Campylobacter coli isolates derived from chickens in Senegal: Diversity, genetic exchange with Campylobacter jejuni and quinolone resistance

Molecular Characterization and Antibiotic Resistant Profiles of Campylobacter Species Isolated From Poultry and Diarrheal Patients in Southeastern China 2017-2019

Campylobacter is a zoonotic pathogen that causes foodborne diarrheal illness globally. To better understand health risks in Southeastern China, Campylobacter spp. were surveyed in humans and representative poultry products over 3 years. One hundred and ninety-five representative isolates (n = 148, Campylobacter jejuni; n = 45, Campylobacter coli; n = 2 Campylobacter hyointestinalis) were examined for genetic relatedness and antimicrobial susceptibility. Nearly all Campylobacter isolates (99.0%, 193/195) were resistant to at least one class of antimicrobials, and 45.6% (89/195) of the isolates exhibited multidrug resistance. Genotypic analysis revealed high diversity among tested strains. Multilocus sequence typing (MLST) displayed 120 sequence types (STs) including 42 novel STs being added to the PubMLST international database. Sixty-two STs belonged to 16 previously characterized clonal complexes (CCs), of which CC-21, CC-45, CC-464, CC-574, CC-353, and CC-828 were most frequently identified. In addition, pulsed-field gel electrophoresis (PFGE) fingerprinting resulted in 66 PFGE SmaI patterns among the 125 isolates, with eight patterns shared between human and poultry sources. Subtyping data did not correlate with antimicrobial resistance phenotypes. Taken together, this large-scale surveillance study highlights high antimicrobial resistance and molecular features of Campylobacter isolates in Southeastern China.

Antibiotic Resistance in Food Animals in Africa: A Systematic Review and Meta-Analysis

OBJECTIVES

This study critically reviewed the published literature and performed a meta-analysis to determine the overall burden of antibiotic-resistant bacteria in food animals in Africa.

METHODS

English and French published articles indexed in EBSCOhost, PubMed, Web of Science, and African Journals Online were retrieved, with searches being conducted up to August, 2015. Data were pooled and meta-analysis performed using a random-effects model, and the results are described as event rates.

RESULTS

According to the predefined inclusion and exclusion criteria, 17 articles out of the 852 retrieved were eligible for the qualitative and quantitative analysis. The studies included were mainly conducted in Nigeria, with Escherichia coli, Salmonella spp., and Campylobacter spp. being the main bacteria. The pooled estimates showed high level of antibiotic resistance (ABR) (86%; p < 0.001) and multidrug resistance (73%; p = 0.003).

CONCLUSION

Our results suggest that ABR is substantively prevalent and poses a serious threat for food safety and security in Africa. These findings shed light on areas for future research concerning antibiotic-resistant and multidrug-resistant bacteria in food animals as etiological agents of infectious diseases in humans. They further yielded some interesting findings on the burden of ABR that could be useful in developing measures to contain this threat in the farm-to-plate continuum in Africa.

Multilocus sequence typing of Campylobacter jejuni and Campylobacter coli isolates from poultry, cattle and humans in Nigeria

AIMS

To determine the genetic diversity of Campylobacter jejuni and Campylobacter coli isolates from Nigeria and to identify the association between multilocus sequence types and hosts (poultry, cattle and humans).

METHODS AND RESULTS

Isolates were identified using multiplex PCR assays. Multilocus sequence typing (MLST) was used to determine the genetic diversity of 36 Camp. jejuni and 24 Camp. coli strains isolated from poultry, cattle and humans. Of the 36 Camp. jejuni genotyped, 21 sequence types (ST) were found, 9 (43%) were new while of the 24 Camp. coli isolates genotyped, 22 STs were identified with 14 (64%) being new. The most prevalent sequence type was ST1932 followed by ST1036 and ST607 while the prevalent clonal complexes were CC-828, CC-460 and CC-353.

CONCLUSIONS

Campylobacter isolates from Nigeria were found to be diverse with novel genotypes. There was overlap of CC-828, CC-460 and CC-353 between the poultry, cattle and human isolates. Genetic exchange was also detected in two of the Camp. coli isolates.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study highlights the genetic diversity of Campylobacter strains in Nigeria, demonstrating that Camp. jejuni and Camp. coli isolates are diverse and have both local and global strains. The predominant sequence types and clonal complexes found in this study differ from other countries; this exemplifies that different predominant Campylobacter populations exist between countries.

Fluoroquinolone-Resistant Enteric Bacteria in Sub-Saharan Africa: Clones, Implications and Research Needs

Fluoroquinolones came into widespread use in African countries in the early 2000s, after patents for the first generation of these drugs expired. By that time, quinolone antibacterial agents had been used intensively worldwide and resistant lineages of many bacterial species had evolved. We sought to understand which Gram negative enteric pandemic lineages have been reported from Africa, as well as the nature and transmission of any indigenous resistant clones. A systematic review of articles indexed in the Medline and AJOL literature databases was conducted. We report on the findings of 43 eligible studies documenting local or pandemic fluoroquinolone-resistant enteric clones in sub-Sahara African countries. Most reports are of invasive non-typhoidal Salmonella and Escherichia coli lineages and there have been three reports of cholera outbreaks caused by fluoroquinolone-resistant Vibrio cholerae O1. Fluoroquinolone-resistant clones have also been reported from commensals and animal isolates but there are few data for non-Enterobacteriaceae and almost none for difficult-to-culture Campylobacter spp. Fluoroquinolone-resistant lineages identified in African countries were universally resistant to multiple other classes of antibacterial agents. Although as many as 972 non-duplicate articles refer to fluoroquinolone resistance in enteric bacteria from Africa, most do not report on subtypes and therefore information on the epidemiology of fluoroquinolone-resistant clones is available from only a handful of countries in the subcontinent. When resistance is reported, resistance mechanisms and lineage information is rarely investigated. Insufficient attention has been given to molecular and sequence-based methods necessary for identifying and tracking resistant clones in Africa and more research is needed in this area.

Multilocus sequence typing reveals genetic diversity of foodborne Arcobacter butzleri isolates in the North of Spain

The emerging pathogen Arcobacter butzleri is being increasingly isolated from different animal food products but the routes of its transmission to human are not well established yet. Typing methods would be useful in gaining such knowledge. Here we report the great genetic diversity observed among A. butzleri isolates from different food products. Forty-five isolates were analyzed by Multilocus Sequence Typing (MLST). A total of 157 alleles were identified across all seven loci, ranging from 16 alleles at glnA to 31 at glyA. MLST differentiated the isolates into 34 sequence types (STs), with the majority of isolates containing a unique sequence type. Seventy-four new alleles were identified, which resulted in the assignment of 33 new STs. No association of alleles or STs with food source was observed. For the first time, lateral gene transfer from Arcobacter skirrowii to A. butzleri at the glyA locus is also reported.

Multilocus sequence typing of Campylobacter jejuni and Campylobacter coli strains isolated from environmental waters in the Mediterranean area

Campylobacter jejuni and Campylobacter coli are important animal-related waterborne pathogens that are distributed worldwide. To further understand Campylobacter populations in water from the Mediterranean area, the genetic diversity of environmental strains was analyzed using multilocus sequence typing (MLST). MLST was also used to determine the potential geographical differences between these bacterial strains and other campylobacters isolated worldwide. The typing study was conducted using 58 strains isolated from the Llobregat river and other water sources, such as urban sewage, animal wastewater and clinical samples. Thirty-nine different sequence types were obtained; eight of these sequences were described for the first time in this study, suggesting the presence of local strains. The identified C. jejuni strains were the most diverse population, whereas the identified C. coli strains showed a high clonal structure, which clustered most of the sequence types into a few clonal complexes. The strains were not exclusively related to specific water sources. However, comparing the identified strains with an international database showed that most of the Mediterranean strains that were exclusively isolated from environmental waters have previously been isolated from similar sources, particularly those obtained from river water. Additional studies, including those in different geographical areas using a wide range of Campylobacter sources, are required to improve the global knowledge concerning Campylobacter dissemination in the environment.

MLST genotypes and antibiotic resistance of Campylobacter spp. isolated from poultry in Grenada

This study determined whether multilocus sequence types (MLST) of Campylobacter from poultry in 2 farms in Grenada, West Indies, differed by farm, antimicrobial resistance and farm antibiotic use. Farm A used fluoroquinolones in the water and Farm B used tetracyclines. The E-test was used to determine resistance of isolates to seven antibiotics. PCR of the IpxA gene confirmed species and MLST was used to characterize 38 isolates. All isolates were either C. jejuni or C. coli. Farm antibiotic use directly correlated with antimicrobial resistance of Campylobacter isolates. Almost 80% of the isolates from Farm A were fluoroquinolone resistant and 17.9% of the isolates from Farm B were fluoroquinolone resistant. All Campylobacter isolates from Farm A were tetracycline sensitive, whereas 35.7% of isolates from Farm B were tetracycline resistant. Six previously recognized sequence types (STs) and 2 novel STs were identified. Previously recognized STs were those overwhelmingly reported from poultry and humans globally. Isolates with the same ST did not always have the same antibiotic resistance profile. There was little ST overlap between the farms suggesting that within-farm transmission of Campylobacter genotypes may dominate. MLST typing was useful for tracking Campylobacter spp. among poultry units and can help elucidate Campylobacter host-species population structure and its relevance to human health.

Evolution of an agriculture-associated disease causing Campylobacter coli clade: evidence from national surveillance data in Scotland

The common zoonotic pathogen Campylobacter coli is an important cause of bacterial gastroenteritis worldwide but its evolution is incompletely understood. Using multilocus sequence type (MLST) data of 7 housekeeping genes from a national survey of Campylobacter in Scotland (2005/6), and a combined population genetic-phylogenetics approach, we investigated the evolutionary history of C. coli. Genealogical reconstruction of isolates from clinical infection, farm animals and the environment, revealed a three-clade genetic structure. The majority of farm animal, and all disease causing genotypes belonged to a single clade (clade 1) which had comparatively low synonymous sequence diversity, little deep branching genetic structure, and a higher number of shared alleles providing evidence of recent clonal decent. Calibration of the rate of molecular evolution, based on within-species genetic variation, estimated a more rapid rate of evolution than in traditional estimates. This placed the divergence of the clades at less than 2500 years ago, consistent with the introduction of an agricultural niche having had an effect upon the evolution of the C. coli clades. Attribution of clinical isolate genotypes to source, using an asymmetric island model, confirmed that strains from chicken and ruminants, and not pigs or turkeys, are the principal source of human C. coli infection. Taken together these analyses are consistent with an evolutionary scenario describing the emergence of agriculture-associated C. coli lineage that is an important human pathogen.

Host association of Campylobacter genotypes transcends geographic variation

Genetic attribution of bacterial genotypes has become a major tool in the investigation of the epidemiology of campylobacteriosis and has implicated retail chicken meat as the major source of human infection in several countries. To investigate the robustness of this approach to the provenance of the reference data sets used, a collection of 742 Campylobacter jejuni and 261 Campylobacter coli isolates obtained from United Kingdom-sourced chicken meat was established and typed by multilocus sequence typing. Comparative analyses of the data with those from other isolates sourced from a variety of host animals and countries were undertaken by genetic attribution, genealogical, and population genetic approaches. The genotypes from the United Kingdom data set were highly diverse, yet structured into sequence types, clonal complexes, and genealogical groups very similar to those seen in chicken isolates from the Netherlands, the United States, and Senegal, but more distinct from isolates obtained from ruminant, swine, and wild bird sources. Assignment analyses consistently grouped isolates from different host animal sources regardless of geographical source; these associations were more robust than geographic associations across isolates from three continents. We conclude that, notwithstanding the high diversity of these pathogens, there is a strong signal of association of multilocus genotypes with particular hosts, which is greater than the geographic signal. These findings are consistent with local and international transmission of host-associated lineages among food animal species and provide a foundation for further improvements in genetic attribution.

Investigation of food and environmental exposures relating to the epidemiology of Campylobacter coli in humans in Northwest England

This study uses multilocus sequence typing (MLST) to investigate the epidemiology of Campylobacter coli in a continuous study of a population in Northwest England. All cases of Campylobacter identified in four Local Authorities (government administrative boundaries) between 2003 and 2006 were identified to species level and then typed, using MLST. Epidemiological information was collected for each of these cases, including food and recreational exposure variables, and the epidemiologies of C. jejuni and C. coli were compared using case-case methodology. Samples of surface water thought to represent possible points of exposure to the populations under study were also sampled, and campylobacters were typed with multilocus sequence typing. Patients with C. coli were more likely to be older and female than patients with C. jejuni. In logistic regression, C. coli infection was positively associated with patients eating undercooked eggs, eating out, and reporting problems with their water supply prior to illness. C. coli was less associated with consuming pork products. Most of the cases of C. coli yielded sequence types described elsewhere in both livestock and poultry, but several new sequence types were also identified in human cases and water samples. There was no overlap between types identified in humans and surface waters, and genetic analysis suggested three distinct clades but with several "intermediate" types from water that were convergent with the human clade. There is little evidence to suggest that epidemiological differences between human cases of C. coli and C. jejuni are a result of different food or behavioral exposures alone.

Campylobacter genotypes from food animals, environmental sources and clinical disease in Scotland 2005/6

A nationwide multi-locus sequence typing (MLST) survey was implemented to analyze patterns of host association among Campylobacter jejuni and Campylobacter coli isolates from clinical disease in Scotland (July 2005-September 2006), food animals (chickens, cattle, sheep, pigs and turkey), non-food animals (wild birds) and the environment. Sequence types (STs) were determined for 5247 clinical isolates and 999 from potential disease sources (augmented with 2420 published STs). Certain STs were over represented among particular sample sets/host groups. These host-associated STs were identified for all sample groups in both Campylobacter species and host associated clonal complexes (groups of related STs) were characterized for C. jejuni. Some genealogical lineages were present in both human disease and food animal samples. This provided evidence for the relative importance of different infection routes/food animal sources in human disease. These results show robust associations of particular genotypes with potential infection sources supporting the contention that contaminated poultry is a major source of human disease.

Genotyping of Campylobacter coli isolated from humans and retail meats using multilocus sequence typing and pulsed-field gel electrophoresis

AIMS

To determine the antimicrobial resistant profiles and clonality of Campylobacter coli isolated from clinically ill humans and retail meats.

METHODS AND RESULTS

A total of 98 C. coli isolates (20 from humans and 78 from retail meats) were phenotypically characterized. Antimicrobial susceptibility testing was done using agar dilution method for ciprofloxacin, gentamicin, erythromycin and doxycycline. Seventy C. coli isolates including humans (n = 20) and retail meats (n = 50) were genotyped by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Resistance to ciprofloxacin was found in 29% and 15% of isolates from retail meats and humans. We observed 61 PFGE profiles using two enzymes (SmaI, KpnI) with an Index of discrimination of 0.99, whereas MLST generated 37 sequence types. Two clonal complexes were identified with 58 (82%) C. coli isolates clustered in the ST-828 complex.

CONCLUSIONS

Resistance to ciprofloxacin and erythromycin was identified in C. coli obtained from retail meats and ill humans. PFGE typing of C. coli isolates was more discriminatory than MLST. Grouping of C. coli isolates (82%) by MLST in ST-828 clonal complex indicates a common ancestry.

SIGNIFICANCE AND IMPACT OF THE STUDY

A high frequency of resistance found to ciprofloxacin and erythromycin is concerning from food safety perspective. PFGE using single or double restriction enzymes was found to be more discriminatory than MLST for genotyping C. coli. Overall, the C. coli populations recovered from humans and retail meats were genotypically diverse.