How scientists can mine wastewater to find drug-resistant bacteria
| May 27, 2023
People often think of wastewater as serving no purpose. But it can be a valuable source of information. Wastewater is increasingly recognised as a significant environmental reservoir for antimicrobial resistance - a growing global public health threat.
Antimicrobials are medicines, including antibiotics and antivirals, used to treat infections in humans, animals and plants. But the excessive use of antimicrobials has resulted in many microorganisms becoming resistant to these important medicines. This, in turn, has led to the development of complicated and sometimes untreatable diseases.
Antimicrobial resistance is expected to kill over 10 million people annually by 2050 if nothing is done to stop it. In sub-Saharan Africa, 23.5 deaths out of every 100,000 are attributed to diseases such as lower respiratory, chest, bloodstream and intra-abdominal infection caused by antimicrobial-resistant organisms.
These organisms are all around us. For instance, research done on pigs in South Africa found resistant bacteria at all the stages of sampling, from the farm to the final packaged meat. Another South African study found that manure from a poultry farm transferred antibiotic-resistant bacteria to the soil. Heavy rainfall could wash these bacteria into nearby rivers. As a result, people who use water from these rivers for drinking and household purposes could get sick.
Wastewater treatment plants receive wastewater from a variety of sources: hospitals, households, industries and farms. This makes the plants useful proxies for determining the burden of antimicrobial resistance in communities. By monitoring wastewater, scientists can determine the types of resistant bacteria circulating in a given population. This approach is becoming the global gold standard for tracking antimicrobial resistance.
But it doesn't seem to have been adopted in many African countries yet. Our recent research looked at studies done on wastewater in African countries between 2012 and 2022. We wanted to identify the challenges in using wastewater surveillance to determine the prevalence of antimicrobial resistance.
We found that using wastewater to study antimicrobial resistance was increasing on the continent. But not in all countries. In most of the studies we found samples were only collected once. This is not sufficient to draw strong conclusions. Furthermore, many studies used only one method to identify resistance in the wastewater. Depending on the method, this either overestimated or underestimated the rate of resistance. With these gaps, studies within the continent could be presenting a false picture of the antimicrobial resistance problem, which could have severe health implications.
We reviewed studies on wastewater-based surveillance of antimicrobial resistance in sub-Saharan Africa. Our study showed that most countries lacked the necessary skills to conduct this research. The lack of skills affected the methods that the studies used, hence the results presented.
Most of the research was done in South Africa. That's largely because most sub-Saharan countries simply do not have enough wastewater treatment plants. Many treat less than 5 per cent of the wastewater they generate. Only a few countries, among them South Africa and neighbouring Botswana, treat 25 per cent to 50 per cent of their wastewater. This means there is more to be learned from these countries.
In South Africa, studies on antimicrobial resistance in wastewater were done in only a few of the provinces. Also, not all the studies were done on wastewater treatment plants. This means the source of the resistance could not be traced. In addition, there were differences in the methods used and the results reported.
We found monitoring challenging even where wastewater treatment plants were available because of the lack of technical skills needed for genomic sequencing. Genomic approaches study the DNA of all the microrganisms in the wastewater, instead of focusing on only a few. Furthermore, there are no standardised approaches to these studies. So, it was difficult to compare findings from different locations.
The absence of wastewater treatment plants in many African countries means that it will be hard for them to actively implement wastewater-based antimicrobial resistance surveillance. Governments must invest in connecting their populations to sewer networks to address this problem. This is crucial for overall hygiene and health. And it will offer important sources of information for researchers trying to detect resistant microorganisms in communities.
Once sewer networks are in place, standardised protocols for assessing antimicrobial resistance in wastewater treatment plants must be established. The protocols should consider the sampling regime and frequency, the organisms targeted, what antibiotics need to be tested, and what methods should be used.
There is also a need to build capacity in sequencing technologies and bioinformatics. This will ensure that there are enough people with the knowledge required to analyse the large volumes of data generated in these studies. Funding bodies must finance researchers in sub-Saharan countries as sequencing technologies are not yet widespread, and the cost of using these facilities is still high.
People may consider wastewater as something undesirable that just needs to be flushed away. But studying this valuable resource could provide early warning about potential disease outbreaks, especially those involving antimicrobial-resistant microorganisms.
[By Akebe Luther King, associate professor, University of KwaZulu-Natal, Afsatou Traore, associate professor, University of Venda, and Natasha Potgieter, executive dean, Faculty of Science, Engineering and Agriculture, University of Venda]
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Jinsi wanasayansi wanavyoweza kuchimba maji taka ili kupata bakteria sugu kwa dawa - Mei 27, 2023 Watu mara nyingi hufikiri maji taka hayana kusudi. Lakini inaweza kuwa chanzo chenye thamani cha habari. Maji ya taka yanatambuliwa zaidi na zaidi kama hifadhi muhimu ya mazingira ya upinzani wa antimicrobial - tishio la afya ya umma la kimataifa linaloongezeka. Antimicrobials ni dawa, ikiwa ni pamoja na antibiotics na antivirals, kutumika kutibu maambukizi katika watu, wanyama na mimea. Lakini matumizi ya kupita kiasi ya dawa za kuua viini yamesababisha viumbe vingi vichache kuwa sugu kwa dawa hizo muhimu. Hilo, kwa upande wake, limesababisha magonjwa magumu na nyakati nyingine yasiyoweza kutibiwa. Inakadiriwa kwamba upinzani wa viini vya kuua wadudu utaua watu milioni 10 kila mwaka kufikia mwaka 2050 ikiwa hakuna kinachofanywa ili kuizuia. Katika nchi za Afrika Kusini mwa Jangwa la Sahara, vifo vya watu 23.5 kati ya kila 100,000 vinatokana na magonjwa kama vile upungufu wa hewa, kifua, damu na maambukizi ya ndani ya tumbo yanayosababishwa na viumbe vinavyopinga dawa za kuua vimelea. Viumbe hawa wako kila mahali karibu nasi. Kwa mfano, utafiti uliofanywa kwenye nguruwe nchini Afrika Kusini uligundua bakteria sugu katika hatua zote za kuchukua sampuli, kutoka shamba hadi nyama ya mwisho iliyofungwa. Uchunguzi mwingine wa Afrika Kusini uligundua kwamba mbolea kutoka shamba la kuku ilihamisha bakteria zisizoweza kutibu viuavijasumu kwenye udongo. Mvua kubwa yaweza kuondoa bakteria hizo katika mito iliyo karibu. Matokeo ni kwamba, watu wanaotumia maji ya mito hiyo kwa ajili ya kunywa na matumizi ya nyumbani wanaweza kuugua. Vituo vya kusafisha maji taka hupokea maji taka kutoka vyanzo mbalimbali: hospitali, nyumba, viwanda na mashamba. Hii inafanya mimea kuwa proxies muhimu kwa kuamua mzigo wa upinzani wa antimicrobial katika jamii. Kwa kuchunguza maji machafu, wanasayansi wanaweza kujua aina za bakteria sugu zinazozunguka katika jamii fulani. Njia hii inakuwa kiwango cha dhahabu cha kimataifa cha kufuatilia upinzani wa antimicrobial. Lakini inaonekana haijachukuliwa katika nchi nyingi za Afrika bado. Utafiti wetu wa hivi karibuni ulichunguza masomo yaliyofanywa juu ya maji taka katika nchi za Kiafrika kati ya 2012 na 2022. Tulitaka kutambua changamoto katika kutumia ufuatiliaji wa maji machafu kuamua kuenea kwa upinzani wa antimicrobial. Kwa mfano, utafiti wa maji taka kwa ajili ya utafiti wa upinzani wa antimicrobial uliongezeka katika nchi za Ulaya. Lakini si katika nchi zote. Katika masomo mengi tuliyopata sampuli zilikusanywa mara moja tu. Hilo si jambo la kutosha ili kufikia mkataa thabiti. Isitoshe, uchunguzi mwingi ulitumia njia moja tu ya kutambua upinzani katika maji machafu. Ikitegemea mbinu, hii ama overestimated au underestimated kiwango cha upinzani. Kwa sababu ya mapungufu haya, tafiti katika bara hilo zinaweza kuwa zinaonyesha picha isiyo sahihi ya tatizo la upinzani wa antimicrobial, ambayo inaweza kuwa na athari mbaya kwa afya. Utafiti wa utafiti wa maji taka ya Afrika Kusini mwa Sahara Utafiti wetu ulionyesha kwamba nchi nyingi hazikuwa na ujuzi unaohitajika kufanya utafiti huu. Ukosefu wa ujuzi uliathiri mbinu ambazo masomo yalitumia, kwa hivyo matokeo yaliyotolewa. Utafiti mwingi ulifanywa katika Afrika Kusini. Hii ni kwa sababu nchi nyingi za kusini mwa Jangwa la Sahara hazina vituo vya kutosha vya kusafisha maji taka. Mengi ya maji hayo yanatumiwa kutengeneza maji machafu ambayo ni chini ya asilimia tano ya maji machafu yanayotoka katika maji. Nchi chache tu, ikiwa ni pamoja na Afrika Kusini na Botswana, hutumia maji ya taka ya asilimia 25 hadi 50 ya maji yao. Hii inamaanisha kuna zaidi ya kujifunza kutoka nchi hizi. Katika Afrika Kusini, masomo juu ya upinzani wa antimicrobial katika maji machafu yalifanywa katika mikoa michache tu. Pia, si masomo yote yaliyofanywa kwenye mitambo ya kusafisha maji machafu. Hii inamaanisha chanzo cha upinzani hakikuweza kufuatiliwa. Kwa kuongezea, kulikuwa na tofauti katika mbinu zilizotumiwa na matokeo yaliyoripotiwa. "Tunapata ufuatiliaji kuwa changamoto hata mahali ambapo viwanda vya kusafisha maji taka vilipatikana kwa sababu ya ukosefu wa ujuzi wa kiufundi unaohitajika kwa mfululizo wa genome. """ Utafiti wa genomics unachunguza DNA ya viumbe vyote katika maji machafu badala ya kuzingatia viumbe vichache tu. Kwa kuongezea, hakuna mbinu za kawaida za kufanya uchunguzi huo. Kwa hiyo, ilikuwa vigumu kulinganisha matokeo kutoka maeneo tofauti-tofauti. Kwa kuwa hakuna viwanda vya kusafisha maji machafu katika nchi nyingi za Afrika, itakuwa vigumu kwa nchi hizo kutekeleza kwa bidii ufuatiliaji wa upinzani wa antimicrobial wa maji machafu. Serikali lazima ziwekeze katika kuunganisha watu wao kwa mitandao ya mifereji ya maji machafu ili kukabiliana na tatizo hili. Hilo ni muhimu kwa ajili ya usafi na afya kwa ujumla. Na itatoa vyanzo muhimu vya habari kwa watafiti wanaojaribu kugundua viumbe wadogo wenye sugu katika jamii. Mara baada ya mitandao ya mifereji ya maji machafu kuwa mahali, itifaki za kawaida kwa ajili ya kutathmini upinzani antimicrobial katika mitambo ya matibabu ya maji taka lazima kuanzishwa. Mipango hiyo inapaswa kuzingatia utaratibu na mzunguko wa kuchukua sampuli, viumbe wanaolengwa, ni viuavijasumu gani vinavyohitaji kupimwa, na ni mbinu zipi zinazopaswa kutumiwa. Pia kuna haja ya kujenga uwezo katika teknolojia ya mfululizo na bioinformatics. Hii itahakikisha kwamba kuna watu wa kutosha na maarifa yanayohitajika kuchambua kiasi kikubwa cha data zinazozalishwa katika masomo haya. "Mashirika ya kifedha lazima kufadhili watafiti katika nchi za kusini mwa Sahara kama teknolojia ya mfululizo bado si kuenea, na gharama ya kutumia vifaa hivi bado ni ya juu. """ Watu huenda wakaona maji machafu kuwa kitu kisichofaa ambacho kinahitaji tu kutupwa. Lakini kuchunguza rasilimali hii yenye thamani kunaweza kutoa onyo la mapema kuhusu milipuko ya magonjwa, hasa yale yanayohusisha viumbe wadogo wasioweza kuambukizwa dawa za kuua viini. 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