Advanced Search

Preplanned Studies: Dissemination of Antibiotic Resistance Genes Among Patients with Diarrhea — Freetown, Sierra Leone, 2018

View author affiliations
  • Summary

    What is already known about this topic?

    Antibiotic resistance (AR) is a serious public health threat worldwide. However, the AR and antibiotic resistance genes (ARGs) data from West Africa, especially from Sierra Leone, are limited.

    What is added by this report?

    The study revealed ARGs’ common dissemination, and multiplex antibiotic resistance genes in one sample. Genes blaNDM and blaOXA-48-like were first discovered in Sierra Leone.

    What are the implications for public health practice?

    Basic information is provided for AR research and surveillance and highlights that effective AR surveillance among diarrhea patients is necessary for Sierra Leone and West Africa.

  • loading...
  • Funding: Supported by the National Key Research and Development Program of China (2020YFE0205700, 2022YFC2303900), the major projects of the National Natural Science Foundation of China (22193064)
  • [1] Wang LL, Wang XC, Pang MF, Hu XQ, Qi XP, Dong XP. The practice of the public health cooperation in the republic of Sierra Leone: contributions and experiences. China CDC Wkly 2020;2(2):28 − 31. http://dx.doi.org/10.46234/ccdcw2020.007CrossRef
    [2] Ssekatawa K, Byarugaba DK, Wampande E, Ejobi F. A systematic review: the current status of carbapenem resistance in East Africa. BMC Res Notes 2018;11(1):629. http://dx.doi.org/10.1186/s13104-018-3738-2CrossRef
    [3] Bernabé KJ, Langendorf C, Ford N, Ronat JB, Murphy RA. Antimicrobial resistance in West Africa: a systematic review and meta-analysis. Int J Antimicrob Agents 2017;50(5):629 − 39. http://dx.doi.org/10.1016/j.ijantimicag.2017.07.002CrossRef
    [4] Che J, Lu JX, Li WG, Zhang YF, Zhao XF, Yuan M, et al. A new high-throughput real-time PCR assay for the screening of multiple antimicrobial resistance genes in broiler fecal samples from China. Biomed Environ Sci 2019;32(12):881 − 92. http://dx.doi.org/10.3967/bes2019.111CrossRef
    [5] Tanfous FB, Raddaoui A, Chebbi Y, Achour W. Epidemiology and molecular characterisation of colistin-resistant Klebsiella pneumoniae isolates from immunocompromised patients in Tunisia. Int J Antimicrob Agents 2018;52(6):861 − 5. http://dx.doi.org/10.1016/j.ijantimicag.2018.08.022CrossRef
    [6] Said HS, Benmahmod AB, Ibrahim RH. Co-production of AmpC and extended spectrum beta-lactamases in cephalosporin-resistant Acinetobacter baumannii in Egypt. World J Microbiol Biotechnol 2018;34(12):189. http://dx.doi.org/10.1007/s11274-018-2571-zCrossRef
    [7] Lakoh S, Li LT, Sevalie S, Guo XJ, Adekanmbi O, Yang G, et al. Antibiotic resistance in patients with clinical features of healthcare-associated infections in an urban tertiary hospital in Sierra Leone: a cross-sectional study. Antimicrob Resist Infect Control 2020;9(1):38. http://dx.doi.org/10.1186/s13756-020-0701-5CrossRef
    [8] Forson AO, Tsidi WB, Nana-Adjei D, Quarchie MN, Obeng-Nkrumah N. Escherichia coli bacteriuria in pregnant women in Ghana: antibiotic resistance patterns and virulence factors. BMC Res Notes 2018;11(1):901. http://dx.doi.org/10.1186/s13104-018-3989-yCrossRef
    [9] Khalifa HO, Soliman AM, Ahmed AM, Shimamoto T, Nariya H, Matsumoto T, et al. High prevalence of antimicrobial resistance in gram-negative bacteria isolated from clinical settings in Egypt: recalling for judicious use of conventional antimicrobials in developing nations. Microb Drug Resist 2019;25(3):371 − 85. http://dx.doi.org/10.1089/mdr.2018.0380CrossRef
    [10] Kanzari L, Ferjani S, Saidani M, Hamzaoui Z, Jendoubi A, Harbaoui S, et al. First report of extensively-drug-resistant Proteus mirabilis isolate carrying plasmid-mediated blaNDM-1 in a Tunisian intensive care unit. Int J Antimicrob Agents 2018;52(6):906 − 9. http://dx.doi.org/10.1016/j.ijantimicag.2018.06.009CrossRef
  • TABLE 1.  Information of diarrheal stool surveillance samples collected from six sentinel hospitals in Sierra Lenoe, 2018.

    Month of collectionSample numberSentinel hospital
    May2MHOS (2)
    June9SZ (1), LH (8)
    July10SZ (1), LH (3), EH (6)
    August9SZ (6), LH (3)
    September5SZ (3), EH (2)
    October10LH (3), WH (5), RH (2)
    November9SZ (8), LH (1)
    December2SZ (1), LH (1)
    Subtotal56MHOS (2), SZ (20), LH (19), EH (8), WH (5), RH (2)
    Abbreviation: SZ=Sierra Leone-China Friendship Hospital; LH=Lumley Hospital; EH=Emergency Hospital; WH=Waterloo Hospital; RH=Rokupa Government Hospital; MHOS=Ministry of Health of Sierra Leone.
    Download: CSV

    TABLE 2.  Positivity information of ARGs/ARG groups detected by real-time PCR in 56 acute diarrheal stool samples from Freetown in Sierra Leone, 2018.

    ARGNumber of positive samples (%)ARGNumber of positive samples (%)
    blaNDM6 (10.7)cfr0 (0)
    blaCTX-M A0 (0)fexA0 (0)
    blaCTX-M E32 (57.1)mcr-10 (0)
    blaSHV A9 (16.1)armA0 (0)
    blaOXA-48-like1 (1.8)aac(6')-Ie-aph(2')-Ia0 (0)
    blaPER1 (1.8)tetA44 (78.6)
    qnrA1 (1.8)intI152 (92.9)
    qnrS0 (0)ISCR130 (53.6)
    aac(6')-Ib-cr0 (0)
    Abbreviation: ARG=antibiotic resistance gene.
    Download: CSV

    TABLE 3.  Coexistence of ARGs/ARG groups in 56 acute diarrheal stool samples from Freetown in Sierra Leone, 2018.

    Number of ARGsCoexisting ARGs/ARG groupsNumber of samplesTotal number of samples
    1intI166
    2blaCTX-M E-intI138
    intI1-ISCR12
    tetA-intI13
    3blaCTX-M E-blaSHV A-tetA218
    blaCTX-M E-intI1-ISCR11
    blaCTX-M E-tetA-intI14
    blaNDM-intI1-ISCR11
    tetA-intI1-ISCR110
    4blaCTX E-tetA-intI1-ISCR1614
    blaCTX-M E-blaSHV A-tetA-intI12
    blaCTX-M E-tetA-intI1-ISCR15
    blaSHV A-blaOXA-48 like-tetA-intI11
    5blaCTX-M E-blaSHV A-tetA-intI1-ISCR136
    blaNDM-blaCTX E-tetA-intI1-ISCR11
    blaNDM-blaCTX-M E-tetA-intI1-ISCR12
    7blaNDM-blaCTX E-blaPER-qnrA-tetA-intI1-ISCR112
    blaNDM-blaCTX-M E-blaSHVA-qnrS-tetA-intI1-ISCR11
    Subtotal56
    Abbreviation: ARG=antibiotic resistance gene.
    Download: CSV

Citation:

通讯作者: 陈斌, bchen63@163.com
  • 1. 

    沈阳化工大学材料科学与工程学院 沈阳 110142

  1. 本站搜索
  2. 百度学术搜索
  3. 万方数据库搜索
  4. CNKI搜索
Turn off MathJax
Article Contents

Article Metrics

Article views(4615) PDF downloads(55) Cited by()

Share

Related

Dissemination of Antibiotic Resistance Genes Among Patients with Diarrhea — Freetown, Sierra Leone, 2018

View author affiliations

Summary

What is already known about this topic?

Antibiotic resistance (AR) is a serious public health threat worldwide. However, the AR and antibiotic resistance genes (ARGs) data from West Africa, especially from Sierra Leone, are limited.

What is added by this report?

The study revealed ARGs’ common dissemination, and multiplex antibiotic resistance genes in one sample. Genes blaNDM and blaOXA-48-like were first discovered in Sierra Leone.

What are the implications for public health practice?

Basic information is provided for AR research and surveillance and highlights that effective AR surveillance among diarrhea patients is necessary for Sierra Leone and West Africa.

  • 1. State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing Municipality, China
  • 2. Sierra Leone-China Friendship Biological Safety Laboratory, Chinese Center for Disease Control and Prevention, Freetown, Sierra Leone and Beijing Municipality, China
  • 3. National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research, Shanghai Municipality, China
  • 4. National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing Municipality, China
  • 5. Center for Global Public Health, Chinese Center for Disease Control and Prevention, Beijing Municipality, China
  • 6. Ministry of Health and Sanitation, Freetown, Sierra Leone
  • Corresponding authors:

    Biao Kan, kanbiao@icdc.cn

    Doris Harding, dorisharding@gmail.com

    Xiaoping Dong, dongxp238@sina.com

  • Funding: Supported by the National Key Research and Development Program of China (2020YFE0205700, 2022YFC2303900), the major projects of the National Natural Science Foundation of China (22193064)
  • Online Date: December 09 2022
    Issue Date: December 09 2022
    doi: 10.46234/ccdcw2022.221
  • Antibiotic resistance (AR), a major public health problem in developed, developing, and undeveloped countries, has increased with rapid globalization. Due to logistical issues and a rapidly migrating population in Africa, AR has become a complicated issue for the general public. Although medical hygiene and public health system in Africa have improved, and the use of antibiotics has also increased in many African countries (1-3), AR has become a prevalent issue. Sierra Leone is categorized as one of the most undeveloped countries in the world with bacterial diarrhea as a common and major disease throughout the country. Antibiotics are an effective treatment option for this disease. Since the medical and public health system in Sierra Leone is still in its infancy, the available data related to AR are limited. Here, 17 antibiotic resistance genes (ARGs)/antibiotic resistance gene (ARG) groups in the stool samples of 56 diarrhea patients were detected in Freetown, Sierra Leone, 2018. Nine ARGs/ARG groups were detected as positive, and most of the samples carried at least 2 ARGs/ARG groups. Two stool samples carrying 7 ARGs/ARG groups highlighted the complexity of ARGs in Freetown, Sierra Leone. Genes blaNDM and blaOXA-48-like are the first reported ARGs from Sierra Leone. The diversity and dissemination data of ARGs in Freetown of Sierra Leone are expected to complement the antibiotic resistance data of West Africa and highlight the need for continued monitoring of antibiotic resistance.

    A total of 56 acute diarrheal stool samples were obtained from six sentinel hospitals of Freetown, Sierra Leone between May 2018 and December 2018 (Table 1). Most samples were collected in July and October (n=10, each), while only two samples were collected in May and December.

    Month of collectionSample numberSentinel hospital
    May2MHOS (2)
    June9SZ (1), LH (8)
    July10SZ (1), LH (3), EH (6)
    August9SZ (6), LH (3)
    September5SZ (3), EH (2)
    October10LH (3), WH (5), RH (2)
    November9SZ (8), LH (1)
    December2SZ (1), LH (1)
    Subtotal56MHOS (2), SZ (20), LH (19), EH (8), WH (5), RH (2)
    Abbreviation: SZ=Sierra Leone-China Friendship Hospital; LH=Lumley Hospital; EH=Emergency Hospital; WH=Waterloo Hospital; RH=Rokupa Government Hospital; MHOS=Ministry of Health of Sierra Leone.

    Table 1.  Information of diarrheal stool surveillance samples collected from six sentinel hospitals in Sierra Lenoe, 2018.

    A total of 17 ARGs/ARG groups, including 249 genes types/subtypes, were detected using the probe method of real-time PCR. The real-time PCR primers and minor groove binder (MGB)-conjugated fluorescent probes used were reported elsewhere (4), except the tet(A) gene. The tet(A) gene was detected using the forward primer (5'-CAT TCT GCA TTC ACT CGC CCA GGC AAT GAT-3'), reverse primer (5'-GAA GCA AGC AGG ACC ATG ATC GGG AAC GC-3'), and the 6-carboxyfluorescein (FAM)-labeled tetA-specific probe (5'-GAT TGC CGA CGG CAC AGG CTA CAT CCT GCT TG-3').

    Seventeen ARGs/ARG groups were detected among the 56 diarrhea stool samples, and the ARG positive detection rates ranged from 0 to 92.9% (Table 2). intI1, ISCR1, blaCTX-M E groups, and tetA gene positive rates were over 50%. Eight ARGs/ARG groups were not detected, including blaCTX-M A, qnrS, aac(6')-Ib-cr, cfr, fexA, mcr-1, armA, and aac(6')-Ie-aph(2')-Ia. At least one ARG/ ARG group was detected from all of the stool samples, and most samples showed ARG/ ARG group coexistence. Forty-two (75%) of the stool samples carried more than two ARGs/ARG groups, and two samples carried seven ARGs/ARG groups. Seventeen different ARG coexistent types were detected. Carbapenem resistance encoding genes blaNDM and blaOXA-48-like were also detected. blaNDM and blaSHV A genes coexisted in some stool samples. ISCR1 and intI1 genes always coexisted with other ARGs/ARG groups. blaNDM gene group coexisted with more than four other ARGs/ARG groups and was detected in five stool samples. Gene group blaOXA-48-like was the first group to be observed in Sierra Leone. Further details of ARGs/ARG groups’ coexistence are summarized in Table 3.

    ARGNumber of positive samples (%)ARGNumber of positive samples (%)
    blaNDM6 (10.7)cfr0 (0)
    blaCTX-M A0 (0)fexA0 (0)
    blaCTX-M E32 (57.1)mcr-10 (0)
    blaSHV A9 (16.1)armA0 (0)
    blaOXA-48-like1 (1.8)aac(6')-Ie-aph(2')-Ia0 (0)
    blaPER1 (1.8)tetA44 (78.6)
    qnrA1 (1.8)intI152 (92.9)
    qnrS0 (0)ISCR130 (53.6)
    aac(6')-Ib-cr0 (0)
    Abbreviation: ARG=antibiotic resistance gene.

    Table 2.  Positivity information of ARGs/ARG groups detected by real-time PCR in 56 acute diarrheal stool samples from Freetown in Sierra Leone, 2018.

    Number of ARGsCoexisting ARGs/ARG groupsNumber of samplesTotal number of samples
    1intI166
    2blaCTX-M E-intI138
    intI1-ISCR12
    tetA-intI13
    3blaCTX-M E-blaSHV A-tetA218
    blaCTX-M E-intI1-ISCR11
    blaCTX-M E-tetA-intI14
    blaNDM-intI1-ISCR11
    tetA-intI1-ISCR110
    4blaCTX E-tetA-intI1-ISCR1614
    blaCTX-M E-blaSHV A-tetA-intI12
    blaCTX-M E-tetA-intI1-ISCR15
    blaSHV A-blaOXA-48 like-tetA-intI11
    5blaCTX-M E-blaSHV A-tetA-intI1-ISCR136
    blaNDM-blaCTX E-tetA-intI1-ISCR11
    blaNDM-blaCTX-M E-tetA-intI1-ISCR12
    7blaNDM-blaCTX E-blaPER-qnrA-tetA-intI1-ISCR112
    blaNDM-blaCTX-M E-blaSHVA-qnrS-tetA-intI1-ISCR11
    Subtotal56
    Abbreviation: ARG=antibiotic resistance gene.

    Table 3.  Coexistence of ARGs/ARG groups in 56 acute diarrheal stool samples from Freetown in Sierra Leone, 2018.

    • From this short-term surveillance, serious AR has already been noticed, with multidrug resistance and first reported carbapenemase-encoding genes blaNDM and blaOXA-48-like from Sierra Leone.

      Isolating bacteria from stool samples is a complex process that includes the probability of bacterial culture having some variable and uncontrollable parameters. In addition, due to the long purchasing period of ordering and receiving special reagents in Sierra Leone, many bacteria cannot be isolated and studied for AR. Considering the existing non-affluent laboratory infrastructure and equipment of Sierra Leone’s lab, ARGs/ARG groups were directly detected from the stool samples by real-time PCR.

      Previous studies about the rapid detection of ARGs by real-time PCR among samples are limited. These studies mainly reported ARG detection among isolates. For instance, a report from Tunisia reported that class 1 integrons, blaTEM, blaCTX-M-1, blaOXA-1, and blaCMY-16 were positive in Klebsiella pneumoniae isolates, and the blaOXA-48 gene was associated with many other ARGs (5). A study from Egypt demonstrated a high prevalence of resistance to β-lactam antibiotics through ESBLs and AmpC β-lactamases production among the Acinetobacter baumannii isolates (6). Rapid detection of ARGs by real-time PCR may reveal the existence of ARGs/ARG groups in diarrhea patients more rapidly and objectively. Our study provided a convenient and accurate method for AR routine surveillance in Sierra Leone, Africa.

      Some highly prevalent ARGs/ARG groups were previously reported from Africa, such as tet(A), int1, and blaCTX-M E. A study that included patients with clinical features of healthcare-associated infections in an urban tertiary hospital in Sierra Leone showed a resistance rate of 1.3% for carbapenem-resistant Enterobacteriaceae but did not reveal related ARGs (7). Carbapenemase-encoding genes blaNDM and blaOXA-48-like were the first reported in Sierra Leone, West Africa. Some investigators have isolated carbapenem-resistant Enterobacteriaceae isolates carrying blaNDM and blaOXA-23 genes from various east-African countries including Kenya, Uganda, Tanzania, Ethiopia, and Rwanda (2). The ARGs in our collected stool samples included tetracycline-, fluoroquinolones-, carbapenem-resistance genes, ESBLs and integrase 1 encoding genes. The findings of this study are consistent with those of previously published studies and demonstrate that carbapenemase genes are disseminated in West Africa. Many common ARGs/ARG groups may also spread in Sierra Leone, which could reduce the effectiveness of anti-infective treatment, accelerating the spread of AR. The presence of the carbapenem-resistance gene along with other ARGs in stool samples is critical and may result in the dissemination of ARGs.

      Coexistence of multiple ARGs/ARG groups was discovered in the tested samples. 89.3% (50/56) and 75.0% (42/56) of the samples carried more than two and more than three groups of ARGs, respectively. Two stool samples carried seven types of ARGs, simultaneously. Six stool samples carried a single intI1 gene that could contribute to ARGs transmission and integration (5). The fact that no other ARGs/ARG groups were detected simultaneously might be because of the limited ARG groups screened in this study. Detection of more ARGs should be the focus of future studies. This study found the diversity and complexity of ARGs in stool samples obtained from Freetown, Sierra Leone. Previous studies demonstrated that multidrug resistance had spread in some African countries. A study in Ghana found that >50% and 7.3% of the Escherichia coli isolates obtained from pregnant women were positive for blaTEM and aph(3)-Ia, respectively (8). A study from Egypt revealed that 75.4% of the tested gram-negative isolates harbored at least one extended-spectrum $ \beta $-lactamase-encoding gene — blaCTX-M, and blaSHV (9). In Tunisia, an extensively drug-resistant clinical isolate of Proteus mirabilis carried plasmid-mediated resistance to carbapenems (blaNDM-1), cephalosporins (blaCMY-4), aminoglycosides (aph3-VIa and aph3-Ia), and fluoroquinolones (qnrA6) (10). The dissemination of ARGs in Africa is alarming and should be given more attention in routine surveillance.

      Our investigation revealed that the common types of ARGs detected in diarrheal stool samples collected in this study included tet(A), int1, ISCR1, and blaCTX-M E. These ARGs might be related to the use or misuse of the above antibiotics. Although no carbapenems antibiotics were available for sale in any hospital or pharmacy during our investigation, carbapenemase-encoding genes blaNDM and blaOXA-48-like were detected in the diarrheal stool samples. The findings of this study provide the direction of research for future studies. By expanding on the origins of sample collection, types of ARGs screened, and antibiotics investigated in Sierra Leone, further detailed insights can be obtained about the dynamics of AR in Sierra Leone.

      This small-scale study revealed AR present situation among a panel of diarrheal stool samples collected from Sierra Leone, but was also subject to some limitations. First, only 56 of stool samples from several public sentinel hospitals in Freetown were involved in this study, because of restrictions for medical technology, sample transportation, and socioeconomic and behavioral factors. Second, limited ARGs were detected here because of long purchase period of special reagents in Africa. AR informantion of int1, ISCR1, tet(A), blaCTX-M E common dissemination, blaNDM gene existence, and multiplex ARGs in one sample, provides basic information for AR research and surveillance and highlights that continued effective AR surveillance is necessary for Sierra Leone and West Africa.

    • Sierra Leonean staff for their wonderful work in the Sierra Leone-China Friendship Biological Safety Laboratory and Sierra Leone-China Second Phase of the Fixed Biological Safety Laboratory Technical Cooperation Project.

Reference (10)

Citation:

Catalog

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return