevention and Control, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, The People’s Republic of China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, The People’s Republic of China; Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Stranmillis Road, Belfast BT9 5AG, UK

Enumeration and Characterization of Campylobacter Species from Retail Chicken Carcasses in Beijing, China

Epidemiological data have implicated contaminated raw or undercooked chicken as primary vehicles of Campylobacter transmission to humans. Risk assessment relating to Campylobacter contamination of poultry products in China is frequently hampered by the lack of quantitative data. In this study, whole chicken carcasses (n=240) were collected from the retail markets of Beijing. The level of Campylobacter contamination was enumerated by the plate-counting method. The representative Campylobacter isolates were characterized for antimicrobial resistance. Selected representative isolates were further analyzed by the multilocus sequencing typing method for genetic relatedness. Overall, 26.3% (63/240) of the retail whole chicken carcasses were contaminated by Campylobacter, and the values ranged from 2.5 to 7050 colony-forming units (CFU)/g. The 50th percentile of Campylobacter value was 45 CFU/g in chicken carcass. Multidrug-resistant profiles were observed in 33 (39.2%) C. jejuni isolates (from 27 chicken carcasses) and 57 (86.4%) C. coli isolates (from 30 chicken carcasses). One dominant ST (ST6322) and one dominant clonal complex (CC828) consisting of multidrug-resistant C. coli isolates were identified. Our findings showed a high prevalence of Campylobacter contamination in retail chicken carcasses, which could be a source of exposure to multidrug-resistant isolates for consumers. This study provided baseline enumeration data for the quantitative risk assessment and evaluation of new control measures of Campylobacter contamination in retail chicken products in China.

Temporal and Spatial Variation in the Abundance of Total and Pathogenic Vibrio parahaemolyticus in Shellfish in China

We investigated the abundance of total and pathogenic Vibrio parahaemolyticus in shellfish sampled from four provinces in China during May 2013 and March 2014 using the most probable number-polymerase chain reaction (MPN-PCR) method. Total V. parahaemolyticus was detected in 67.7% of 496 samples. A total of 38.1% and 10.1% of samples exceeded 1,000 MPN g-1 and 10,000 MPN g-1, respectively. V. parahaemolyticus densities followed a seasonal and geographical trend, with Guangxi and Sichuan shellfish possessing total V. parahaemolyticus levels that were 100-fold higher than those of the Liaoning and Shandong regions. Moreover, the levels of V. parahaemolyticus were at least 10-fold higher in the summer and autumn than in the cooler seasons. Pathogenic V. parahaemolyticus levels were generally lower than total V. parahaemolyticus levels by several log units and tended to be high in samples contaminated with high total V. parahaemolyticus levels. The aqua farms had a lower prevalence but higher abundance of total V. parahaemolyticus compared to retail markets. The catering markets showed the lowest levels of total V. parahaemolyticus, but 20.0% of samples exceeded 1,000 MPN g-1. The levels of both total and pathogenic V. parahaemolyticus in oysters were higher than in clams. The log-transformed abundance of V. parahaemolyticus was significantly correlated with both water temperature and air temperature but not water salinity. These results provide baseline contamination data of V. parahaemolyticus in shellfish in China, which can be applied to local risk assessments to prioritize risk control to key sectors and evaluate the effectiveness of future control measures.

Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Indiana C629, a Carbapenem-Resistant Bacterium Isolated from Chicken Carcass in China.

ABSTRACT The carbapenem-resistant Salmonella enterica subsp. enterica serovar Indiana strain C629 was isolated from a chicken carcass collected from a slaughterhouse in Qingdao, China. The complete genome sequence of C629 contains a circular 4,791,723-bp chromosome and a circular 210,106-bp plasmid. Genes involved in carbapenem resistance of this bacterium were identified by whole-genome analysis.

Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale

Genetic information about Enterococcus hirae is limited, a feature that has compromised our understanding of these clinically challenging bacteria. In this study, comparative analysis was performed of E. hirae R17, a daptomycin‐resistant strain isolated from pork purchased from a retail market in Beijing, China, and three other enterococcal genomes (Enterococcus faecium DO, Enterococcus faecalis V583, and E. hirae ATCC™9790). Some 1,412 genes were identified that represented the core genome together with an additional 139 genes that were specific to E. hirae R17. The functions of these R17 strain‐specific coding sequences relate to the COGs categories of carbohydrate transport and metabolism and transcription, a finding that suggests the carbohydrate utilization capacity of E. hirae R17 may be more extensive when compared with the other three bacterial species (spp.). Analysis of genomic islands and virulence genes highlighted the potential that horizontal gene transfer played as a contributor of variations in pathogenicity in this isolate. Drug‐resistance gene prediction and antibiotic susceptibility testing indicated E. hirae R17 was resistant to several antimicrobial compounds, including bacitracin, ciprofloxacin, daptomycin, erythromycin, and tetracycline, thereby limiting chemotherapeutic treatment options. Further, tolerance to biocides and metals may confer a phenotype that facilitates the survival and adaptation of this isolate against food preservatives, disinfectants, and antibacterial coatings. The genomic plasticity, mediated by IS elements, transposases, and tandem repeats, identified in the E. hirae R17 genome may support adaptation to new environmental niches, such as those that are found in hospitalized patients. A predicted transmissible plasmid, pRZ1, was found to carry several antimicrobial determinants, along with some predicted pathogenic genes. These data supported the previously determined phenotype confirming that the foodborne E. hirae R17 is a multidrug‐resistant pathogenic bacterium with evident genome plasticity and environmental adaptability.

Prevalence and Molecular Characteristics of Extended-Spectrum β-Lactamase Genes in Escherichia coli Isolated from Diarrheic Patients in China

Background: The emergence and spread of antimicrobial resistance has become a major global public health concern. A component element of this is the spread of the plasmid-encoded extended-spectrum b-lactamase (ESBL) genes, conferring resistance to third-generation cephalosporins. The purpose of this study was to investigate the molecular characteristics of ESBL-encoding genes identified in Escherichia coli cultured from diarrheic patients in China from 2013 to 2014. Materials and Methods: A total of 51 E. coli were confirmed as ESBL producers by double-disk synergy testing of 912 E. coli isolates studied. Polymerase chain reaction (PCR) and DNA sequencing were performed to identify the corresponding ESBL genes. Susceptibility testing was tested by the disk diffusion method. Plasmids were typed by PCR-based replicon typing and their sizes were determined by S1-nuclease pulsed-field gel electrophoresis. Multi-locus sequence typing (MLST) and phylogrouping were also performed. Broth mating assays were carried out for all isolates to determine whether the ESBL marker could be transferred by conjugation. Results: Of the 51 ESBL-positive isolates identified, blaCTX-M, blaTEM, blaOXA, and blaSHV were detected in 51, 26, 3, 1 of these isolates, respectively. Sequencing revealed that 7 blaCTX-M subtypes were detected, with blaCTX-M-14 being the most common, followed by blaCTX-M-79 and blaCTX-M-28. Of the 26 TEM-positive isolates identified, all of these were blaTEM-1 genotypes. All isolates contained one to three large plasmids and 10 replicon types were detected. Of these, IncFrep (n = 50), IncK/B (n = 31), IncFIB (n = 26), IncB/O (n = 14), and IncI1-Ir (n = 8) replicon types were the predominating incompatibility groups. Twenty-six isolates demonstrated the ability to transfer their cefotaxime resistance marker at high transfer rates. MLST typing identified 31 sequence types and phylogenetic grouping showed that 12 of the 51 donor strains belonged to phylogroup B2. Conclusion: This study highlights the diversity of the ESBL producing E. coli and also the diversity of ESBL genes and plasmids carrying these genes in China, which poses a threat to public health.

Complete Genome Sequence of Enterococcus hirae R17, a Daptomycin-Resistant Bacterium Isolated from Retail Pork in China.

ABSTRACT Daptomycin-resistant Enterococcus hirae R17 was isolated from retail pork sold at a free-trade market in Beijing, China. The complete genome sequence of R17 contains a circular 2,886,481-bp chromosome and a circular 73,574-bp plasmid. Genes involved in cell envelope homeostasis of this bacterium were identified by whole-genome analysis.

Effects of metal and metalloid pollutants on the microbiota composition of feces obtained from twelve commercial pig farms across China

Understanding the metal and metalloid contamination and microbiota composition of pig feces is an important step required to support the design and implementation of effective pollution control and prevention strategies. A survey was implemented in 12 locations across China to investigate the content of metals and metalloids, and the main composition of the microbial communities of commercially reared pigs during two growth periods, defined as the early (Q group) and the later fattening growth phases (H group). These data showed widespread Al, Mn, Cu, Zn, and Fe pollution in pig feces. The concentration of Zn in the Q group feces was nearly two times higher than the levels measured in the H group. The microbial composition of the Q group exhibited greater richness of operational taxonomic units (OTUs) and fewer bacteria associated with zoonotic diseases compared with the microbial composition of the H group. Spearman rank correlation analysis showed that Cu and northern latitudes had a significant positive effect on the richness of bacterial communities in pig feces. Zn and Cd exhibited the biggest impact on microbial community composition based on canonical correspondence analysis. Functional metagenomic prediction indicated that about 0.8% genes present in the pig feces bacteria community are related to human diseases, and significantly more predicted pathogenic genes were detected in the H group than in the Q group. These results support the need to monitor heavy metal contamination and to control for zoonotic pathogens disseminated from pig feces in Chinese pig farms.